bluuebunny/crossref_metadata_2025_split 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

Abstract
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

Abstract
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

Abstract
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.
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.
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

AimThe purpose of this study is to describe our experience with the implementation of a protocol for small bowel obstruction (SBO).MethodologyA retrospective review of patients who presented with SBO between 1 March 2012 and 30 November 2014 were reviewed.ResultsBetween 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).ConclusionThis 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

SummaryComplement 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

Summary
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

AbstractThe 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

AbstractBackground and objectiveWhile 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 participantsGroup 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.ResultsViews 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 conclusionWhile 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

ObjectivesTo examine the benefit of drain placement during open partial nephrectomy.MethodsOverall, 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.ResultsThere 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).ConclusionsThe 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.