Classifying behavior from short‐interval biologging data: An example with GPS tracking of birds

1. Recent advances in digital data collection have spurred accumulation of immense quantities of data that have potential to lead to remarkable ecological insight, but that also present analytic challenges. In the case of biologging data from birds, common analytical approaches to classifying movement behaviors are largely inappropriate for these massive data sets.
2. We apply a framework for using K‐means clustering to classify bird behavior using points from short time interval GPS tracks. K‐means clustering is a well‐known and computationally efficient statistical tool that has been used in animal movement studies primarily for clustering segments of consecutive points. To illustrate the utility of our approach, we apply K‐means clustering to six focal variables derived from GPS data collected at 1–11 s intervals from free‐flying bald eagles (Haliaeetus leucocephalus) throughout the state of Iowa, USA. We illustrate how these data can be used to identify behaviors and life‐stage‐ and age‐related variation in behavior.
3. After filtering for data quality, the K‐means algorithm identified four clusters in >2 million GPS telemetry data points. These four clusters corresponded to three movement states: ascending, flapping, and gliding flight; and one non‐moving state: perching. Mapping these states illustrated how they corresponded tightly to expectations derived from natural history observations; for example, long periods of ascending flight were often followed by long gliding descents, birds alternated between flapping and gliding flight.
4. The K‐means clustering approach we applied is both an efficient and effective mechanism to classify and interpret short‐interval biologging data to understand movement behaviors. Furthermore, because it can apply to an abundance of very short, irregular, and high‐dimensional movement data, it provides insight into small‐scale variation in behavior that would not be possible with many other analytical approaches.

     

Effect of anti-mycobacterial antibodies on activation of the alternative pathway of the human complement system

Abstract Genome analysis of Pseudomonas aeruginosa was performed by digestion with rare-cutting restriction endonucleases and subsequent one- and two-dimensional field inversion gel electrophoresis (FIGE). The frequency of chromosomal recognition sites increased in the order Spe I, Dra I, Xba I, Ssp I, Nhe I. The genome size of strain PAO and the 17 IATS strains varied from 4.4 × 10⁶ to 5.4 × 10⁶ base pairs. Double restriction digests and two-dimensional FIGE provide a genome fingerprint which is useful for the identification and typing of the respective strains.     

Seasonal variations in the mating-related traits of Drosophila melanogaster

The Indian subcontinent shows high levels of seasonal weather variation, but the extent to which mating-related traits (mating latency, copulation duration and number of progeny produced) are being affected by such variations in Drosophila species remain poorly understood. In the present study, we analyzed the effects of seasonal change (humidity and temperature) on mating-related traits of Drosophila melanogaster by mimicking natural conditions in the laboratory. The light body color phenotype is collected in large numbers during the rainy season, while the dark phenotype is prevalent in the winter. We found that a short-term stress, in the form of reduced humidity or temperature, causes a strong climatic selection pressure, which leads to assortative mating and longer copulation duration of the dark phenotype. By contrast, the light phenotype shows higher assortative mating and longer copulation duration after short-term high humidity or high temperature stress. Higher assortative mating and increased copulation duration results in high progeny numbers which may be a cause for the high prevalence of the dark phenotype in winter and the light phenotype in the rainy season. Thus, besides plasticity, seasonal changes in mating propensity can be a potential cause of the change in the frequency of the dark and light phenotypes of D. melanogaster during different seasons.     

Gender distribution in irritable bowel syndrome is proportional to the severity of constipation relative to diarrhea

Background: A significant gender disparity has been observed in individuals with irritable bowel syndrome (IBS), with females outnumbering males, especially in constipation-predominant IBS (C-IBS). However, this observation is based on Rome criteria categorization and does not take into account the severity of constipation or diarrhea.Objective: In a large prospective data set, gender differences across the severity of constipation and diarrhea were examined in patients with IBS.Methods: Consecutive adult patients with Rome I positive IBS who were referred to a tertiary care medical center (Cedars-Sinai Medical Center, Los Angeles, California) in 1999–2003 were given a questionnaire. The questionnaire asked subjects to rate their constipation and diarrhea according to perceived severity using a scale from 0 (none) to 5 (very severe). C-IBS was determined to be present if the severity of constipation was greater than the severity of diarrhea (sevC > sevD). If sevD > sevC, subjects were considered to have diarrhea-predominant IBS (D-IBS). To further categorize their symptoms, subjects were then grouped by the difference between the severity of constipation and diarrhea, creating a range of values from ?5 to +5. For each of these 11 constipation/diarrhea severity values, the female:male ratio was determined. The severity of constipation to diarrhea was compared by Spearman rank correlation.Results: A total of 429 subjects with IBS (325 women: mean [SD] age, 42.5 [0.8] years; 104 men: mean age, 42.2 [1.7] years) completed the questionnaire. Constipation occurred more frequently in women (79.7%) compared with men (61.5%) (odds ratio [OR] = 2.49; 95% CI, 1.55–4.02). The prevalence of diarrhea was similar between the sexes. Whereas C-IBS was more common in women (31.8%) than in men (26.0%) (OR = 2.03; 95% CI, 1.24–3.30), D-IBS was more prevalent in men (62.5%) than in women (36.3%) (OR = 2.39; 95% CI, 1.53–3.75). When the female:male ratio was evaluated across the 11 severity score categories of constipation and diarrhea, the greater the sevC — sevD score, the higher the proportion of women (R = 0.80; P = 0.003).Conclusion: In this study of patients with IBS, the observation of the association of constipation and gender in IBS is extended to indicate that the female:male ratio significantly increases according to the severity of constipation relative to the severity of diarrhea.     

Efforts in diagnosing early leprosy using serological techniques

Skin scrapings obtained from the lesions of leprosy patients of all types showed 96 % positivity to the serum antibody competition test using monoclonal antibody (ML04)to 35 kDa antigen of Mycobacterium leprae. Further, in vitro culture of full thickness skin biopsies from lepromatous patients were noted to release IgG antibodies toM. leprae with a peak antibody response at 48 h. The significance of this local antibody response toM. leprae in skin has been discussed for its possible use in diagnosing early leprosy.     

Cardiac resynchronization therapy: a meta-analysis of randomized controlled trials

Background

Studies of cardiac resynchronization therapy in addition to an implantable cardioverter defibrillator in patients with mild to moderate congestive heart failure had not been shown to reduce mortality until the recent RAFT trial (Resynchronization/Defibrillation for Ambulatory Heart Failure Trial). We performed a meta-analysis including the RAFT trial to determine the effect of cardiac resynchronization therapy with or without an implantable defibrillator on mortality.

Methods

We searched electronic databases and other sources for reports of randomized trials using a parallel or crossover design. We included studies involving patients with heart failure receiving optimal medical therapy that compared cardiac resynchronization therapy with optimal medical therapy alone, or cardiac resynchronization therapy plus an implantable defibrillator with a standard implantable defibrillator. The primary outcome was mortality. The optimum information size was considered to assess the minimum amount of information required in the literature to reach reliable conclusions about cardiac resynchronization therapy.

Results

Of 3071 reports identified, 12 studies (n = 7538) were included in our meta-analysis. Compared with optimal medical therapy alone, cardiac resynchronization therapy plus optimal medical therapy significantly reduced mortality (relative risk [RR] 0.73, 95% confidence interval [CI] 0.62–0.85). Compared with an implantable defibrillator alone, cardiac resynchronization therapy plus an implantable defibrillator significantly reduced mortality (RR 0.83, 95% CI 0.72–0.96). This last finding remained significant among patients with New York Heart Association (NYHA) class I or II disease (RR 0.80, 95% CI 0.67–0.96) but not among those with class III or IV disease (RR 0.84, 95% CI 0.69–1.07). Analysis of the optimum information size showed that the sequential monitoring boundary was crossed, which suggests no need for further clinical trials.

Interpretation

The cumulative evidence is now conclusive that the addition of cardiac resynchronization to optimal medical therapy or defibrillator therapy significantly reduces mortality among patients with heart failure.Congestive heart failure is currently reaching epidemic proportions in Canada, with 500 000 Canadians affected and 50 000 new patients identified each year.¹ It accounts for more than 100 000 hospital admissions per year and has a one-year mortality ranging from 15% to 50%, depending on the severity of heart failure.² By 2050, the number of patients with heart failure is projected to increase threefold.²Advances in medical therapies have resulted in substantial reductions in mortality associated with congestive heart failure.^3–7 The use of devices has recently become an important adjuvant therapy.⁸ Cardiac resynchronization therapy involves pacing from both the right and left ventricles simultaneously to improve myocardial efficiency (see radiographs in Appendix 1, at www.cmaj.ca/cgi/content/full/cmaj.101685/DC1). Cardiac resynchronization therapy has been shown to reduce morbidity and, when compared with medical therapy alone, to reduce mortality.^9–13 Until recently, it was not shown to reduce mortality among patients who also received an implantable cardioverter defibrillator. Among patients receiving optimal medical therapy, the Resynchronization/Defibrillation for Ambulatory Heart Failure Trial (RAFT) showed the superiority of cardiac resynchronization therapy in addition to an implantable defibrillator over a standard implantable defibrillator in reducing mortality and the combined outcome of death from any cause or hospital admission related to heart failure.¹⁴We performed a meta-analysis to further assess the effect on mortality of cardiac resynchronization therapy with and without an implantable defibrillator among patients with mildly symptomatic and advanced heart failure.     

Low-dosage inhibition of Dll4 signaling promotes wound healing by inducing functional neo-angiogenesis

Recent findings regarding Dll4 function in physiological and pathological conditions indicate that this Notch ligand may constitute an important therapeutic target. Dll4 appears to be a major anti-angiogenic agent, occupying a central role in various angiogenic pathways. The first trials of anti-Dll4 therapy in mice demonstrated a paradoxical effect, as it reduced tumor perfusion and growth despite leading to an increase in vascular density. This is seen as the result of insufficient maturation of the newly formed vasculature causing a circulatory defect and increased tumor hypoxia. As Dll4 function is known to be closely dependent on expression levels, we envisioned that the therapeutic anti-Dll4 dosage could be modulated to result in the increase of adequately functional blood vessels. This would be useful in conditions where vascular function is a limiting factor for recovery, like wound healing and tissue hypoxia, especially in diabetic patients. Our experimental results in mice confirmed this possibility, revealing that low dosage inhibition of Dll4/Notch signaling causes improved vascular function and accelerated wound healing.     

Antagonistic lipopolysaccharides block E. coli lipopolysaccharide function at human TLR4 via interaction with the human MD-2 lipopolysaccharide binding site

Lipopolysaccharides containing underacylated lipid A structures exhibit reduced abilities to activate the human (h) Toll-like receptor 4 (TLR4) signalling pathway and function as potent antagonists against lipopolysaccharides bearing canonical lipid A structures. Expression of underacylated lipopolysaccharides has emerged as a novel mechanism utilized by microbial pathogens to modulate host innate immune responses. Notably, antagonistic lipopolysaccharides are prime therapeutic candidates for combating Gram negative bacterial sepsis. Penta-acylated msbB and tetra-acylated Porphyromonas gingivalis lipopolysaccharides functionally antagonize hexa-acylated Escherichia coli lipopolysaccharide-dependent activation of hTLR4 through the coreceptor, hMD-2. Here, the molecular mechanism by which these antagonistic lipopolysaccharides act at hMD-2 is examined. We present evidence that both msbB and P. gingivalis lipopolysaccharides are capable of direct binding to hMD-2. These antagonistic lipopolysaccharides can utilize at least two distinct mechanisms to block E. coli lipopolysaccharide-dependent activation of hTLR4. The main mechanism consists of direct competition between the antagonistic lipopolysaccharides and E. coli lipopolysaccharide for the same binding site on hMD-2, while the secondary mechanism involves the ability of antagonistic lipopolysaccharide-hMD-2 complexes to inhibit E. coli lipopolysaccharide-hMD-2 complexes function at hTLR4. It is also shown that both hTLR4 and hMD-2 contribute to the species-specific recognition of msbB and P. gingivalis lipopolysaccharides as antagonists at the hTLR4 complex.