bluuebunny/crossref_metadata_2025 huggingface dataset:
Path2PPI: an R package to predict protein–protein interaction networks for a set of proteins
Authors: Philipp Oliver , Osiewacz Heinz D. , Koch Ina
Published: February 2016

Summary: We introduce Path2PPI, a new R package to identify protein–protein interaction (PPI) networks for fully sequenced organisms for which nearly none PPI are known. Path2PPI predicts PPI networks based on sets of proteins from well-established model organisms, providing an intuitive visualization and usability. It can be used to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism.

Availability and implementation: Path2PPI is an open-source tool implemented in R. It can be obtained from the Bioconductor project: http://bioconductor.org/packages/Path2PPI/

Contact: ina.koch@bioinformatik.uni-frankfurt.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
ProQ2: estimation of model accuracy implemented in Rosetta
Authors: Uziela Karolis , Wallner Björn
Published: February 2016

Motivation: Model quality assessment programs are used to predict the quality of modeled protein structures. They can be divided into two groups depending on the information they are using: ensemble methods using consensus of many alternative models and methods only using a single model to do its prediction. The consensus methods excel in achieving high correlations between prediction and true quality measures. However, they frequently fail to pick out the best possible model, nor can they be used to generate and score new structures. Single-model methods on the other hand do not have these inherent shortcomings and can be used both to sample new structures and to improve existing consensus methods.

Results: Here, we present an implementation of the ProQ2 program to estimate both local and global model accuracy as part of the Rosetta modeling suite. The current implementation does not only make it possible to run large batch runs locally, but it also opens up a whole new arena for conformational sampling using machine learned scoring functions and to incorporate model accuracy estimation in to various existing modeling schemes. ProQ2 participated in CASP11 and results from CASP11 are used to benchmark the current implementation. Based on results from CASP11 and CAMEO-QE, a continuous benchmark of quality estimation methods, it is clear that ProQ2 is the single-model method that performs best in both local and global model accuracy.

Availability and implementation:  https://github.com/bjornwallner/ProQ_scripts

Contact:  bjornw@ifm.liu.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ocean warming and elevated carbon dioxide: multiple stressor impacts on juvenile mussels from southern Chile
Authors: Navarro Jorge M. , Duarte Cristian , Manríquez Patricio H. , Lardies Marco A. , Torres Rodrigo , Acuña Karin , Vargas Cristian A. , Lagos Nelson A.
Published: February 2016

The combined effect of increased ocean warming and elevated carbon dioxide in seawater is expected to have significant physiological and ecological consequences at many organizational levels of the marine ecosystem. In the present study, juvenile mussels Mytilus chilensis were reared for 80 d in a factorial combination of two temperatures (12 and 16°C) and three pCO2 levels (380, 700, and 1000 µatm). We investigated the combined effects of increasing seawater temperature and pCO2 on the physiological performance (i.e. feeding, metabolism, and growth). Lower clearance rate (CR) occurred at the highest pCO2 concentration (1000 µatm) compared with the control (380 µatm) and with the intermediate concentration of pCO2 (700 µatm). Conversely, CR was significantly higher at 16°C than at 12°C. Significant lower values of oxygen uptake were observed in mussels exposed to 1000 µatm pCO2 level compared with those exposed to 380 µatm pCO2. Scope for growth (SFG) was significantly lower at the highest pCO2 concentration compared with the control. Mussels exposed to 700 µatm pCO2 did not show significantly different SFG from the other two pCO2 treatments. SFG was significantly higher at 16°C than at 12°C. This might be explained because the experimental mussels were exposed to temperatures experienced in their natural environment, which are within the range of thermal tolerance of the species. Our results suggest that the temperature rise within the natural range experienced by M. chilensis generates a positive effect on the processes related with energy gain (i.e. feeding and absorption) to be allocated to growth. In turn, the increase in the pCO2 level of 1000 µatm, independent of temperature, adversely affects this species, with significantly reduced energy allocated to growth (SFG) compared with the control treatment.
Skewness Preference and Seasoned Equity Offers
Authors: Autore Don M. , DeLisle Jared R.
Published: February 2016

We find that the degree of expected idiosyncratic skewness in seasoned equity issuers’ stock returns is an important determinant of flotation costs and subsequent abnormal stock performance. High skewness issuers incur significantly greater offer price discounts, particularly when institutional share allocation is largest, pay higher gross underwriting spreads, and exhibit poorer stock performance in the three years after issuance, all compared to low skewness issuers. These results suggest that skewness-induced overpricing increases the flotation costs of seasoned equity offers and leads to poor subsequent stock performance.

Received November 18, 2014; accepted December 17, 2015 by Editor Paolo Fulghieri.
Sphenoid Wing Meningioma With Extraocular Muscle Involvement Mimicking Idiopathic Orbital Inflammation
Authors: Rodríguez-Colón Gabriela , Bratton Emily M. , Serracino Hilary , Bennett Jeffrey L. , Hink Eric M.
Published: February 2016

Meningiomas are slow growing, typically benign, tumors originating from arachnoid cap cells. Specifically, sphenoid wing or spheno-orbital meningiomas infiltrate the lesser wing of the sphenoid, lateral orbital wall, and orbital roof with occasional extension to the superior orbital fissure, optic canal, anterior clinoid process, and middle cranial fossa where neurologic and ophthalmologic functions are impaired by compressive injury. The extraocular muscles are rarely involved. The authors present a rare case of an spheno-orbital meningioma causing extraocular muscle enlargement mimicking idiopathic orbital inflammation and highlight important diagnostic clues to meningioma.
Giant Ocular Horn Occurring in a 10-Year-Old Female
Authors: Armstrong Blair K. , Rabinowitz Michael P. , Levin Alex V. , Eagle Ralph C. , Snitzer Melanie , Carrasco Jacqueline
Published: February 2016

Cutaneous horns uncommonly involve the periocular region. Involvement of the ocular surface is particularly rare. The authors present a patient who underwent a perinatal buccal mucosal graft for corneal perforation due to congenital corneal ectasia, most likely resulting from Peters anomaly. She developed a giant ocular horn 10 years later.
Nodular Fasciitis of the Orbit: A Case Report Confirmed by Molecular Cytogenetic Analysis
Authors: Anzeljc Andrew J. , Oliveira Andre M. , Grossniklaus Hans E. , Kim Hee Joon , Hayek Brent
Published: February 2016

Nodular fasciitis is a benign fibroblastic proliferation typically found in the subcutaneous tissue or superficial fascia of the extremities that is often confused for malignancy. These lesions rarely occur on the eyelids and ocular adnexa and are seldom analyzed by ophthalmic pathologists. USP6 gene rearrangement has been recently demonstrated in nodular fasciitis and this rearrangement may lead to the formation of a fusion gene MYH9-USP6 in some cases. Herein, the authors describe a 38-year-old woman with a 6-month history of a progressively enlarging mass beneath her right medial upper eyelid. Histopathologic analysis of the excisional biopsy confirmed classic features of nodular fasciitis. Molecular cytogenetic analysis revealed a rearrangement of the USP6 locus, confirming the diagnosis of benign nodular fasciitis.
Eyelid Mycetoma Masquerading as Sebaceous Carcinoma
Authors: Zoroquiain Pablo , Alghamdi Sarah , Arthurs Bryan , Levin Leonard , Sheppard Donald C. , Ralph Benjamin , Burnier Julia , Burnier Miguel N.
Published: February 2016

A 56-year-old Asian woman presented with an upper eyelid mass. The lesion was exposed after eversion of the eyelid revealing a thickened tarsus with yellowish areas. Working diagnosis was sebaceous carcinoma. Biopsy was performed. Histopathological studies showed a mycotic eumycetoma with Splendore-Hoeppli phenomena and - microbiologic cultures grew Scedosporium apiospermum. The patient was started on voriconazole 200 mg po bid with adequate serum levels. A complete response was observed after 18 weeks of voriconazole therapy. To the best of our knowledge, this is the first published case of S. apiospermum eumycotic mycetoma of the eyelid. It is important to consider mycotic infection in the differential diagnosis of eyelid tumors even in healthy patients.
Assessing the Outcomes of Powered Endoscopic Dacryocystorhinostomy in Adults Using the Lacrimal Symptom (Lac-Q) Questionnaire
Authors: Ali Mohammad Javed , Iram Sadiya , Ali Mohammad Hasnat , Naik Milind N.
Published: February 2016

Purpose:

The objective of this study was to assess the quality of outcomes of powered endoscopic dacryocystorhinostomy using the lacrimal symptom (Lac-Q) questionnaire.

Methods:

Prospective interventional case series of 50 consecutive patients who underwent primary powered endoscopic dacryocystorhinostomy were included in the study. All the patients had stent placement which were removed at 4 weeks. The Lac-Q questionnaire was administered preoperatively and at 4 weeks and 16 weeks following the surgery. Outcomes assessed were anatomical success, functional success, and changes in the social impact and lacrimal symptoms scores. Statistical analysis was performed using Dunnette’s procedure with bonferroni correction.

Results:

Fifty-five powered endoscopic dacryocysto rhinostomies were performed on 50 patients. A total of 150 questionnaire responses were analyzed. At the 16 week follow up, the anatomical and functional success rates were 98% and 94%, respectively. The mean social impact scores showed significant improvement postoperatively from 3.88 to 0.3 (p ≤ 0.001). The changes in the total scores (12.5 preoperatively to 1.0 at 16 weeks follow up) were statistically significant (p ≤ 0.001). Postoperative scoring correlated well with the anatomical and functional success rates. The symptom scores reflected changes with change in the clinical condition.

Conclusion:

The Lac-Q questionnaire is a simple and useful tool to evaluate the quality of outcomes of powered endoscopic dacryocystorhinostomy.
Comparative Study of Clinical, Pathological, Radiological, and Genetic Features of Patients With Adult Ocular Adnexal Xanthogranulomatous Disease, Erdheim-Chester Disease, and IgG4-Related Disease of the Orbit/Ocular Adnexa
Authors: McKelvie Penelope , McNab Alan A. , Hardy Thomas , Rathi Vivek
Published: February 2016

Purpose:

To compare and contrast the clinical, radiologic, pathologic, and genetic features of patients with ocular adnexal IgG4-related disease (IgG4-RD) and patients with adult ocular adnexal xanthogranulomatous disease (XG).

Methods:

This retrospective review study identified patients with histological evidence of either disease from records of the pathology department of our hospital from 1996 to 2014. Clinical, imaging, and a variety of histopathologic features were collected for 23 patients with IgG4-RD and 13 patients with XG. Next generation sequencing with a 50-gene cancer screening panel was performed on biopsy tissues from 10 patients in each group.

Results:

Statistical differences between the 2 groups include eyelid (67%; p = 0.0002) and anterior orbital (75%; p = 0.0352) predilection for XG except for Erdheim-Chester disease subgroup which was more posterior and diffuse. Eyelid involvement was rare (4%) for IgG4-RD. Involvement of orbital nerves was seen in 30% of IgG4-RD and 0% in XG (p = 0.0695). Five patients with IgG4-RD developed malignancy (4 lymphoma, 1 leiomyosarcoma), but none of XG patients. Discriminating pathological features were the presence of any IgG4+ plasma cells (p = 0.0121) and the ratio of IgG4+/IgG+ plasma cells (p =0.0294) for IgG4-RD. Five of 12 (42%) patients with XG had sufficient numbers of IgG4+ plasma cells/high power field to fulfill published diagnostic criteria for IgG4-RD, and 5 (42%) had a ratio of IgG4+/IgG+ plasma cells over 40%, but the numbers overall were less than seen in the IgG4-RD patients. The only genetic difference between the 2 groups was that BRAF V600E mutation was found in 1 of the 2 Erdheim-Chester disease patients, which form a subgroup of XG.

Conclusions:

IgG4-RD and XG share clinical, imaging, and histopathological features including IgG4+ plasma cells. Significant differences were the eyelid involvement in XG, orbital nerve involvement, and an elevated IgG4+/IgG+ ratio in IgG4-RD and the only genetic abnormality found was BRAF V600E mutation in the Erdheim-Chester disease subgroup of XG.
Upper Eyelid and Pupillary Effects of Topical Dilute Epinephrine
Authors: Garcia Giancarlo A. , Ngai Philip , Vemuri Swapna , Tao Jeremiah P.
Published: February 2016

Purpose:

Adrenergic medications may elevate the upper eyelid and dilate the pupil. The effects of topical phenylephrine on Müller’s muscle have been well described. Dilute epinephrine (DE) is a sympathomimetic agent commonly administered in blepharoptosis surgery, and has been shown to elevate the upper eyelid margin when injected subcutaneously. The effects of DE applied topically to the eye, whether intentional or inadvertent during surgery have not been characterized. The purpose of this investigation was to quantify and compare the effects of topical DE and phenylephrine on upper eyelid position and pupil size.

Methods:

Prospective, nonrandomized trial of 41 adults without (n = 25, 25 eyes) and with ptosis (n = 16, 16 eyes). Upper eyelid margin reflex distance (MRD1) and pupil diameter were primary measures and pupil reactivity to light was a secondary measure. MRD1 and pupil diameter were recorded at baseline and at 30-second intervals for 5 minutes after administration of topical 1% lidocaine with epinephrine 1:100,000 (DE). After a washout period of >24 hours, the same measurements were recorded after administration of topical phenylephrine 2.5%.

Results:

No statistically significant difference was observed between mean baseline and postexposure MRD1 after application of topical DE (p = 0.181). In contrast, a mean increase in MRD1 of 0.51 ± 0.09 mm (effect size 0.33) was observed after exposure to phenylephrine 2.5% (p < 0.001). Baseline-adjusted postexposure mean MRD1 was significantly greater for phenylephrine compared with DE (p < 0.001, analysis of covariance). Mean pupil diameter increased 0.29 ± 0.09 mm (effect size 0.48) in response to DE and 0.27 ± 0.11 mm (effect size 0.41) after application of phenylephrine (p = 0.004 and p = 0.001, respectively). All pupils maintained a constrictive response to light.

Conclusions:

Although DE is similar to topical phenylephrine in causing mydriasis, it did not have a similar effect on elevating the upper eyelid. These findings may have implications on intraoperative assessment during eyelid surgery. The pupillary changes due to DE offer one explanation for cases of transient pupil dilation during orbitofacial surgery.
Response to “Commentary on ‘Limitations of GCTA as a solution to the missing heritability problem”
Authors: Kumar Siddharth Krishna , Feldman Marcus W. , Rehkopf David H. , Tuljapurkar Shripad
Published: February 2016

In a recent manuscript [18], Yang and colleagues criticized our paper, ‘Limitations of GCTA as a solution to the missing heritability problem’ [9]. Henceforth we refer to our original paper as SK and the critique as YC.

Here we show that their main claims are statistically invalid. We begin with an overview and the mathematical details follow in subsequent sections.
Concerted activities of Mcm4, Sld3, and Dbf4 in control of origin activation and DNA replication fork progression
Authors: Sheu Yi-Jun , Kinney Justin B. , Stillman Bruce
Published: February 2016

Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins in a temporally specific manner during S phase. The replicative helicase Mcm2-7 functions in both initiation and fork progression and thus is an important target of regulation. Mcm4, a helicase subunit, possesses an unstructured regulatory domain that mediates control from multiple kinase signaling pathways, including the Dbf4-dependent Cdc7 kinase (DDK). Following replication stress in S phase, Dbf4 and Sld3, an initiation factor and essential target of Cyclin-Dependent Kinase (CDK), are targets of the checkpoint kinase Rad53 for inhibition of initiation from origins that have yet to be activated, so-called late origins. Here, whole-genome DNA replication profile analysis is used to access under various conditions the effect of mutations that alter the Mcm4 regulatory domain and the Rad53 targets, Sld3 and Dbf4. Late origin firing occurs under genotoxic stress when the controls on Mcm4, Sld3, and Dbf4 are simultaneously eliminated. The regulatory domain of Mcm4 plays an important role in the timing of late origin firing, both in an unperturbed S phase and in dNTP limitation. Furthermore, checkpoint control of Sld3 impacts fork progression under replication stress. This effect is parallel to the role of the Mcm4 regulatory domain in monitoring fork progression. Hypomorph mutations in sld3 are suppressed by a mcm4 regulatory domain mutation. Thus, in response to cellular conditions, the functions executed by Sld3, Dbf4, and the regulatory domain of Mcm4 intersect to control origin firing and replication fork progression, thereby ensuring genome stability.
Implementation of a small bowel obstruction protocol at an urban public hospital
Authors: Martinez Antonio , Goldberg Ross F. , Dixon Robert M. , Thomas Eric L. , Davis Karole M. , Bogert James N.
Published: February 2016

Aim

The purpose of this study is to describe our experience with the implementation of a protocol for small bowel obstruction (SBO).

Methodology

A retrospective review of patients who presented with SBO between 1 March 2012 and 30 November 2014 were reviewed.

Results

Between 1 March 2012 and 30 November 2014, the protocol was administered to 49 patients with SBO and 49 patients were treated conventionally. Operative rates for the protocol group and the non‐protocol group were 6% and 18%, respectively (P = 0.06). Patients who received the protocol had an average hospital stay of 5.2 days. The non‐protocol group had an average stay of 7.2 days (P = 0.34). Time from admission to operating room (OR) was 35.2 h for the protocol group and 161.2 h for those who did not receive the protocol (P = 0.57). Mean OR time was 2.6 h for the protocol group and 2.3 h for the non‐protocol group (P = 0.68).

Conclusion

This study describes an urban public hospital's experience with a protocol for SBO. These findings suggest that an SBO protocol can be successfully implemented to decrease operative rates, length of stay, and time from admission to OR.
New insight into the effects of heparinoids on complement inhibition by C1-inhibitor
Authors: Poppelaars F , Damman J , de Vrij E L , Burgerhof J G M , Saye J , Daha M R , Leuvenink H G , Uknis M E , Seelen M A J
Published: February 2016

Complement activation is of major importance in numerous pathological conditions. Therefore, targeted complement inhibition is a promising therapeutic strategy. C1-esterase inhibitor (C1-INH) controls activation of the classical pathway (CP) and the lectin pathway (LP). However, conflicting data exist on inhibition of the alternative pathway (AP) by C1-INH. The inhibitory capacity of C1-INH for the CP is potentiated by heparin and other glycosaminoglycans, but no data exist for the LP and AP. The current study investigates the effects of C1-INH in the presence or absence of different clinically used heparinoids on the CP, LP and AP. Furthermore, the combined effects of heparinoids and C1-INH on coagulation were investigated. C1-INH, heparinoids or combinations were analysed in a dose-dependent fashion in the presence of pooled serum. Functional complement activities were measured simultaneously using the Wielisa®-kit. The activated partial thrombin time was determined using an automated coagulation analyser. The results showed that all three complement pathways were inhibited significantly by C1-INH or heparinoids. Next to their individual effects on complement activation, heparinoids also enhanced the inhibitory capacity of C1-INH significantly on the CP and LP. For the AP, significant potentiation of C1-INH by heparinoids was found; however, this was restricted to certain concentration ranges. At low concentrations the effect on blood coagulation by combining heparinoids with C1-INH was minimal. In conclusion, our study shows significant potentiating effects of heparinoids on the inhibition of all complement pathways by C1-INH. Therefore, their combined use is a promising and a potentially cost-effective treatment option for complement-mediated diseases.
Expansion of highly activated invariant natural killer T cells with altered phenotype in acute dengue infection
Authors: Kamaladasa A , Wickramasinghe N , Adikari T N , Gomes L , Shyamali N L A , Salio M , Cerundolo V , Ogg G S , Malavige G Neelika
Published: February 2016

Invariant natural killer T (iNKT) cells are capable of rapid activation and production of cytokines upon recognition of antigenic lipids presented by CD1d molecules. They have been shown to play a significant role in many viral infections and were observed to be highly activated in patients with acute dengue infection. In order to characterize further their role in dengue infection, we investigated the proportion of iNKT cells and their phenotype in adult patients with acute dengue infection. The functionality of iNKT cells in patients was investigated by both interferon (IFN)-γ and interleukin (IL)−4 ex-vivo enzyme-linked immunospot (ELISPOT) assays following stimulation with alpha-galactosyl-ceramide (αGalCer). We found that circulating iNKT cell proportions were significantly higher (P = 0·03) in patients with acute dengue when compared to healthy individuals and were predominantly of the CD4+ subset. iNKT cells of patients with acute dengue had reduced proportions expressing CD8α and CD161 when compared to healthy individuals. The iNKT cells of patients were highly activated and iNKT activation correlated significantly with dengue virus-specific immunoglobulin (Ig)G antibody levels. iNKT cells expressing Bcl-6 (P = 0·0003) and both Bcl-6 and inducible T cell co-stimulator (ICOS) (P = 0·006) were increased significantly in patients when compared to healthy individuals. Therefore, our data suggest that in acute dengue infection there is an expansion of highly activated CD4+ iNKT cells, with reduced expression of CD161 markers.
Volatiles released from foliar extract of host plant enhance landing rates of gravid Polygonia c‐album females, but do not stimulate oviposition
Authors: Mozūraitis Raimondas , Radžiutė Sandra , Apšegaitė Violeta , Cravcenco Alexei , Būda Vincas , Nylin Sören
Published: February 2016

The role of olfactory cues for host search is much less investigated in day‐active butterflies than in their relatives, the nocturnal moths. The goal of this study was to investigate whether host‐plant volatiles from foliar extracts of hop, Humulus lupulus L. (Cannabaceae), evoke electroantennographic (EAG) responses, increase landing rates, and stimulate egg‐laying behavior of gravid Polygonia c‐album L. (Lepidoptera: Nymphalidae) females. Eighty‐nine volatile compounds were detected in a non‐concentrated methanol extract of hop by gas chromatography–mass spectrometry, 11 of which elicited an EAG response. Concentration of the crude extract significantly reduced landing rates on artificial leaves treated with the sample due to loss of volatile compounds, but after landing the oviposition response of gravid females was not affected. A mixture of eight commercially available EAG‐active volatiles increased the landing rate of gravid females to their source but did not act as oviposition stimulants. Dividing the volatile compounds into two groups – consisting of (1) hexanal, (E)‐2‐hexenal, octanal, nonanal, and decanal, and (2) sulcatone, humulene, and benzyl alcohol – obliterated effectiveness, revealing synergism between compounds. Although volatiles did not stimulate oviposition, they significantly contributed to the distribution of eggs by increasing the landing rates on treated artificial leaves.
The use of decision aids on early detection of prostate cancer: views of men and general practitioners
Authors: Engelen Annelies , Vanderhaegen Joke , Van Poppel Hendrik , Van Audenhove Chantal
Published: February 2016

Background and objective

While decision support tools such as decision aids can contribute to shared decision making, implementing these tools in daily practice is challenging. To identify and address issues around the use of decision support tools in routine care, this study explores the views of men and general practitioners on using a DA for early detection of prostate cancer.

Methods, setting and participants

Group discussions and semi‐structured interviews were carried out with 43 men and 16 general practitioners familiar with a previously developed decision aid. Data were analysed using qualitative description.

Results

Views on using the decision support tool could be classified into four categories: no need for decision making, need for support, perceived benefit and practical barriers. For each category, several underlying themes could be identified that reflect the absence or presence of prerequisites to successful decision support delivery.

Discussion and conclusion

While men and general practitioners generally have positive attitudes to shared decision making, for both parties attitudes such as not agreeing that there is a decision to be made and doubts on the beneficence of using DAs were identified as factors that may hinder the use of a DA in clinical practice. Participants formulated strategies to support the use of DAs, mainly supplementing DAs with short tools and investing in both training programmes and large‐scale awareness raising of the general public.
Drain placement can safely be omitted for open partial nephrectomy: Results from a prospective randomized trial
Authors: Kriegmair Maximilian C , Mandel Philipp , Krombach Patrick , Dönmez Hasan , John Axel , Häcker Axel , Michel Maurice S
Published: February 2016

Objectives

To examine the benefit of drain placement during open partial nephrectomy.

Methods

Overall, 106 patients treated with open partial nephrectomy were enrolled in a prospective randomized trial. Based on the randomization, a drain was placed or omitted. Complications were assessed according to the Clavien classification. Pain level and requirement for analgesics was evaluated according to a customized pattern.

Results

There was no significant difference in the two groups regarding age, body mass index, American Society of Anesthesiologists score, tumor size and nephrometry (preoperative aspects and dimensions used for an anatomical classification). In terms of overall and drain‐related complications, no advantage of placing a drain could be proven (P = 0.249). Patients with a drain suffered from a significantly higher pain level (P = 0.01) and showed prolonged mobilization (P < 0.001). There was no difference in bowel movements and requirement of additional analgesics (P = 0.347 and 0.11).

Conclusions

The results of the study suggest that drain placement during open partial nephrectomy can safely be omitted, even in cases with violation of the collecting system.
Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad‐leaved forests
Authors: Xiang Xiao‐Guo , Mi Xiang‐Cheng , Zhou Hai‐Lang , Li Jian‐Wu , Chung Shih‐Wen , Li De‐Zhu , Huang Wei‐Chang , Jin Wei‐Tao , Li Zhen‐Yu , Huang Lu‐Qi , Jin Xiao‐Hua
Published: February 2016

Aim

Evergreen broad‐leaved forests (EBLFs) occupy most tropical and subtropical regions of mainland Asia and exhibit high species diversity, productivity and richness. Understanding the historical dynamics of EBLFs is important for biodiversity conservation and regional carbon storage and cycling under global climate change. However, little is known about the historical dynamics of EBLFs in mainland Asia. Dendrobium, an epiphytic orchid genus found in EBLFs, was used to gain new insights of the historical establishment and extension of EBLFs in mainland Asia.

Location

Mainland Asia.

Methods

We sampled c. 80% of the currently recognized species of Dendrobium found in mainland Asia. A phylogeny was generated using maximum parsimony, maximum likelihood and Bayesian inference methods. A calibrated chronogram was obtained using a Bayesian relaxed‐clock model approach. Biogeographical scenarios were investigated using the statistical dispersal–vicariance analysis and dispersal–extinction–cladogenesis methods. Ancestral states were constructed by mesquite and bayestraits, and diversification of Dendrobium was investigated by APE and LASER packages.

Results

Our results indicate that Asian Dendrobium was present on mainland Asia since the Oligocene, after which this genus diversified in this region and dispersed into higher elevations. The ancestral habit of Dendrobium was epiphytic and terrestrial and lithophytic habits each have multiple, recently independent origins.

Main conclusions

Our results support the hypothesis that EBLFs have been established in mainland Asia at least since the Oligocene and further suggest that the EBLFs of mainland Asia expanded into higher elevations prior to the late Cenozoic. The diversification of Asian Dendrobium coincided with a warmer climate during the late Oligocene and middle Miocene and the expansion of key groups (including Fagaceae, Lauraceae, Magnoliaceae and Theaceae) of EBLFs during the early Cenozoic.
Quantifying the similarity between genes and geography across Alaska's alpine small mammals
Authors: Knowles L. Lacey , Massatti Rob , He Qixin , Olson Link E. , Lanier Hayley C.
Published: February 2016

Aim

Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species‐specific or shared manner.

Location

Alaska and adjacent north‐western Canada.

Methods

For each taxon we generated 3500–7500 single‐nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between principal components analysis maps of genetic variation and geographical maps of sample locations. We generate stability maps using projected distributions from ecological niche models of the Last Glacial Maximum and the present.

Results

Significant similarity between genes and geography exists across taxa. However, the extent to which geography is predictive of patterns of genetic variation not only differs among taxa, but the correspondence between genes and geography varies over space. Geographical areas where genetic structure aligns poorly with the geographical coordinates are of particular interest because they indicate regions where processes other than isolation by distance (IBD) have influenced genetic variation. The clustering of individuals according to their sample location does not support suppositions of admixture, despite the presumed high vagility of some species (e.g. arctic ground squirrels).

Main conclusions

Genomic data indicate a more nuanced biogeographical history for the taxa than suggested by previous studies based on mtDNA alone. These include departures from IBD that are shared among taxa, which suggest some shared processes structuring genetic variation, including new potential ancestral source populations. In addition, some regions fit expectations of IBD where incremental migration and gene flow play a strong role in population structure, despite any ecological difference among taxa. Differences in dispersal capabilities do not result in different species‐specific local patterns of population structure, at least at the sampling scale examined here. We highlight how the general fit to, as well as departures from, expectations for patterns of genetic variation based on the Procrustes analyses can be used to generate hypotheses about the underlying processes.
Ecological, evolutionary and human‐mediated determinants of poeciliid species richness on Caribbean islands
Authors: Furness Andrew I. , Reznick David N. , Avise John C.
Published: February 2016

Aim

The theory of island biogeography provides a predictive framework relating species richness to island size and distance from the mainland. However, the theory as originally formulated does not necessarily scale to large islands and continental landmasses that are capable of generating species through in situ speciation (rather than entirely by colonization), nor does it necessarily account for how human introduction of species alters traditional biogeographical patterns. Here, we examine the ecological (colonization and extinction), evolutionary (in situ speciation) and human‐mediated (deliberate introductions) determinants of species richness in a taxonomic group that has undergone a radiation on Caribbean islands: live‐bearing fishes of the family Poeciliidae.

Location

The Caribbean.

Methods

We created a database of both native and introduced poeciliid species occurrence on Caribbean islands through literature review, and estimated the number of colonizations versus speciation events on each island using a molecular phylogeny. Linear regression and other statistical tests were used to explore species–area and species–isolation relationships.

Results

Species richness on small islands results entirely from colonization and does not significantly increase with island area, whereas on larger islands species richness increases dramatically as a function of area due primarily to in situ speciation. Poeciliid fishes have been introduced widely, both as a by‐product of their popularity in the aquarium hobby and as a means of mosquito control. We show that such establishments have occurred disproportionately on islands depauperate in native species, and that introduced species richness is positively correlated with economic interconnectedness (shipping traffic) and human population size.

Main conclusions

On large Caribbean islands in situ speciation has elevated the number of poeciliid species beyond that predicted from ecological processes alone. Introduced species significantly alter biogeographical patterns.
Factors driving structure of natural and anthropogenic forest edges from temperate to boreal ecosystems
Authors: Esseen Per‐Anders , Hedström Ringvall Anna , Harper Karen Amanda , Christensen Pernilla , Svensson Johan
Published: February 2016

Questions

What factors control broad‐scale variation in edge length and three‐dimensional boundary structure for a large region extending across two biomes? What is the difference in structure between natural and anthropogenic edges?

Location

Temperate and boreal forests across all of Sweden, spanning latitudes 55–69° N.

Methods

We sampled more than 2000 forest edges using line intersect sampling in a monitoring programme (National Inventory of Landscapes in Sweden). We compared edge length, ecosystem attributes (width of adjacent ecosystem, canopy cover, canopy height, patch contrast in canopy height, forest type) and boundary attributes (profile, abruptness, shape) of natural edges (lakeshore, wetland) with anthropogenic edges (clear‐cut, agricultural, linear disturbance) in five regions.

Results

Anthropogenic edges were nearly twice as abundant as natural edges. Length of anthropogenic edges was largest in southern regions, while the abundance of natural edges increased towards the north. Edge types displayed unique spectrums of boundary structures, but abrupt edges dominated, constituting 72% of edge length. Anthropogenic edges were more abrupt than natural edges; wetland edges had the most gradual and sinuous boundaries. Canopy cover, canopy height, patch contrast and forest type depended on region, whereas overall boundary abruptness and shape showed no regional pattern. Patch contrast was related to temperature sum (degree days ≥ 5 °C), suggesting that regional variability can be predicted from climate‐controlled forest productivity. Boundary abruptness was coupled with the underlying environmental gradient, land use and forest type, with higher variability in deciduous than in conifer forest.

Conclusions

Edge origin, land use, climate and tree species are main drivers of broad‐scale variability in forest edge structure. Our findings have important implications for developing ecological theory that can explain and predict how different factors affect forest edge structure, and help to understand how land use and climate change affect biodiversity at forest edges.
Woody species composition in an African savanna: determined by centuries of termite activity but modulated by 50 years of ungulate herbivory
Authors: Seymour Colleen L. , Joseph Grant S. , Makumbe Milton , Cumming Graeme S. , Mahlangu Zacheus , Cumming David H.M.
Published: February 2016

Questions

Ungulate herbivory and formation of large termite mounds occur over different time scales, but both can affect plant community composition in savannas. Human‐managed savanna systems are increasingly dominated by domesticated grazing herbivores. These have replaced a mix of indigenous browsers and grazers, leading to changes in plant communities such as increased bush encroachment. We compared the relative impacts of five decades of different types of ungulate herbivory (cattle grazing, browsing and grazing by wild herbivores, and exclusion of all larger herbivores) on woody plant assemblages in two habitats, namely, large termite mounds, which may be thousands of years old, and the surrounding matrix.

Location

Miombo woodland savanna, Zimbabwe.

Methods

To determine the influence of termite mounds and herbivory on spatial distribution and composition of woody assemblages, we compared 40 paired mound–matrix plots from the three herbivory treatments using PERMANOVA. We assessed whether mound plots were more similar to each other than matrix plots were to each other, and whether herbivory influenced similarity. We used SIMPER analysis to identify changes in abundance of indicator species for each habitat (i.e. mound or matrix).

Results

Species composition differed significantly between mound and matrix and also between herbivory treatments. Woody plant assemblages on mounds were more similar to each other than woody plant assemblages in matrix plots were to each other, regardless of type of herbivory, but herbivory reduced the mound/matrix contrast. Sample location (i.e. on mound or in matrix) explained 23% of the variation in woody species composition, compared to 12% explained by herbivory. Woody plant abundance was lowest where there were both grazers and browsers.

Conclusions

The influence of large termite mounds on plant assemblages was roughly double that of herbivory, which has occurred over five decades. Type of herbivory emerged as relatively influential on woody plant species composition, given that the time periods involved were short by comparison to the slow formation of termite mounds. Type of herbivory also influenced species composition and vegetation structure, with a diversity of herbivores necessary to reduce encroachment by woody species.
The Category of the Supernatural: A Valid Anthropological Term?
Authors: Dein Simon
Published: February 2016

This paper is a survey of the anthropological literature pertaining to the term ‘supernatural’. It considers a number of questions: Is the distinction between natural and supernatural universal? Can the distinction be applied to non‐western cultures? What does the term mean as a cultural construction and as a response to reality? Finally, it examines the use of the term supernatural in the contemporary cognitive science of religion. The inspiration for the paper arose from the way that anthropologists often fail to problematise the uses and cross‐cultural applicability of the term supernatural.
Dose‐Response Modeling for Inhalational Anthrax in Rabbits Following Single or Multiple Exposures
Authors: Gutting Bradford W. , Rukhin Andrey , Marchette David , Mackie Ryan S. , Thran Brandolyn
Published: February 2016

There is a need to advance our ability to characterize the risk of inhalational anthrax following a low‐dose exposure. The exposure scenario most often considered is a single exposure that occurs during an attack. However, long‐term daily low‐dose exposures also represent a realistic exposure scenario, such as what may be encountered by people occupying areas for longer periods. Given this, the objective of the current work was to model two rabbit inhalational anthrax dose‐response data sets. One data set was from single exposures to aerosolized Bacillus anthracis Ames spores. The second data set exposed rabbits repeatedly to aerosols of B. anthracis Ames spores. For the multiple exposure data the cumulative dose (i.e., the sum of the individual daily doses) was used for the model. Lethality was the response for both. Modeling was performed using Benchmark Dose Software evaluating six models: logprobit, loglogistic, Weibull, exponential, gamma, and dichotomous‐Hill. All models produced acceptable fits to either data set. The exponential model was identified as the best fitting model for both data sets. Statistical tests suggested there was no significant difference between the single exposure exponential model results and the multiple exposure exponential model results, which suggests the risk of disease is similar between the two data sets. The dose expected to cause 10% lethality was 15,600 inhaled spores and 18,200 inhaled spores for the single exposure and multiple exposure exponential dose‐response model, respectively, and the 95% lower confidence intervals were 9,800 inhaled spores and 9,200 inhaled spores, respectively.
Injury, inflammation and the emergence of human‐specific genes
Authors: Baird Andrew , Costantini Todd , Coimbra Raul , Eliceiri Brian P.
Published: February 2016

In light of the central role of inflammation in normal wound repair and regeneration, we hypothesize that the preponderance of human‐specific genes expressed in human inflammatory cells is commensurate with the genetic versatility of inflammatory response and the emergence of injuries associated with uniquely hominid behaviors, like a bipedal posture and the use of tools, weapons and fire. The hypothesis underscores the need to study human‐specific signaling pathways in experimental models of injury and infers that a selection of human‐specific genes, driven in part by the response to injury, may have facilitated the emergence of multifunctional genes expressed in other tissues.
Response of human macrophages to wound matrices in vitro
Authors: Witherel Claire E. , Graney Pamela L. , Freytes Donald O. , Weingarten Michael S. , Spiller Kara L.
Published: February 2016

Chronic wounds remain a major burden to the global healthcare system. Myriad wound matrices are commercially available but their mechanisms of action are poorly understood. Recent studies have shown that macrophages are highly influenced by their microenvironment, but it is not known how different biomaterials affect this interaction. Here, it was hypothesized that human macrophages respond differently to changes in biomaterial properties in vitro with respect to phenotype, including pro‐inflammatory M1, anti‐inflammatory M2a, known for facilitating extracellular matrix deposition and proliferation, and M2c, which has recently been associated with tissue remodeling. Using multiple donors, it was found that collagen scaffolds cross‐linked with 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide and N‐hydroxysuccinimide (EDC/NHS) promoted the least inflammatory phenotype in primary human macrophages compared with scaffolds cross‐linked with formaldehyde or glutaraldehyde. Importantly, gene expression analysis trends were largely conserved between donors, especially TNFa (M1), CCL22 (M2a), and MRC1 (M2a). Then the response of primary and THP1 monocyte‐derived macrophages to four commercially available wound matrices were compared—Integra Dermal Regeneration Template (Integra), PriMatrix Dermal Repair Scaffold (PriMatrix), AlloMend Acellular Dermal Matrix (AlloMend), and Oasis Wound Matrix (Oasis). Gene expression trends were different between primary and THP1 monocyte‐derived macrophages for all six genes analyzed in this study. Finally, the behavior of primary macrophages cultured onto the wound matrices over time was analyzed. Integra and Oasis caused down‐regulation of M2a markers CCL22 and TIMP3. PriMatrix caused up‐regulation of TNFa (M1) and CD163 (M2c) and down‐regulation of CCL22 and TIMP3 (both M2a). AlloMend caused up‐regulation in CD163 (M2c). Lastly, Oasis promoted the largest increase in the combinatorial M1/M2 score, defined as the sum of M1 genes divided by the sum of M2 genes. This preliminary study suggested that biomaterials influenced the wound microenvironment to affect macrophage phenotype.
A case of acquired laryngomalacia in an infant, with endoscopy before and after establishing the diagnosis for the first time
Authors: Gazzaz Malak Jamal , El-Hakim Hamdy
Published: February 2016

A 12-week-old infant girl born at 27 weeks gestation, with multiple comorbidities, was referred to the paediatric otolaryngology team due to stridor and feeding difficulties. Initial airway endoscopy was performed, showing no abnormal findings. The infant underwent frequent hospitalisations for recurrent cyanotic spells. Despite initial laryngoscopy and bronchoscopy not showing abnormalities, a repeat endoscopy demonstrated laryngomalacia, significant enough to require a supraglottoplasty. This is the first report to confirm, with video evidence, that some cases of laryngomalacia are acquired rather than congenital, even in infancy.