bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance
Authors: Wei Wei-Qi , Teixeira Pedro L , Mo Huan , Cronin Robert M , Warner Jeremy L , Denny Joshua C
Published: September 2015

Objective To evaluate the phenotyping performance of three major electronic health record (EHR) components: International Classification of Disease (ICD) diagnosis codes, primary notes, and specific medications.

Materials and Methods We conducted the evaluation using de-identified Vanderbilt EHR data. We preselected ten diseases: atrial fibrillation, Alzheimer’s disease, breast cancer, gout, human immunodeficiency virus infection, multiple sclerosis, Parkinson’s disease, rheumatoid arthritis, and types 1 and 2 diabetes mellitus. For each disease, patients were classified into seven categories based on the presence of evidence in diagnosis codes, primary notes, and specific medications. Twenty-five patients per disease category (a total number of 175 patients for each disease, 1750 patients for all ten diseases) were randomly selected for manual chart review. Review results were used to estimate the positive predictive value (PPV), sensitivity, and F -score for each EHR component alone and in combination.

Results The PPVs of single components were inconsistent and inadequate for accurately phenotyping (0.06–0.71). Using two or more ICD codes improved the average PPV to 0.84. We observed a more stable and higher accuracy when using at least two components (mean ± standard deviation: 0.91 ± 0.08). Primary notes offered the best sensitivity (0.77). The sensitivity of ICD codes was 0.67. Again, two or more components provided a reasonably high and stable sensitivity (0.59 ± 0.16). Overall, the best performance ( F score: 0.70 ± 0.12) was achieved by using two or more components. Although the overall performance of using ICD codes (0.67 ± 0.14) was only slightly lower than using two or more components, its PPV (0.71 ± 0.13) is substantially worse (0.91 ± 0.08).

Conclusion Multiple EHR components provide a more consistent and higher performance than a single one for the selected phenotypes. We suggest considering multiple EHR components for future phenotyping design in order to obtain an ideal result.
Cognitive–behavioural assessment
Authors: Kirk Joan
Published: September 2015

This chapter considers cognitive–behavioural assessment, its goals, modes of assessment, measurement in cognitive–behavioural assessment and treatment, and sources of information (behavioural interviewing, self-monitoring, self-report questionnaires, information from third parties, direct observation, and physiological measures).
Depression
Authors: Fennell Melanie J. V.
Published: September 2015

Chapter 6 explores depression. The chapter outlines the nature of depression, the development of psychological treatments, the cognitive model of depression, cognitive behaviour therapy for depression, the structure of treatment sessions, major cognitive behaviour therapy strategies and preventative strategies, and options for if cognitive behaviour therapy fails.
Problem-solving
Authors: Hawton Keith , Kirk Joan
Published: September 2015

This chapter explores problem-solving and provides practical guidance on a general approach to helping people manage personal issues. It discusses problem-solving from a cognitive–behavioural viewpoint, the application of problem-solving, assessment of efficacy, stages and strategies in problem-solving.
Tenacious Goal Pursuits and Striving Toward Personal Growth: Proactive Coping
Authors: Schwarzer Ralf , Taubert Steffen
Published: September 2015

Chapter 2 discusses goal pursuits, personal growth, and proactive coping. This includes trends in stress and coping theory (response-based perspective, stimulus-based perspective, cognitive-transactional theory of stress, antecedents of stress and coping, and dimensions of coping), proactive coping theory, and research into proactive coping.
The Associations Between Pain-related Beliefs, Pain Intensity, and Patient Functioning
Authors: Jensen Mark P. , Galer Peter D. , Johnson Linea L. , George Holly R. , Mendoza M. Elena , Gertz Kevin J.
Published: September 2015

Objectives:

On the basis of the idea that thoughts held about pain may represent “self-suggestions” and evidence indicating that people with higher levels of trait hypnotizability are more responsive to suggestions, the current study evaluated hypothesized moderating effects of hypnotizability on the associations between pain-related thoughts and both pain intensity and pain interference.

Methods:

Eighty-five individuals with chronic pain were given measures of hypnotizability, pain intensity, pain interference, and pain-related thoughts (control beliefs, catastrophizing).

Results:

Analyses supported a moderating role of hypnotizability on the association between control beliefs and pain interference. Specifically, the negative association between pain control beliefs and pain interference were stronger among those with higher trait hypnotizability than between those with lower trait hypnotizability.

Discussion:

The study findings, if replicated in additional samples of individuals with chronic pain, have important clinical and theoretical implications. For example, if trait hypnotizability is found to predict an individual’s response to a particular technique of cognitive therapy—such as focusing on and repeating pain control belief self-statements—measures of hypnotizability could be used to identify individuals who might be most responsive to this technique. The current findings indicate that research to further examine this possibility is warranted.
Basal Ganglia Perfusion in Fibromyalgia is Related to Pain Disability and Disease Impact
Authors: Shokouhi Mahsa , Davis Karen D. , Moulin Dwight E. , Morley-Forster Pat , Nielson Warren R. , Bureau Yves , St. Lawrence Keith
Published: September 2015

Objectives:

Pain disability is a major impediment to fibromyalgia (FM) patients’ quality of life. Neuroimaging studies have demonstrated abnormal pain processing in FM. However, it is not known whether there are brain abnormalities linked to pain disability. Understanding neural correlates of pain disability in FM, independent from pain intensity, could provide a framework to guide future more efficient therapy strategies to improve patients’ functional ability.

Methods:

We used arterial spin labeling to image cerebral blood flow (CBF) in 23 FM patients and 16 controls. Functional connectivity was also estimated using blood oxygenation level–dependent imaging to further investigate the possible underpinnings of the observed CBF changes.

Results:

Among patients, CBF in the basal ganglia correlated negatively with pain disability index and positively with the overall impact of FM (Fibromyalgia Impact Questionnaire) but did not correlate with pain intensity. Whole-brain analysis revealed no CBF differences between the 2 groups; however, post hoc analysis in the basal ganglia showed CBF reductions mainly in the right putamen and right lateral globus pallidus in patients, likely reflecting the negative correlation with the pain disability index. However, the connectivity of the corresponding corticobasal ganglia-thalamus loop, that is, motor network (the connection between supplementary motor area, putamen, and thalamus) remained intact.

Discussion:

Basal ganglia perfusion reflects long-term symptoms, including somatic and psychological components of FM rather than pain intensity. These CBF findings may reflect differences in behavioral and psychological responses between patients.
β-Blocker use and mortality in cancer patients: systematic review and meta-analysis of observational studies
Authors: Zhong Shanliang , Yu Dandan , Zhang Xiaohui , Chen Xiu , Yang Sujin , Tang Jinhai , Zhao Jianhua , Wang Shukui
Published: September 2015

A number of epidemiologic studies have attempted to link the use of β blockers to mortality in cancer patients, but their findings have been inconclusive. A meta-analysis was carried out to derive a more precise estimation. Relevant studies were identified by searching PubMed and EMBASE to May 2015. We calculated the summary hazard ratios (HRs) and 95% confidence intervals (CIs) using random-effects models. Twenty cohort studies and four case–control studies involving 76 538 participants were included. The overall results showed that patients who used β blockers after diagnosis had an HR of 0.89 (95% CI 0.81–0.98) for all-cause mortality compared with nonusers. Those who used β blockers after diagnosis (vs. nonusers) had an HR of 0.89 (95% CI 0.79–0.99) for cancer-specific mortality. Prediagnostic use of β blockers showed no beneficial effect on all-cause mortality or cancer-specific mortality. Stratifying by cancer type, only breast cancer patients who used β blockers after diagnosis had a prolonged overall survival. A linear but nonsignificant trend was found between postdiagnostic β-blocker use and mortality of cancer patients. In conclusion, the average effect of β-blocker use after diagnosis but not before diagnosis is beneficial for the survival of cancer patients.
Effect of reminders mailed to general practitioners on colorectal cancer screening adherence: a cluster-randomized trial
Authors: Le Breton Julien , Ferrat Émilie , Attali Claude , Bercier Sandrine , Le Corvoisier Philippe , Brixi Zahida , Veerabudun Kalaivani , Renard Vincent , Bastuji-Garin Sylvie
Published: September 2015

Reminders have been used in various settings, but failed to produce convincing evidence of benefits on patient adherence to colorectal cancer (CRC) screening. The aim of this study was to assess the effectiveness of sending general practitioners (GPs) printed reminders about CRC screening. We conducted a cluster-randomized controlled trial involving 144 GPs in the Val-de-Marne district (France), who provided care for any reason to 20 778 patients eligible for CRC screening between June 2010 and November 2011. Data were collected from the main statutory health-insurance programme and local cancer screening agency. GPs were randomly assigned in a 1 : 1 proportion to the intervention or the control group. Every 4 months, intervention-group GPs received a computer-generated printed list of patients who had not performed scheduled faecal occult blood test (FOBT) screening. The primary outcome was patient adherence to FOBT screening or exclusion from CRC screening for medical reasons. The screening adherence rate was 31.2% [95% confidence interval (CI) 30.3–32.1] in the control group and 32.9% (95% CI 32.0–33.8) in the intervention group [crude relative risk, 1.05 (95% CI 1.01–1.09), P<0.01]. This rate was not significantly different between groups by multilevel modelling accounting for clustering and confounding variables [adjusted relative risk, 1.07 (95% CI 0.95–1.20), P=0.27]. Computer-generated printed reminders sent to GPs did not significantly improve patient adherence to organized CRC screening by the FOBT.
A New Fitting Approach for Providing Adequate Comfort and Visual Performance in Keratoconus: Soft HydroCone (Toris K) Lenses
Authors: Gumus Koray , Kahraman Nisa
Published: September 2015

Objective:

To evaluate the comfort and visual performance of soft HydroCone (Toris K) silicone hydrogel lenses in keratoconus patients.

Methods:

Fifty eyes of 50 keratoconic patients who were fitted with the Toris K lens were included in the study. All patients were evaluated at baseline and after 2 weeks of lens wear. Uncorrected and best-corrected visual acuities were measured. Corneal topography, ocular aberrations, and point spread function (PSF) were obtained using NIDEK-OPD Scan. Comfort level and visual performance in daytime and nighttime conditions were scored from 0 to 5 after 2 weeks of lens wear.

Results:

Best-corrected visual acuity was significantly better with the Toris K lens (P<0.001). Mean increase in visual acuity with the lens was 4.5 lines. Mean K1, K2, and Kmax values significantly decreased with the lens (P<0.001). Both total and higher-order root-mean-square errors were significantly corrected with the Toris K lens (P<0.001 and P=0.038, respectively). A significant correction of total coma and trefoil aberrations was achieved with the lens. Also, PSF values were significantly increased with the lens (P<0.001). Although comfort scores in 46 eyes (92.0%) were classified as good/excellent, only 4 eyes (8.0%) had moderate comfort scores. Visual acuity was classified as good/excellent in 46 eyes (92.0%) in daytime and in 38 eyes (76%) in nighttime conditions.

Conclusions:

Soft HydroCone silicone hydrogel keratoconus lenses should be considered as alternative visual correction for keratoconus patients. The soft and full-custom design provides optimal comfort and visual performance for the patients' daily requirements.
Endoscopic Surveillance After Repair of Oesophageal Atresia
Authors: Koivusalo Antti I. , Pakarinen Mikko P. , Lindahl Harry G. , Rintala Risto J.
Published: September 2015

Aim:

After repair of oesophageal atresia (OA), the need for endoscopic follow‐up (EFU) remains unclear. To end this, we assessed the trends of oesophageal mucosal changes in successive follow‐up biopsies.

Methods:

EFU records of 264 patients including histological grades of oesophagitis (from 0 to III), gastric (GM) or intestinal (IM) metaplasia and dysplasia (mild to severe) at 1, 3, 5 10, 15, and >15 years after repair of OA were reviewed.

Results:

Included were 209 patients with 616 biopsies. A total of 60 patients had undergone antireflux surgery and 24 had long‐gap OA (LG). Median follow‐up was 12 (range 1–17) years with 3 (1–6) endoscopies per patient. Highest grade of oesophagitis was Gr 0 (no oesophagitis) in 47%, Gr I in 37%, and Gr II or III in 16%. Metaplasia, GM (n = 31), IM (n = 4), occurred in 17% of patients and reached 15% prevalence by 15 years. Dysplasia and cancer were not found. From 1 to 15 years after repair grade of histological oesophagitis often fluctuated between Gr 0 and Gr I, but further progression was unlikely, hazard ratio = 0.2–3.4 (95% confidence interval 0.0–29), P = 0.06–0.87. LG and antireflux surgery predicted early detection of metaplasia (P < 0.001). Only 9% of patients with metaplasia and 32% with Gr II oesophagitis were symptomatic. A total of 6 (3%) patients had a symptomatic anastomotic stenosis at 1 year.

Conclusions:

EFU revealed frequent oesophagitis and metaplasia, but no dysplasia or cancer. Routine endoscopic surveillance had limited benefit and seems unnecessary during childhood after repair of OA.
Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago
Authors: Pansu Johan , Winkworth Richard C. , Hennion Françoise , Gielly Ludovic , Taberlet Pierre , Choler Philippe
Published: September 2015

During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities at sites on the sub-Antarctic Kerguelen Islands with contrasting histories of disturbance by rabbits. Our results suggest that on these islands, the simplification of plant communities and increased erosion resulting from the introduction of rabbits have driven compositional changes, including diversity reductions, in indigenous soil fungal communities. Moreover, there is no indication of recovery at sites from which rabbits were removed 20 years ago. These results imply that introduced herbivores have long-lasting and multifaceted effects on fungal biodiversity as well as highlight the low resiliency of sub-Antarctic ecosystems.
Claude Ambrose Rogers. 1 November 1920 — 5 December 2005
Authors: Falconer Kenneth , Gruber Peter M. , Ostaszewski Adam , Stuart Trevor
Published: September 2015

Claude Ambrose Rogers and his identical twin brother, Stephen Clifford, were born in Cambridge in 1920 and came from a long scientific heritage. Their great-great-grandfather, Davies Gilbert, was President of the Royal Society from 1827 to 1830; their father was a Fellow of the Society and distinguished for his work in tropical medicine. After attending boarding school at Berkhamsted with his twin brother from the age of 8 years, Ambrose, who had developed very different scientific interests from those of his father, entered University College London in 1938 to study mathematics. He completed the course in 1940 and graduated in 1941 with first-class honours, by which time the UK had been at war with Germany for two years. He joined the Applied Ballistics Branch of the Ministry of Supply in 1940, where he worked until 1945, apparently on calculations using radar data to direct anti-aircraft fire. However, this did not lead to research interests in applied mathematics, but rather to several areas of pure mathematics. Ambrose's PhD research was at Birkbeck College, London, under the supervision of L. S. Bosanquet and R. G. Cooke. Although his first paper was a short note on linear transformations of convergent series, his substantive early work was on the geometry of numbers. Later, Rogers became known for his very wide interests in mathematics, including not only geometry of numbers but also Hausdorff measures, convexity and analytic sets, as described in this memoir. Ambrose was married in 1952 to Joan North, and they had two daughters, Jane and Petra, to form a happy family.
Sperm metabolism is altered during storage by female insects: evidence from two-photon autofluorescence lifetime measurements in bedbugs
Authors: Reinhardt Klaus , Breunig Hans Georg , Uchugonova Aisada , König Karsten
Published: September 2015

We explore the possibility of characterizing sperm cells without the need to stain them using spectral and fluorescence lifetime analyses after multi-photon excitation in an insect model. The autofluorescence emission spectrum of sperm of the common bedbug,
Cimex lectularius
, was consistent with the presence of flavins and NAD(P)H. The mean fluorescence lifetimes showed smaller variation in sperm extracted from the male (tau m,
τ
m
= 1.54–1.84 ns) than in that extracted from the female sperm storage organ (tau m,
τ
m
= 1.26–2.00 ns). The fluorescence lifetime histograms revealed four peaks. These peaks (0.18, 0.92, 2.50 and 3.80 ns) suggest the presence of NAD(P)H and flavins and show that sperm metabolism can be characterized using fluorescence lifetime imaging. The difference in fluorescence lifetime variation between the sexes is consistent with the notion that female animals alter the metabolism of sperm cells during storage. It is not consistent, however, with the idea that sperm metabolism represents a sexually selected character that provides females with information about the male genotype.
Cell cycle progression is an essential regulatory component of phospholipid metabolism and membrane homeostasis
Authors: Sanchez-Alvarez Miguel , Zhang Qifeng , Finger Fabian , Wakelam Michael J. O. , Bakal Chris
Published: September 2015

We show that phospholipid anabolism does not occur uniformly during the metazoan cell cycle. Transition to S-phase is required for optimal mobilization of lipid precursors, synthesis of specific phospholipid species and endoplasmic reticulum (ER) homeostasis. Average changes observed in whole-cell phospholipid composition, and total ER lipid content, upon stimulation of cell growth can be explained by the cell cycle distribution of the population. TORC1 promotes phospholipid anabolism by slowing S/G2 progression. The cell cycle stage-specific nature of lipid biogenesis is dependent on p53. We propose that coupling lipid metabolism to cell cycle progression is a means by which cells have evolved to coordinate proliferation with cell and organelle growth.
Amplifiers of selection
Authors: Adlam B. , Chatterjee K. , Nowak M. A.
Published: September 2015

When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement—that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two.
On rate-dependent polycrystal deformation: the temperature sensitivity of cold dwell fatigue
Authors: Zhang Zhen , Cuddihy M. A. , Dunne F. P. E.
Published: September 2015

A temperature and rate-dependent crystal plasticity framework has been used to examine the temperature sensitivity of stress relaxation, creep and load shedding in model Ti-6Al polycrystal behaviour under dwell fatigue conditions. A temperature close to 120°C is found to lead to the strongest stress redistribution and load shedding, resulting from the coupling between crystallographic slip rate and slip system dislocation hardening. For temperatures in excess of about 230°C, grain-level load shedding from soft to hard grains diminishes because of the more rapid stress relaxation, leading ultimately to the diminution of the load shedding and hence, it is argued, the elimination of the dwell debit. Under conditions of cyclic stress dwell, at temperatures between 20°C and 230°C for which load shedding occurs, the rate-dependent accumulation of local slip by ratcheting is shown to lead to the progressive cycle-by-cycle redistribution of stress from soft to hard grains. This phenomenon is termed
cyclic load shedding
since it also depends on the material's creep response, but develops over and above the well-known dwell load shedding, thus providing an additional rationale for the incubation of facet nucleation.
Constructing more informative plant–pollinator networks: visitation and pollen deposition networks in a heathland plant community
Authors: Ballantyne G. , Baldock Katherine C. R. , Willmer P. G.
Published: September 2015

Interaction networks are widely used as tools to understand plant–pollinator communities, and to examine potential threats to plant diversity and food security if the ecosystem service provided by pollinating animals declines. However, most networks to date are based on recording visits to flowers, rather than recording clearly defined effective pollination events. Here we provide the first networks that explicitly incorporate measures ofpollinator effectiveness(PE) from pollen deposition on stigmas per visit, andpollinator importance(PI) as the product of PE and visit frequency. These more informative networks, here produced for a low diversity heathland habitat, reveal that plant–pollinator interactions are more specialized than shown in most previous studies. At the studied site, the specialization indexwas lower for the visitation network than the PE network, which was in turn lower thanfor the PI network. Our study shows that collecting PE data is feasible for community-level studies in low diversity communities and that including information about PE can change the structure of interaction networks. This could have important consequences for our understanding of threats to pollination systems.
Pleistocene megafaunal interaction networks became more vulnerable after human arrival
Authors: Pires Mathias M. , Koch Paul L. , Fariña Richard A. , de Aguiar Marcus A. M. , dos Reis Sérgio F. , Guimarães Paulo R.
Published: September 2015

The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions.
Multimodal cues improve prey localization under complex environmental conditions
Authors: Rhebergen F. , Taylor R. C. , Ryan M. J. , Page R. A. , Halfwerk W.
Published: September 2015

Predators often eavesdrop on sexual displays of their prey. These displays can provide multimodal cues that aid predators, but the benefits in attending to them should depend on the environmental sensory conditions under which they forage. We assessed whether bats hunting for frogs use multimodal cues to locate their prey and whether their use varies with ambient conditions. We used a robotic set-up mimicking the sexual display of a male túngara frog (
Physalaemus pustulosus
) to test prey assessment by fringe-lipped bats (
Trachops cirrhosus
). These predatory bats primarily use sound of the frog's call to find their prey, but the bats also use echolocation cues returning from the frog's dynamically moving vocal sac. In the first experiment, we show that multimodal cues affect attack behaviour: bats made narrower flank attack angles on multimodal trials compared with unimodal trials during which they could only rely on the sound of the frog. In the second experiment, we explored the bat's use of prey cues in an acoustically more complex environment. Túngara frogs often form mixed-species choruses with other frogs, including the hourglass frog (
Dendropsophus ebraccatus
). Using a multi-speaker set-up, we tested bat approaches and attacks on the robofrog under three different levels of acoustic complexity: no calling
D. ebraccatus
males, two calling
D. ebraccatus
males and five
D. ebraccatus
males. We found that bats are more directional in their approach to the robofrog when more
D. ebraccatus
males were calling. Thus, bats seemed to benefit more from multimodal cues when confronted with increased levels of acoustic complexity in their foraging environments. Our data have important consequences for our understanding of the evolution of multimodal sexual displays as they reveal how environmental conditions can alter the natural selection pressures acting on them.
Affinity for natal environments by dispersers impacts reproduction and explains geographical structure of a highly mobile bird
Authors: Fletcher Robert J. , Robertson Ellen P. , Wilcox Rebecca C. , Reichert Brian E. , Austin James D. , Kitchens Wiley M.
Published: September 2015

Understanding dispersal and habitat selection behaviours is central to many problems in ecology, evolution and conservation. One factor often hypothesized to influence habitat selection by dispersers is the natal environment experienced by juveniles. Nonetheless, evidence for the effect of natal environment on dispersing, wild vertebrates remains limited. Using 18 years of nesting and mark–resight data across an entire North American geographical range of an endangered bird, the snail kite (Rostrhamus sociabilis), we tested for natal effects on breeding-site selection by dispersers and its consequences for reproductive success and population structure. Dispersing snail kites were more likely to nest in wetlands of the same habitat type (lacustrine or palustrine) as their natal wetland, independent of dispersal distance, but this preference declined with age and if individuals were born during droughts. Importantly, dispersing kites that bred in natal-like habitats had lower nest success and productivity than kites that did not. These behaviours help explain recently described population connectivity and spatial structure across their geographical range and reveal that assortative breeding is occurring, where birds are more likely to breed with individuals born in the same wetland type as their natal habitat. Natal environments can thus have long-term and large-scale effects on populations in nature, even in highly mobile animals.
Pathogen evolution under host avoidance plasticity
Authors: McLeod David V. , Day Troy
Published: September 2015

Host resistance consists of defences that limit pathogen burden, and can be classified as either adaptations targeting recovery from infection or those focused upon infection avoidance. Conventional theory treats avoidance as a fixed strategy which does not vary from one interaction to the next. However, there is increasing empirical evidence that many avoidance strategies are triggered by external stimuli, and thus should be treated as phenotypically plastic responses. Here, we consider the implications of avoidance plasticity for host–pathogen coevolution. We uncover a number of predictions challenging current theory. First, in the absence of pathogen trade-offs, plasticity can restrain pathogen evolution; moreover, the pathogen exploits conditions in which the host would otherwise invest less in resistance, causing resistance escalation. Second, when transmission trades off with pathogen-induced mortality, plasticity encourages avirulence, resulting in a superior fitness outcome for both host and pathogen. Third, plasticity ensures the sterilizing effect of pathogens has consequences for pathogen evolution. When pathogens castrate hosts, selection forces them to minimize mortality virulence; moreover, when transmission trades off with sterility alone, resistance plasticity is sufficient to prevent pathogens from evolving to fully castrate.
The legacy effects of keystone individuals on collective behaviour scale to how long they remain within a group
Authors: Pruitt Jonathan N. , Pinter-Wollman Noa
Published: September 2015

The collective behaviour of social groups is often strongly influenced by one or few individuals, termed here ‘keystone individuals’. We examined whether the influence of keystone individuals on collective behaviour lingers after their departure and whether these lingering effects scale with their tenure in the group. In the social spider,Stegodyphus dumicola, colonies' boldest individuals wield a disproportionately large influence over colony behaviour. We experimentally manipulated keystones' tenure in laboratory-housed colonies and tracked their legacy effects on collective prey capture following their removal. We found that bolder keystones caused more aggressive collective foraging behaviour and catalysed greater inter-individual variation in boldness within their colonies. The longer keystones remained in a colony, the longer both of these effects lingered after their departure. Our data demonstrate that, long after their disappearance, keystones have large and lasting effects on social dynamics at both the individual and colony levels.
Eukaryotic origins
Authors: Lake James A.
Published: September 2015

The origin of the eukaryotes is a fundamental scientific question that for over 30 years has generated a spirited debate between the competing Archaea (or three domains) tree and the eocyte tree. As eukaryotes ourselves, humans have a personal interest in our origins. Eukaryotes contain their defining organelle, the nucleus, after which they are named. They have a complex evolutionary history, over time acquiring multiple organelles, including mitochondria, chloroplasts, smooth and rough endoplasmic reticula, and other organelles all of which may hint at their origins. It is the evolutionary history of the nucleus and their other organelles that have intrigued molecular evolutionists, myself included, for the past 30 years and which continues to hold our interest as increasingly compelling evidence favours the eocyte tree. As with any orthodoxy, it takes time to embrace new concepts and techniques.
Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist
Authors: Katz Laura A.
Published: September 2015

While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.
Endosymbiotic theories for eukaryote origin
Authors: Martin William F. , Garg Sriram , Zimorski Verena
Published: September 2015

For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.
What's in a genome? The C-value enigma and the evolution of eukaryotic genome content
Authors: Elliott Tyler A. , Gregory T. Ryan
Published: September 2015

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.
New substitution models for rooting phylogenetic trees
Authors: Williams Tom A. , Heaps Sarah E. , Cherlin Svetlana , Nye Tom M. W. , Boys Richard J. , Embley T. Martin
Published: September 2015

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.
Psittacosis associated with pet bird ownership: a concern for public health
Authors: Ferreira Vivian Lindmayer , Silva Marcos Vinícius , Nascimento Rodrigo Delfino , Raso Tânia Freitas
Published: September 2015

Introduction:

Psittacosis is a zoonotic infectious disease caused by Chlamydia psittaci and most cases involve avian contact history. In humans, psittacosis induces symptoms ranging from mild ‘flu-like’ symptoms to serious atypical pneumonia. Unless specifically thought of, the diagnosis of psittacosis can be missed and the disease is usually treated as atypical pneumonia. Here, we detail cases of psittacosis related to pet birds.

Case presentation:

A 16-year-old male was admitted with fever and persistent cough. The patient reported previous treatment with broad-spectrum antibiotics that led to limited improvement of his condition, and owning pet birds; thus, psittacosis was suspected. Serum samples from the patient were obtained and tested using a microimmunofluorescence assay, revealing an IgG titre of 64. An epidemiological investigation was conducted in five family members related to the patient; two possessed anti-C. psittaci antibodies (IgG titre = 64 and IgM titre = 20; IgG titre = 128 and IgA titre = 20). Additionally, C. psittaci DNA was detected by PCR carried out on the family's pet birds.

Conclusion:

Psittacosis probably occurs more often than reported. Individuals with milder cases may not seek medical attention, and physicians may not inquire about bird exposure. There is a need for awareness campaigns directed at health workers and birds owners.
Small Heat Shock Proteins and Eicosanoid Pathways Modulate Caspase-1 Activity in the Fat Bodies ofAntheraea pernyi
Authors: Zhang Congfen , Wang Lei , Wei Guoqing , Qian Cen , Dai Lishang , Sun Yu , Zhu Baojian , Liu Chaoliang
Published: September 2015

After heat shock injury, a group of proteins that regulate protein-folding processes are synthesised to prevent damage. Caspase is an enzyme responsible for the execution ostress-induced apoptosis. Heat shock proteins (Hsp) are capable of modulating caspase activity. In addition to changes in protein synthesis, heat shock causes the release of arachidonic acid (AA) from plasma membranes and the subsequent synthesis of eicosanoids, i.e., activation of the AA pathways. The development of cytoprotective strategies might depend on whether caspase-1 activity is affected by heat shock preconditioning and the associated pharmacological modulations after heat shock injury. Therefore, we studied the effects of heat shock preconditioning and modulations of the eicosanoid pathways onAp-sHSP20.8and on the final apoptotic effector enzyme caspase-1 to clarify whether these effects were modulated in the fat bodies ofAntheraea pernyiinjured by heat shock. We concluded that eicosanoid biosynthesis inhibitors might be utilised to simultaneously decrease Hsp 20.8 synthesis and to increase caspase-1 activity. Modifications of the eicosanoid pathways might also be used to mediate caspase-1 activity under hyperthermic conditions, suggesting a novel mechanism for regulation of caspase-1 in the fat bodies ofA. pernyi
A Comparison of Methods: Normalizing High-Throughput RNA Sequencing Data
Authors: Reddy Rahul
Published: September 2015

As RNA-Seq and other high-throughput sequencing grow in use and remain critical for gene expression studies, technical variability in counts data impedes studies of differential expression studies, data across samples and experiments, or reproducing results. Studies likeDillies et al. (2013)compare several between-lane normalization methods involving scaling factors, whileHansen et al. (2012)andRisso et al. (2014)propose methods that correct for sample-specific bias or use sets of control genes to isolate and remove technical variability. This paper evaluates four normalization methods in terms of reducingintra-group, technical variability and facilitating differential expression analysis or other research where the biological,inter-groupvariability is of interest. To this end, the four methods were evaluated in differential expression analysis between data fromPickrell et al. (2010)andMontgomery et al. (2010)and between simulated data modeled on these two datasets. Though the between-lane scaling factor methods perform worse on real data sets, they are much stronger for simulated data. We cannot reject the recommendation of Dillies et al. to use TMM and DESeq normalization, but further study of power to detect effects of different size under each normalization method is merited.
Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England
Authors: Jeffries Daniel L , Copp Gordon H , Handley Lori Lawson , Sayer Carl D , Hänfling Bernd
Published: September 2015

A fundamental consideration for the conservation of a species is the extent of its native range, however defining a native range is often challenging as changing environments drive shifts in species distributions over time. The crucian carp,Carassius carassius(L.) is a threatened freshwater fish native to much of Europe, however the extent of this range is ambiguous. One particularly contentious region is England, in whichC. carassiusis currently considered native on the basis of anecdotal evidence. Here, we use 13 microsatellite loci, population structure analyses and approximate bayesian computation (ABC), to empirically test the native status ofC. carassiusin England. Contrary to the current consensus, ABC yields strong support for introduced origins ofC. carassiusin England, with posterior distribution estimates placing their introduction in the 15th century, well after the loss of the doggerland landbridge. This result brings to light an interesting and timely debate surrounding our motivations for the conservation of species. We discuss this topic, and make arguments for the continued conservation ofC. carassiusin England, despite its non-native origins.