bluuebunny/crossref_metadata_2025 huggingface dataset:
Intraobserver and Interobserver Reliability of the Oberg-Manske-Tonkin (OMT) Classification: Establishing a Registry on Congenital Upper Limb Differences
Authors: Bae Donald S. , Canizares Maria F. , Miller Patricia E. , Roberts Summer , Vuillermin Carley , Wall Lindley B. , Waters Peter M. , Goldfarb Charles A.
Published: February 2016

Background:

The purpose of this investigation was to determine the reliability of the Oberg-Manske-Tonkin (OMT) classification system applied to patients enrolled in a prospective, multicenter cohort study of congenital upper limb differences. Our hypothesis was that the OMT classification would exhibit high intraobserver and interobserver reliability and thus would be an appropriate tool for the new Congenital Upper Limb Differences registry.

Methods:

Four pediatric hand surgeons independently reviewed the medical records, clinical photographs, and radiographs of 60 randomly selected patients previously enrolled in the Congenital Upper Limb Differences registry. Patient’s information was summarized and shared electronically (PowerPoint). Each rater classified each congenital anomaly according to the OMT classification system. Responses were recorded using a web-based data capture tool (REDCap). Three weeks later, the surgeons repeated the process. Intraobserver reliability for each rater was assessed using Fleiss’ κ. Interobserver reliability was assessed using percent exact agreement (when all 4 raters were in agreement) as well as Fleiss’ κ.

Results:

Using the OMT classification, intraobserver reliability for the 4 pediatric hand surgeons showed almost perfect agreement, with κ values in the range of 0.89 to 0.93. Interobserver reliability demonstrated substantial agreement, with κ value of 0.79 (95% confidence interval, 0.77-0.82) in the first reading and 0.80 (95% confidence interval, 0.77-0.83) in the second reading. The highest possible agreement (κ=1) was seen for the following diagnoses: congenital dislocation of radial head (OMT I.A.2.v), Madelung deformity (I.A.2.vii), radial polydactyly (I.B.2.iii), triphalangeal thumb (I.B.2.iv), Kirner deformity (I.B.4.vi), and osteochondromatosis (3.B.4.i).

Conclusions:

The OMT classification of congenital upper limb differences exhibits substantial to almost perfect intraobserver and interobserver reliability among pediatric hand surgeons at different institutions. The OMT is therefore well-suited for classification of congenital upper limb anomalies in patients enrolled in a multicenter registry.

Level of Evidence:

Level II—diagnostic.
Trajectories and Prognosis of Older Patients Who Have Prolonged Mechanical Ventilation After High-Risk Surgery
Authors: Nabozny Michael J. , Barnato Amber E. , Rathouz Paul J. , Havlena Jeffrey A. , Kind Amy J. , Ehlenbach William J. , Zhao Qianqian , Ronk Katie , Smith Maureen A. , Greenberg Caprice C. , Schwarze Margaret L.
Published: February 2016

Objectives:

Surgical patients often receive routine postoperative mechanical ventilation with excellent outcomes. However, older patients who receive prolonged mechanical ventilation may have a significantly different long-term trajectory not fully captured in 30-day postoperative metrics. The objective of this study is to describe patterns of mortality and hospitalization for Medicare beneficiaries 66 years old and older who have major surgery with and without prolonged mechanical ventilation.

Design:

Retrospective cohort study.

Setting:

Hospitals throughout the United States.

Patients:

Five percent random national sample of elderly Medicare beneficiaries (age ≥ 66 yr) who underwent 1 of 227 operations previously defined as high risk during an inpatient stay at an acute care hospital between January 1, 2005, and November 30, 2009.

Interventions:

None.

Measurements and Main Results:

We identified 117,917 episodes for older patients who had high-risk surgery; 4% received prolonged mechanical ventilation during the hospitalization. Patients who received prolonged mechanical ventilation had higher 1-year mortality rate than patients who did not have prolonged ventilation (64% [95% CI, 62–65%] vs 17% [95% CI, 16.4–16.9%]). Thirty-day survivors who received prolonged mechanical ventilation had a 1-year mortality rate of 47% (95% CI, 45–48%). Thirty-day survivors who did not receive prolonged ventilation were more likely to be discharged home than patients who received prolonged ventilation 71% versus 10%. Patients who received prolonged ventilation and were not discharged by postoperative day 30 had a substantially increased 1-year mortality (adjusted hazard ratio, 4.39 [95% CI, 3.29–5.85]) compared with patients discharged home by day 30. Hospitalized 30-day survivors who received prolonged mechanical ventilation and died within 6 months of their index procedure spent the majority of their remaining days hospitalized.

Conclusions:

Older patients who require prolonged mechanical ventilation after high-risk surgery and survive 30 days have a significant 1-year risk of mortality and high burdens of treatment. This difficult trajectory should be considered in surgical decision making and has important implications for surgeons, intensivists, and patients.
Sustained Clostridium tertium Bacteremia in a Nonneutropenic Patient
Authors: Nambiar Puja H. , Belden Katherine A. , Roslund Brian , Silibovsky Randi
Published: February 2016

We report a case of sustained Clostridium tertium bacteremia mimicking an endovascular infection in a nonneutropenic patient with metastatic pancreatic neuroendocrine cancer. Clostridium tertium infection has been increasingly recognized in immunocompromised patients. The significance of this organism in nonneutropenic host, however, is unclear. The diagnosis and treatment can be challenging owing to morphology and antibiotic resistance patterns. Newer rapid identification testing with mass spectrometry enables for early diagnosis and treatment. We discuss the clinical significance of C. tertium as an emerging pathogen with review of the literature.
Chronic Hepatitis B Virus Infection
Authors: Yuen Man-Fung , Ahn Sang Hoon , Chen Ding-Shinn , Chen Pei-Jer , Dusheiko Geoffrey M. , Hou Jin-Lin , Maddrey Willis C. , Mizokami Masashi , Seto Wai-Kay , Zoulim Fabien , Lai Ching-Lung
Published: February 2016

Chronic hepatitis B virus (HBV) infection evolves from immune-tolerance phase, through immune clearance phase to a quiescent phase or reactivation as hepatitis B e antigen-negative hepatitis. Persistent infection may result in the development of cirrhosis and hepatocellular carcinoma (HCC). Host factors including gender, age, family history, HLA-DP, and viral factors including HBV DNA, genotypes, precore mutations, pre-S deletions, and hepatitis B surface antigen (HBsAg) level are associated with the development of these complications. Risk scores for the development of HCC have been derived. Patients with persistently elevated alanine aminotransferase levels (>30 for males; >19 U/L for females) and HBV DNA levels >2000 IU/mL should be treated. Patients with established cirrhosis with detectable HBV DNA should also be treated. The recommended first-line agents include pegylated interferon and 2 nucleos(t)ide analogs, entecavir and tenofovir. NAs require long-term treatment to maintain suppression of HBV DNA. They have been shown to decrease hepatic fibrosis, or reverse cirrhosis and to reduce the development of HCC. They have very low rates (0% to 1.2%) of resistance. HBsAg seroclearance, although the ideal endpoint, is only achievable in 10% to 12% of patients by multicenter trials usually studying relatively young patients. Patients on long-term treatment should be monitored for viral breakthrough that may be due to noncompliance or the development of resistance. Newer agents are under trials to enhance the rate of HBsAg seroclearance. However, even with the current NAs, long-term treatment of >6 years can markedly reduce the covalently closed circular DNA, the viral component responsible for initiation of viral replication.
Effectiveness of Systemic Fluconazole in Adult Patients With Asymptomatic Candiduria: A Systematic Review and Meta-Analysis
Authors: Chaari Anis , Ismail Mohamed , Abdel Hakim Karim , Said Mahmoud Tarek , Boussalmi Kamel , Elsaka Ahmed , Al Khaja Mariem , Kauts Vipin , Casey William Francis
Published: February 2016

Asymptomatic candiduria is a common finding in hospitalized patients. Its management modalities are still a matter of debate. Urinary catheter should be removed or replaced in all cases. In the current meta-analysis, we aimed to compare 2 different strategies in term of candida clearance from the urinary tract: Systemic fluconazole versus conservative management. A systematic search was performed in Pubmed, Web of science, and Cochrane Library database by 2 investigators. Three studies were included (421 patients). Data were extracted and the quality of each study was assessed. Systemic fluconazole was associated with a significantly higher short-term clearance of the funguria after 14 days of treatment [odds ratio = 0.43; confidence interval (CI) 95% (0.26–0.65)]. No significant heterogeneity was found among the included studies (Q statistic test = 0.38; I2 = 0). In conclusion, fluconazole significantly hasten short-term candida clearance from the urinary tract.
Efficacy and Safety of Opioids for the Prevention of Etomidate-Induced Myoclonus: A Meta-Analysis
Authors: Wang Jiang , Li Qing-Bo , Wu Yuan-Yuan , Wang Bao-Ning , Kang Jin-Long , Xu Xue-Wu
Published: February 2016

Etomidate is a widely used hypnotic drug for induction of general anesthesia and sedation, especially in elderly patients and hemodynamically unstable patients. Myoclonus, however, is the most prominent problem during induction of anesthesia with etomidate. Many agents have been used to prevent it and opioid is one of them. This meta-analysis was to evaluate effects of opioids pretreatment for preventing etomidate-induced myoclonus. We searched the PubMed, EMBASE, and the Cochrane Library databases and published studies in English updated to September 2015. Randomized controlled trials of opioids versus placebo/control in patients were included. We evaluated the prophylactic effect of opioids on etomidate-induced myoclonus. All statistical analysis was performed using RevMan 5.2 software. Nine randomized controlled trials involving 604 participants were included. The results indicated that compared with placebo/control, opioids allow more patients to experience no myoclonic movements after etomidate injection [risk ratio (RR) 2.76, 95% confidence interval (CI) 1.75–4.37, P < 0.0001]. The numbers of patients with mild myoclonus [(RR) 0.53, 95% (CI) 0.36–0.78, P = 0.001], moderate myoclonus [(RR) 0.36, 95% (CI) 0.23–0.55, P < 0.00001], and severe myoclonus [(RR) 0.20, 95% (CI) 0.08–0.52, P = 0.0009] after etomidate injection were significantly decreased with the pretreatment of opioids. This meta-analysis suggests that pretreatment with opioids before injecting etomidate was effective for preventing etomidate-induced myoclonus and can reduce the intensity of myoclonus without any adverse effects.
Gardner Fibroma: Clinical and Histopathologic Implications of Germline APC Mutation Association
Authors: Dahl Nathan A. , Sheil Amy , Knapke Sarah , Geller James I.
Published: February 2016

The proportion and clinical characteristics of Gardner fibromas (GAFs) that are sporadic versus familial adenomatous polyposis (FAP)-associated have not been clearly established. We report on 7 patients diagnosed with GAF who underwent APC sequencing and duplication/deletion testing. Three (43%) were found to have underlying APC germline perturbations consistent with FAP; these patients had multifocal (1) or large; unresectable (2) GAFs. The 4 patients with negative APC testing each had a single resectable GAF. β-catenin reactivity was noted in all FAP-associated GAFs and in 1/4 APC wild-type cases. FAP-associated GAFs may be less common than sporadic GAFs and can demonstrate clinically distinct features.
Using Virtual Patients to Teach Empathy
Authors: Foster Adriana , Chaudhary Neelam , Kim Thomas , Waller Jennifer L. , Wong Joyce , Borish Michael , Cordar Andrew , Lok Benjamin , Buckley Peter F.
Published: February 2016

Introduction

Physician empathy is a complex phenomenon known to improve illness outcomes; however, few tools are available for deliberate practice of empathy. We used a virtual patient (VP) to teach empathic communication to first-year medical students. We then evaluated students’ verbal empathy in a standardized patient (SP) interaction.

Methods

Seventy medical students, randomly assigned to 3 separate study groups, interacted with (1) a control VP portraying depression, (2) a VP with a backstory simulating patient shadowing, or (3) a VP able to give immediate feedback about empathic communication (empathy-feedback VP). Subsequently, the students interviewed an SP portraying a scenario that included opportunities to express empathy. All SP interviews were recorded and transcribed. The study outcomes were (1) the students’ verbal response to the empathic opportunities presented by the SP, as coded by reliable assessors using the Empathic Communication Coding System, and (2) the students’ responses as coded by the SPs, using a communication checklist.

Results

There were no significant differences in student demographics between groups. The students who interacted with the empathy-feedback VP showed higher empathy in the SP interview than did the students in the backstory VP and the control VP groups [mean (SD) empathy scores coded on a 0–6 scale were 2.91 (0.16) vs. 2.20 (0.22) and 2.27 (0.21), respectively). The difference in scores was significant only for the empathy-feedback VP versus the backstory VP group (P = 0.027). The SPs rated the empathy-feedback and the backstory VP groups significantly higher than the control VP group on offering empathic statements (P < 0.0001), appearing warm and caring (P = 0.015), and forming rapport (P = 0.004).

Conclusions

Feedback on empathy in a VP interaction increased students’ empathy in encounters with SPs, as rated by trained assessors, whereas a simulation of patient shadowing did not. Both VP interventions increased students’ empathy as rated by SPs, compared with the control VP group.
Dementia and Cognitive Impairment Prevalence and Associated Factors in Indigenous Populations
Authors: de Souza-Talarico Juliana N. , de Carvalho Anna P. , Brucki Sonia M.D. , Nitrini Ricardo , Ferretti-Rebustini Renata E.de.L.
Published: February 2016

Population aging has been accompanied by worldwide growth in dementia. However, little is known about the prevalence of dementia and cognitive impairment not dementia in ethnically diverse populations, such as indigenous populations conceptualized as groups of persons who self-identify as indigenous and who are recognized as distinctive communities reproducing ancestral, historical, and territorial culture. This is particularly relevant in view of increasing life expectancy in indigenous populations and, consequently, in the number of elderly people, as well as the changes in their multimorbidity profile. In this study, a systematic review of the literature on the subject “cognitive impairment in indigenous elderly population” in the databases MEDLINE via PubMed, Lilacs, and Scopus showed that the prevalence of dementia in indigenous populations between 45 and 94 years old, originally from different countries, varied between 0.5% and 26.8% for age 60 and older, whereas the prevalence of cognitive impairment not dementia varied between 4.4% and 17.7%. Early onset of the disease, older age, low education level, and several poor health conditions were associated with prevalence rates and conversion from normal to any cognitive impairment. Cultural inadequacy of neuropsychological tests was the main factor reported in the selected studies, which makes the investigation of dementia a challenge in indigenous populations. These data reveal that the prevalence rates of dementia ranged from low to very high for those aged 60 years and older, with early onset of the disease and elevated mortality rate after initial diagnosis compared with the current global prevalence studies, suggesting that these individuals may be more vulnerable to cognitive disorders. Cognitive reserve and exposure to poor health status throughout life span may be considered in the interpretation of results.
Ophthalmological Assessment of OCT and Electrophysiological Changes in Migraine Patients
Authors: Verroiopoulos George V. , Nitoda Eirini , Ladas Ioannis D. , Brouzas Dimitrios , Antonakaki Dimitra , Moschos Marilita M.
Published: February 2016

Background:

A cross-sectional study to investigate the morphological and functional changes of the visual pathway taking place in patients with migraine.

Methods:

Fifteen patients (14 female, 1 male) diagnosed with migraine with aura and 23 patients (21 female, 2 male) diagnosed with migraine without aura were compared with 20 healthy volunteers (18 female, 2 male). All the participants underwent optical coherence tomography scan, electroretinogram (ERG), visual evoked potentials, and multifocal electroretinogram (mf-ERG) recording.

Results:

Assessing ERG recordings, no significant differences in mean N1-P1 amplitudes were measured among the groups. The mean visual evoked potentials N80-P100 amplitudes were not significantly different among the three groups (one way analysis of variance: P = 0.075, F = 2.718). No significant difference was found in P100 latency times among groups. The mean retinal response density of mf-ERG in ring 1 was higher in healthy individuals compared with migraineurs, with statistical significance (Kruskal–Wallis analysis of variance and Dunn multiple comparisons test; P < 0.001, mean rank difference = −24.857 and P < 0.001, mean rank difference = −20.9, for migraine with aura-control and migraine without aura-control comparisons, respectively). In migraine with aura subjects, retinal nerve fiber layer thickness in superior and inferior quadrants was significantly decreased compared with healthy individuals, whereas in migraine without aura group, only the superior quadrant was significantly thinner compared with the control group.

Conclusions:

Retinal response density in mfERG of all migraineurs was significantly lessened compared with healthy individuals. There was no significant difference in visual evoked potentials N80-P100 amplitudes or P100 latencies among the groups. Moreover, retinal nerve fiber layer thinning observed in patients with migraine compared with control subjects, appeared statistically significant in some quadrants. The authors may be able to defend the retinal blood flow decrease theory in migraine. The results also indicate that several levels of the visual pathway seem to be affected in migraineurs.
Ancient hybrid origin of the eastern wolf not yet off the table: a comment on Rutledgeet al. (2015)
Authors: Sefc Kristina M. , Koblmüller Stephan
Published: February 2016

A recent study of North American canids by Rutledgeet al.(Biol. Lett.11, 20150303 (doi:10.1098/rsbl.2015.0303)) refutes the hypothesized hybrid origin of the eastern wolf (EW) based on genomic evidence against very recent hybridization. However, the analyses do not rule out the possibility of more ancient hybridization. Claims to have resolved the evolutionary origin of the EW are therefore inappropriate. Importantly, though, we plead that uncertainty about the ancient history of the taxon should not affect current conservation policy.
Pharmacological removal of serum amyloid P component from intracerebral plaques and cerebrovascular Aβ amyloid depositsin vivo
Authors: Al-Shawi Raya , Tennent Glenys A. , Millar David J. , Richard-Londt Angela , Brandner Sebastian , Werring David J. , Simons J. Paul , Pepys Mark B.
Published: February 2016

Human amyloid deposits always contain the normal plasma protein serum amyloid P component (SAP), owing to its avid but reversible binding to all amyloid fibrils, including the amyloid β (Aβ) fibrils in the cerebral parenchyma plaques and cerebrovascular amyloid deposits of Alzheimer's disease (AD) and cerebral amyloid angiopathy (CAA). SAP promotes amyloid fibril formationin vitro, contributes to persistence of amyloidin vivoand is also itself directly toxic to cerebral neurons. We therefore developed (R)-1-[6-[(R)-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid (CPHPC), a drug that removes SAP from the blood, and thereby also from the cerebrospinal fluid (CSF), in patients with AD. Here we report that, after introduction of transgenic human SAP expression in the TASTPM double transgenic mouse model of AD, all the amyloid deposits contained human SAP. Depletion of circulating human SAP by CPHPC administration in these mice removed all detectable human SAP from both the intracerebral and cerebrovascular amyloid. The demonstration that removal of SAP from the blood and CSF also removes it from these amyloid deposits crucially validates the strategy of the forthcoming ‘Depletion of serum amyloid P component in Alzheimer's disease (DESPIAD)’ clinical trial of CPHPC. The results also strongly support clinical testing of CPHPC in patients with CAA.
Computational exploration of the reaction mechanism of the Cu
+
-catalysed synthesis of indoles from
N
-aryl enaminones
Authors: Bernardo Carlos E. P. , Silva Pedro J.
Published: February 2016

We have studied the role of Cu
+
-phenantroline as a catalyst in the cyclization of
N
-aryl-enaminones using density-functional theory computations. The catalyst was found to bind the substrate upon deprotonation of its eneaminone, and to dramatically increase the acidity of the carbon adjacent to the ketone functionality. The deprotonation of this carbon atom yields a carbanion which attacks the aryl moiety, thereby closing the heterocycle in the rate-determining step. This C–C bond forming reaction was found to proceed much more rapidly when preceded by re-protonation of the substrate N-atom (which had lost H
+
in the initial step). Hydride transfer to the catalyst then completes the indole synthesis, in a very fast step. The influence of Li
+
and K
+
on the regio-selectivity of the cyclization of bromo-substituted analogues could not, however, be reproduced by our model. Alternative pathways involving either single-electron transfer from the catalyst to the substrate or ring cyclization without previous carbon
α
-deprotonation were found to be kinetically or thermodynamically inaccessible.
Unified analytical expressions of the three-dimensional fundamental solutions and their derivatives for linear elastic anisotropic materials
Authors: Xie Longtao , Zhang Chuanzeng , Sladek Jan , Sladek Vladimir
Published: February 2016

Novel unified analytical displacement and stress fundamental solutions as well as the higher order derivatives of the displacement fundamental solutions for three-dimensional, generally anisotropic and linear elastic materials are presented in this paper. Adequate integral expressions for the displacement and stress fundamental solutions as well as the higher order derivatives of the displacement fundamental solutions are evaluated analytically by using the Cauchy residue theorem. The resulting explicit displacement fundamental solutions and their first and second derivatives are recast into convenient analytical forms which are valid for non-degenerate, partially degenerate, fully degenerate and nearly degenerate cases. The correctness and the accuracy of the novel unified and closed-form three-dimensional anisotropic fundamental solutions are verified by using some available analytical expressions for both transversely isotropic (non-degenerate or partially degenerate) and isotropic (fully degenerate) linear elastic materials.
Explanation of
ν
= −½ fractional quantum Hall state in bilayer graphene
Authors: Jacak J. , Jacak L.
Published: February 2016

The commensurability condition is applied to determine the hierarchy of fractional filling of Landau levels for fractional quantum Hall effect (FQHE) in monolayer and bilayer graphene. Good agreement with experimental data is achieved. The presence of even-denominator filling fractions in the hierarchy of the FQHE in bilayer graphene is explained, including the state at

ν
=
−

1
2

.
Asymmetric bifurcation of thermally and electrically actuated functionally graded material microbeam
Authors: Chen X. , Meguid S. A.
Published: February 2016

In this paper, we investigate the symmetric snap-through buckling and the asymmetric bifurcation behaviours of an initially curved functionally graded material (FGM) microbeam subject to the electrostatic force and uniform/non-uniform temperature field. The beam model is developed in the framework of Euler–Bernoulli beam theory, accounting for the through-thickness power law variation of the beam material and the physical neutral plane. Based on the Galerkin decomposition method, the beam model is simplified as a 2 d.f. reduced-order model, from which the necessary snap-through and symmetry breaking criteria are derived. The results of our work reveal the significant effects of the power law index on the snap-through and symmetry breaking criteria. Our results also reveal that the non-uniform temperature field can actuate the FGM microbeam and induce the snap-through and asymmetric bifurcation behaviours.
Predators inhibit brain cell proliferation in natural populations of electric fish,
Brachyhypopomus occidentalis
Authors: Dunlap Kent D. , Tran Alex , Ragazzi Michael A. , Krahe Rüdiger , Salazar Vielka L.
Published: February 2016

Compared with laboratory environments, complex natural environments promote brain cell proliferation and neurogenesis. Predators are one important feature of many natural environments, but, in the laboratory, predatory stimuli tend to inhibit brain cell proliferation. Often, laboratory predatory stimuli also elevate plasma glucocorticoids, which can then reduce brain cell proliferation. However, it is unknown how natural predators affect cell proliferation or whether glucocorticoids mediate the neurogenic response to natural predators. We examined brain cell proliferation in six populations of the electric fish,
Brachyhypopomus occidentalis
, exposed to three forms of predator stimuli: (i) natural variation in the density of predatory catfish; (ii) tail injury, presumably from predation attempts; and (iii) the acute stress of capture. Populations with higher predation pressure had lower density of proliferating (PCNA+) cells, and fish with injured tails had lower proliferating cell density than those with intact tails. However, plasma cortisol did not vary at the population level according to predation pressure or at the individual level according to tail injury. Capture stress significantly increased cortisol, but only marginally decreased cell proliferation. Thus, it appears that the presence of natural predators inhibits brain cell proliferation, but not via mechanisms that depend on changes in basal cortisol levels. This study is the first demonstration of predator-induced alteration of brain cell proliferation in a free-living vertebrate.
Ancient origin of high taxonomic richness among insects
Authors: Clapham Matthew E. , Karr Jered A. , Nicholson David B. , Ross Andrew J. , Mayhew Peter J.
Published: February 2016

Insects are a hyper-diverse group, comprising nearly three-quarters of all named animal species on the Earth, but the environmental drivers of their richness and the roles of ecological interactions and evolutionary innovations remain unclear. Previous studies have argued that family-level insect richness increased continuously over the evolutionary history of the group, but inclusion of extant family records artificially inflated the relative richness of younger time intervals. Here we apply sampling-standardization methods to a species-level database of fossil insect occurrences, removing biases present in previous richness curves. We show that insect family-richness peaked 125 Ma and that Recent values are only 1.5–3 times as high as the Late Palaeozoic. Rarefied species-richness data also tentatively suggest little or no net increase in richness over the past 125 Myr. The Cretaceous peak in family richness was coincident with major radiations within extant groups but occurred prior to extinctions within more basal groups. Those extinctions may in part be linked to mid-Cretaceous floral turnover following the evolution of flowering plants. Negligible net richness change over the past 125 Myr implies that major radiations within extant groups were offset by reduced richness within groups that are now relict or extinct.
High proportion of smaller ranged hummingbird species coincides with ecological specialization across the Americas
Authors: Sonne Jesper , Martín González Ana M. , Maruyama Pietro K. , Sandel Brody , Vizentin-Bugoni Jeferson , Schleuning Matthias , Abrahamczyk Stefan , Alarcón Ruben , Araujo Andréa C. , Araújo Francielle P. , Mendes de Azevedo Severino , Baquero Andrea C. , Cotton Peter A. , Ingversen Tanja Toftemark , Kohler Glauco , Lara Carlos , Guedes Las-Casas Flor Maria , Machado Adriana O. , Machado Caio Graco , Maglianesi María Alejandra , Moura Alan Cerqueira , Nogués-Bravo David , Oliveira Genilda M. , Oliveira Paulo E. , Ornelas Juan Francisco , Rodrigues Licléia da Cruz , Rosero-Lasprilla Liliana , Rui Ana Maria , Sazima Marlies , Timmermann Allan , Varassin Isabela Galarda , Wang Zhiheng , Watts Stella , Fjeldså Jon , Svenning Jens-Christian , Rahbek Carsten , Dalsgaard Bo
Published: February 2016

Ecological communities that experience stable climate conditions have been speculated to preserve more specialized interspecific associations and have higher proportions of smaller ranged species (SRS). Thus, areas with disproportionally large numbers of SRS are expected to coincide geographically with a high degree of community-level ecological specialization, but this suggestion remains poorly supported with empirical evidence. Here, we analysed data for hummingbird resource specialization, range size, contemporary climate, and Late Quaternary climate stability for 46 hummingbird–plant mutualistic networks distributed across the Americas, representing 130 hummingbird species (
ca
40% of all hummingbird species). We demonstrate a positive relationship between the proportion of
SRS of hummingbirds
and community-level specialization, i.e. the division of the floral niche among coexisting hummingbird species. This relationship remained strong even when accounting for climate, furthermore, the effect of SRS on specialization was far stronger than the effect of specialization on SRS, suggesting that climate largely influences specialization through species' range-size dynamics. Irrespective of the exact mechanism involved, our results indicate that communities consisting of higher proportions of SRS may be vulnerable to disturbance not only because of their small geographical ranges, but also because of their high degree of specialization.
Regulatory links between imprinted genes: evolutionary predictions and consequences
Authors: Patten Manus M. , Cowley Michael , Oakey Rebecca J. , Feil Robert
Published: February 2016

Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect tocis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes actsin transon the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of thesetrans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.
Phylogeny and adaptation shape the teeth of insular mice
Authors: Ledevin Ronan , Chevret Pascale , Ganem Guila , Britton-Davidian Janice , Hardouin Emilie A. , Chapuis Jean-Louis , Pisanu Benoit , da Luz Mathias Maria , Schlager Stefan , Auffray Jean-Christophe , Renaud Sabrina
Published: February 2016

By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation.
Inter- and intraspecific conflicts between parasites over host manipulation
Authors: Hafer Nina , Milinski Manfred
Published: February 2016

Host manipulation is a common strategy by which parasites alter the behaviour of their host to enhance their own fitness. In nature, hosts are usually infected by multiple parasites. This can result in a conflict over host manipulation. Studies of such a conflict in experimentally infected hosts are rare. The cestodeSchistocephalus solidus(S) and the nematodeCamallanus lacustris(C) use copepods as their first intermediate host. They need to grow for some time inside this host before they are infective and ready to be trophically transmitted to their subsequent fish host. Accordingly, not yet infective parasites manipulate to suppress predation. Infective ones manipulate to enhance predation. We experimentally infected laboratory-bred copepods in a manner that resulted in copepods harbouring (i) an infective C plus a not yet infective C or S, or (ii) an infective S plus a not yet infective C. An infective C completely sabotaged host manipulation by any not yet infective parasite. An infective S partially reduced host manipulation by a not yet infective C. We hence show experimentally that a parasite can reduce or even sabotage host manipulation exerted by a parasite from a different species.
Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins
Authors: Grosser Stefanie , Rawlence Nicolas J. , Anderson Christian N. K. , Smith Ian W. G. , Scofield R. Paul , Waters Jonathan M.
Published: February 2016

The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (
Eudyptula novaehollandiae
) in southeastern New Zealand may potentially represent an additional ‘cryptic’ invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical
Eudyptula
remains to reveal that the arrival of
E. novaehollandiae
in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic
Eudyptula minor
. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
Authors: Lees John A. , Vehkala Minna , Välimäki Niko , Harris Simon R. , Chewapreecha Claire , Croucher Nicholas J. , Marttinen Pekka , Davies Mark R. , Steer Andrew C. , Tong Stephen Y. C. , Honkela Antti , Parkhill Julian , Bentley Stephen D. , Corander Jukka
Published: February 2016

Bacterial genomes vary extensively in terms of both gene content and gene sequence – this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogensStreptococcus pneumoniaeandStreptococcus pyogenes, SEER identifies relevant previously characterised resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness ofS. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.
Predicting protein thermal stability changes upon point mutations using statistical potentials: IntroducingHoTMuSiC
Authors: Pucci Fabrizio , Bourgeas Raphael , Rooman Marianne
Published: February 2016

The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTmupon point mutations, given the protein structure and, when available, the melting temperatureTmof the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTmvalues of 4.2°C that reduces to 2.9°C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use atsoft.dezyme.com.
Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population
Authors: Timothée Bonnet , Peter Wandeler , Glauco Camenisch , Erik Postma
Published: February 2016

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions: Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called ‘stasis paradox’ highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e. with a lowpotentialadult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non-causal (i.e. non-genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level thereby enabled us to uncover adaptive evolution in action, and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change.
gEVAL – A web based browser for evaluating genome assemblies
Authors: Chow William , Brugger Kim , Caccamo Mario , Sealy Ian , Torrance James , Howe Kerstin
Published: February 2016

Motivation

For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. While gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.

Availability

Web Browser:http://geval.sanger.ac.uk, Plugin:http://wchow.github.io/wtsi-geval-plugin.

Contact

kj2@sanger.ac.uk

Supplementary information

Supplementary data are available atBioinformaticsonline.
Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns
Authors: Shao Zhu-Qing , Xue Jia-Yu , Wu Ping , Zhang Yan-Mei , Wu Yue , Hang Yue-Yu , Wang Bin , Chen Jian-Qun
Published: February 2016

Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.
On ethnicity of idiosyncratic risk and stock returns puzzle
Authors: Al Rahahleh Naseem , Adeinat Iman , Bhatti Ishaq
Published: February 2016

Purpose

– The purpose of this paper is to understand the controversial issue of whether stock returns and idiosyncratic risks are related positively or negatively in case of Singaporean ethically poor screened stocks.

Design/methodology/approach

– To achieve the major objectives of this paper, it uses a multiple regression to explore the relationship between expected stock returns and idiosyncratic risk. The paper replicates the Lee and Faff’s (2009) three-factor capital asset-pricing model (CAPM) model in creating the six size/book-to-market portfolios from which it constructs the small minus big (SMB) and high minus low (HML) portfolios that capture the size and book-to-market equity factors, respectively.

Findings

– The basic finding of the paper is that there is a strong relation between idiosyncratic risk and the expected stock returns. In more details, we observe that the portfolio of stocks with the highest idiosyncratic volatility generates higher average returns (4.36 per cent) than the portfolio of stocks with the lowest idiosyncratic volatility (0.79 per cent) over the sample period. The paper observes that the stock’s idiosyncratic volatility is inversely correlated with the size of the underlying firm. Moreover, there is a pattern of relationships nearer the periods of financial crises: Asian and global financial crises.

Research limitations/implications

– This paper uses only a three-factor model on a single country. So it cannot be generalized to a multi-country level in the Association of Southeast Asian Nations (ASEAN) region, as the structure of each member country is different.

Practical implications

– This paper provides guidelines for policymakers and foreign investors in Singapore about the relationship. This research can also be extended to other ASEAN countries to understand this puzzle.

Social implications

– Ethically sensitive and faithful investors with small investment can benefit from the findings of this paper.

Originality/value

– The work reported in this paper is original, unpublished and is also not under consideration for publication elsewhere.
Eduselling: The Role of Customer Education In Selling to Corporate Clients in the Sport Industry
Authors: Sutton William A. , Lachowetz Tony , Clark John
Published: February 2016

Eduselling is a unique form of selling as it combines needs assessments, relationship building, customer education and aftermarketing in a process that originates at the prospect targeting stage and progresses to an on-going partnership agreement. Results of proprietary research indicate that certain professional sport organizations fall short of educating corporate clients with respect to all of the benefits and attributes of the products they offer: these results led to the development of a nine-step conceptual framework designed to assist corporate salespeople in professional sport. Future research should focus on specific selling activities and attempt to identify those activities that lead to higher retention rates of corporate sponsors.