Text similarity: an alternative way to search MEDLINE

MOTIVATION: The most widely used literature search techniques, such as those offered by NCBI's PubMed system, require significant effort on the part of the searcher, and inexperienced searchers do not use these systems as effectively as experienced users. Improved literature search engines can save researchers time and effort by making it easier to locate the most important and relevant literature. RESULTS: We have created and optimized a new, hybrid search system for Medline that takes natural text as input and then delivers results with high precision and recall. The combination of a fast, low-sensitivity weighted keyword-based first pass algorithm to cast a wide net to gather an initial set of literature, followed by a unique sentence-alignment based similarity algorithm to rank order those results was developed that is sensitive, fast and easy to use. Several text similarity search algorithms, both standard and novel, were implemented and tested in order to determine which obtained the best results in information retrieval exercises. AVAILABILITY: Literature searching algorithms are implemented in a system called eTBLAST, freely accessible over the web at http://invention.swmed.edu. A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities. CONTACT: Harold.Garner@UTSouthwestern.edu.     

Dynamics of Nosema pyrausta in natural populations of the European corn borer, Ostrinia nubilalis: A six-year study

Nosema pyrausta (Paillot) (Microsporida: Nosematidae) is an obligatory intracellular parasite of the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). This pathogen is maintained in natural populations of O. nubilalis by both horizontal and vertical transmission. The impact of N. pyrausta on fecundity of adults and survival of larvae has been well documented in laboratory and field research. In an extensive study covering a 6 year period at one site, we described the effect of N. pyrausta within O. nubilalis populations in a continuous corn following corn ecosystem. We documented the presence of the pathogen through all life stages of O. nubilalis (egg, larva, pupa, adult), by collecting throughout the crop season and examining each insect stage in the laboratory for the frequency of infection with N. pyrausta. The percentage of infection with N. pyrausta and magnitude of the O. nubilalis population fluctuated throughout generation 1 and generation 2. Both horizontal and vertical transmission played a role in maintaining N. pyrausta in the population in both generations. There were strong correlations between percentage adults with N. pyrausta and percentage larvae with N. pyrausta, and between percentage eggs with N. pyrausta and percentage larvae with N. pyrausta. There was a weak correlation between percentage adults with N. pyrausta and percentage eggs with N. pyrausta. The percentage of insects infected with N. pyrausta was always lowest in the egg.     

The Spatial Structure of Variability in a Semi-arid, Fluvial Ecosystem

The arrangement and composition of flowpath types within a given network are thought to govern its functioning. This concept assumes that different flowpath types are functionally distinct. We investigated this assumption in a fluvial ecosystem by comparing the riparian zone, parafluvial zone (in-channel gravel bars), and surface stream. We hypothesized that differences in advection, uptake, and sorption would render material cycles more (a) open and (b) mutable in the surface stream, whereas the converse would occur in the riparian zone, and an intermediate state would be seen in the intervening parafluvial zone. To test our first hypothesis, we predicted that spatial heterogeneity in solute concentrations would be least in the surface stream, greater in the parafluvial zone, and greatest in the riparian zone. Using a null model, we ascertained that this pattern was shown by all solute species we examined (nitrate, ammonium, total dissolved inorganic nitrogen [DIN], dissolved organic N, total dissolved N, soluble reactive phosphorus, dissolved organic carbon, and chloride). To test our second hypothesis, we predicted that temporal change in spatial heterogeneity would be greatest in the surface stream, less in the parafluvial zone, and least in the riparian zone. Nitrate, DIN, and chloride showed this pattern. In particular, surface stream inorganic N was less spatially variable following months of high rainfall. According to an extant hypothesis, these results suggest that inorganic N processing may be a stable function in this ecosystem. Other solute species did not support our second prediction, perhaps because their retention and release dynamics are influenced principally by geochemistry. Generally, our findings indicate that a geomorphic template can generate spatial patterns in ecosystem function, warranting an expansion of the spiraling framework to a variety of flowpath types.     

Steroid analysis in saliva: an overview

The first report of steroid analysis in saliva was more than thirty years ago. Since that time its popularity has increased due to the attractiveness of non-invasive, repeated and simple stress-free sampling. It has proved a popular sampling fluid for psychobiology, sports medicine, pharmacology and paediatric studies as well as in the area of complementary medicine. In the diagnostic laboratory, salivary progesterone and oestradiol have been used for assessing ovarian function and 17alpha-OH progesterone for the diagnosis of congenital adrenal hyperplasia (CAH). Salivary cortisol is used for investigating adrenal function and recently there has been considerable interest in the use of bedtime salivary cortisol levels as a screening test for Cushing's disease. However, there are several caveats on the use of saliva including collection techniques, the variable matrix of saliva, sensitivity, steroid stability, the presence of binding proteins and reference range anomalies. This brief review will attempt to address these issues and provide a balanced approach to steroid analysis in saliva.     

In vitro assessment of a motion-based optimization method for locating the talocrural and subtalar joint axes

The locations of the joint axes of the ankle complex vary considerably between subjects, yet no noninvasive method with demonstrated accuracy exists for locating these axes. The moments of muscle and ground reaction forces about the joint axes are dependent on axis locations, making knowledge of these locations critical to accurate musculoskeletal modeling of the foot and ankle. The accuracy of a computational optimization method that fits a two-revolute model to measured motion was assessed using computer-generated data, a two-revolute mechanical linkage, and three lower-leg cadaver specimens. Motions were applied to cadaver specimens under axial load while bone-mounted markers attached to the tibia, talus, and calcaneus were tracked using a video-based motion analysis system. Estimates of the talocrural and subtalar axis locations were computed from motions of the calcaneus relative to the tibia using the optimization method. These axes were compared to mean helical axes computed directly from tibia, talus, and calcaneus motions. The optimization method performed well when the motions were computer-generated or measured in the mechanical linkage, with angular differences between optimization and mean helical axes ranging from 1 deg to 5 deg. In the cadaver specimens, however, these differences exceeded 20 deg. Optimization methods that locate the anatomical joint axes of the ankle complex by fitting two revolute joints to measured tibia-calcaneus motions may be limited because of problems arising from non-revolute behavior.     

The molecular scaffold kinase suppressor of Ras 1 is a modifier of RasV12-induced and replicative senescence

In primary mouse embryo fibroblasts (MEFs), oncogenic Ras induces growth arrest via Raf/MEK/extracellular signal-regulated kinase (ERK)-mediated activation of the p19ARF/p53 and INK4/Rb tumor suppressor pathways. Ablation of these same pathways causes spontaneous immortalization in MEFs, and oncogenic transformation by Ras requires ablation of one or both of these pathways. We show that Kinase Suppressor of Ras 1 (KSR1), a molecular scaffold for the Raf/MEK/ERK cascade, is necessary for RasV12-induced senescence, and its disruption enhances primary MEF immortalization. RasV12 failed to induce p53, p19ARF, p16INK4a, and p15INK4b expression in KSR1-/- MEFs and increased proliferation instead of causing growth arrest. Reintroduction of wild-type KSR1, but not a mutated KSR1 construct unable to bind activated ERK, rescued RasV12-induced senescence. On continuous culture, deletion of KSR1 accelerated the establishment of spontaneously immortalized cultures and increased the proportion of cultures escaping replicative crisis. Despite enhancing escape from both RasV12-induced and replicative senescence, however, both primary and immortalized KSR1-/- MEFs are completely resistant to RasV12-induced transformation. These data show that escape from senescence is not necessarily a precursor for oncogenic transformation. Furthermore, these data indicate that KSR1 is a member of a unique class of proteins whose deletion blocks both senescence and transformation.     

Feast or Famine: The Sympathetic Nervous System Response to Nutrient Intake

  1. The use of tritiated norepinephrine (NE) to measure the turnover rate of NE in sympathetically innervated organs was pioneered in the laboratory of Julius Axelrod. This technique provides an organ specific assessment of sympathetic activity, integrated over a 24 h period, in free living laboratory animals. As such it has proved useful in estimating changes in sympathetic outflow in different physiologic and patho-physiologic states.2. Studies employing NE turnover techniques in laboratory rodents have demonstrated conclusively that fasting suppresses and overfeeding stimulates the sympathetic nervous system (SNS). These changes in sympathetic activity also occur in humans.3. Diet-induced changes in SNS activity are regulated by insulin-mediated glucose uptake and metabolism in central neurons sensitive to insulin and located anatomically in the ventro-medial hypothalamus. The regulation is imposed by descending inhibition of tonically active sympathetic brainstem centers.4. Diet-induced changes in SNS activity mediate changes in energy production known as dietary thermogenesis. The capacity for dietary thermogenesis serves as a potential buffer against weight gain.5. Insulin stimulated SNS activity contributes to obesity-related hypertension. The insulin resistance of obesity, and consequent hyperinsulinemia, drives sympathetically mediated thermogenesis, restoring energy balance at the expense of SNS over activity. The association of obesity and hypertension, therefore, may be the unintended consequence of mechanisms recruited in the obese to limit further weight gain.     

Scent marking in sifaka: no one function explains it all

Various hypotheses to explain possible functions of scent-marking have been put forth and basically fall into five categories: territorial demarcation, ownership of resources, mate attraction, noncombative fighting, and self-advertisement. Verreaux's sifaka (Propithecus verreauxi verreauxi), like many prosimians, use scent-marking as one form of communication. The goal of this study was to determine the function of scent-marking in sifaka. All-occurrence of scent-marks, scent-mark context, and scent-mark style were collected on 23 sifaka in the Kirindy Forest of western Madagascar for 7 months (September 2001-March 2002). Scent-mark rates were collected using continuous focal animal sampling from November 2000-March 2002. Home range data were collected using monthly censuses and instantaneous focal sampling throughout the 17 months. Scent-marking behavior was exhibited almost exclusively by adults. Scent-mark rates were not related to the number of resident adult males, number of resident adult females, rank, or group size. The majority of scent-marks occurred in the perimeter of the home range; however, less than a quarter of the home range was used by only a single group. Sifaka did not preferentially mark food trees, mark during the mating season, or mark during intergroup encounters. The results from this study indicate that none of the five hypothesized functions best explains all scent-marking in Verreaux's sifaka. Rather, scent-marking may serve different functions for different individuals.