bluuebunny/crossref_metadata_2025_split huggingface dataset:
State aggregation for fast likelihood computations in molecular evolution
Authors: Davydov Iakov I. , Robinson-Rechavi Marc , Salamin Nicolas 
Published: December 2015

AbstractMotivationCodon models are widely used to identify the signature of selection at the molecular level and to test for changes in selective pressure during the evolution of genes encoding proteins. The large size of the state space of the Markov processes used to model codon evolution makes it difficult to use these models with large biological datasets. We propose here to use state aggregation to reduce the state space of codon models and, thus, improve the computational performance of likelihood estimation on these models.ResultsWe show that this heuristic speeds up the computations of the M0 and branch-site models up to 6.8 times. We also show through simulations that state aggregation does not introduce a detectable bias. We analysed a real dataset and show that aggregation provides highly correlated predictions compared to the full likelihood computations. Finally, state aggregation is a very general approach and can be applied to any continuous-time Markov process-based model with large state space, such as amino acid and coevolution models. We therefore discuss different ways to apply state aggregation to Markov models used in phylogenetics.AvailabilityThe heuristic is implemented in thegodonpackage (https://bitbucket.org/Davydov/godon) and in a version of FastCodeML (https://gitlab.isb-sib.ch/phylo/fastcodeml).
Lipocalin‐2 exacerbates psoriasiform skin inflammation by augmenting T‐helper 17 response
Authors: Hau Carren S. , Kanda Naoko , Tada Yayoi , Shibata Sayaka , Uozaki Hiroshi , Fukusato Toshio , Sato Shinichi , Watanabe Shinichi 
Published: December 2015

AbstractLipocalin‐2 (LCN2) is an antimicrobial protein and adipokine associated with insulin resistance, obesity and atherosclerotic disease. Psoriasis is a T‐helper (Th)1/Th17‐mediated, chronic inflammatory dermatosis related to metabolic syndromes and serum LCN2 levels are elevated in psoriatic patients. We examined the in vivo effects of LCN2 on topical imiquimod (IMQ)‐induced psoriasiform skin in BALB/c mice and in vitro on human keratinocytes (KC). Clinically, i.p. injected LCN2 exacerbated erythema and scaling in IMQ‐treated murine skin compared with phosphate‐buffered saline injection alone, and it augmented interleukin (IL)‐17A, IL‐17F, IL‐22, IL‐23p19, IL‐12p40, CCL20, tumor necrosis factor‐α, chemokine (C‐X‐C motif) ligand (CXCL)1, CXCL2, DEFB4, DEFB14, LCN2 and S100A7 mRNA levels of IMQ‐treated murine skin while it did not increase the mRNA levels of interferon‐γ, IL‐12p35 or CXCL10. LCN2 in synergy with IL‐17 increased mRNA levels of CCL20, LCN2 and DEFB4A but not of CXCL10 in human KC in vitro. These results suggest that LCN2 enhances the expression of Th17 cytokines/chemokines and antimicrobial peptides in murine IMQ‐treated psoriatic skin and KC. LCN2 may potentiate the development of psoriasis via the enhancement of Th17‐ and antimicrobial peptide‐mediated inflammation.
Mast cell chymase in experimentally induced psoriasis
Authors: Suttle Mireille‐Maria , Harvima Ilkka T. 
Published: December 2015

AbstractMast cell chymase can have a pro‐inflammatory or an immunosuppressive function in psoriasis, but the outcome may depend on the level of chymase activity. Therefore, mast cells showing chymase activity (Chyact) and immunoreactivity (Chyprot) were studied during the Köbner reaction (0 days, 2 h, 1 day, 3 days and 7 days) of psoriasis induced by the tape‐stripping technique. Also, the effect of recombinant human chymase (rh‐chymase) or human LAD2 mast cells (LAD2) on the 3H‐thymidine uptake of psoriatic peripheral blood mononuclear cells (PBMC) or total T cells was studied. The Chyact/Chyprot ratio tended to be higher in all time‐point biopsies in the Köbner‐negative (n = 10) than ‐positive (n = 8) group (P = 0.073), although chymase activity decreased significantly at 2 h to 1 day only in the Köbner‐negative group. rh‐chymase (0.05–0.5 μg/mL) stimulated to a varying extent PBMC in eight out of nine cultures, but in all cultures 5 μg/mL rh‐chymase turned the stimulation towards inhibition. The effect of rh‐chymase on T cells varied from stimulation to inhibition, but in 11 of 15 cultures rh‐chymase, at least at 5 μg/mL, produced a change to inhibition. In co‐cultures, LAD2 inhibited PBMC in the absence of soybean trypsin inhibitor (SBTI). In the presence of SBTI, LAD2 stimulated PBMC in the majority of seven cultures. In summary, the psoriatic immunopathogenesis may be promoted at low, but controlled at high, activity status of chymase.
Microorganisms inhabiting follicular contents of facial acne are not only Propionibacterium but also Malassezia spp.
Authors: Akaza Narifumi , Akamatsu Hirohiko , Numata Shigeki , Yamada Shunji , Yagami Akiko , Nakata Satoru , Matsunaga Kayoko 
Published: December 2015

AbstractTo clarify the relationship between major cutaneous microorganisms (Propionibacterium, Staphylococcus and Malassezia spp.) and acne vulgaris (acne), we examined the microbiota quantitatively in the follicular contents of inflammatory acne and on the facial skin of patients with acne. Fifteen Japanese untreated acne outpatients were studied. The follicular contents from inflammatory acne lesions of the face were collected using a comedo extractor. The skin surface samples were obtained by the swab method from 10 cm2 of facial skin. The microbiota was analyzed using polymerase chain reaction. The microbiota in follicular contents was similar to that on the skin surface, namely, there were large populations of Propionibacterium spp., Staphylococcus spp. and Malassezia spp. Moreover, the number of Malassezia spp. on the skin surface was correlated with that of inflammatory acne and that in follicular contents. This study clarified that there are large populations of Propionibacterium spp., Staphylococcus spp. and Malassezia spp. in follicular contents. These results suggest the possibility that not only Propionibacterium acnes but also other cutaneous resident microorganisms are related to acne. Particularly, we considered that Malassezia spp. is closely related.
Temporal variability of a single population can determine the vulnerability of communities to perturbations
Authors: Mrowicki Robert J. , O'Connor Nessa E. , Donohue Ian 
Published: December 2015

Summary

Many aspects of global change affect the variability of species population densities, in terms of both the magnitude and pattern of density fluctuations. However, we have limited empirical understanding of the consequences of altered temporal variability of populations, independent of changes in their mean densities, for the structure and stability of natural communities and the responses of ecosystems to additional stressors.

We used a field experiment to test the effects of altered temporal variability of a single consumer species on community structure and stability. Specifically, we manipulated the temporal variability of populations of a key grazer species on temperate rocky shores (Littorina littorea), independent of their mean densities, over 12 months and measured the responses of algal communities in terms of multiple measures of structure and stability. Further, we tested whether consumer variability determined the effects of an additional perturbation, elevated sedimentation, on algal communities.

The effects of sedimentation on the structure and stability of algal communities were regulated by the temporal variability of consumer populations. In particular, elevated sedimentation led to a decrease in algal evenness, but only when consumer densities were held constant, and resulted in a decrease in the rate of local algal extinctions, but only when consumer temporal variability was increased.

Independent of sedimentation, increased temporal variability of consumer populations led to a shift in algal assemblage structure and affected the stability of algal communities in terms of both compositional turnover and resistance to environmental perturbations. Further, these effects varied according to the temporal pattern of consumer density fluctuations.

Synthesis. Our results demonstrate that changes in the temporal variability of a single species can modify multiple aspects of both the structure and stability of natural communities and alter their responses to perturbations. However, the effects of consumer variability cannot be predicted without knowledge of the temporal pattern of density fluctuations. These findings have profound implications for our understanding of the effects of multiple disturbances on ecosystems.
Pricing to market behaviour of India's high value agri‐food exporters: an empirical analysis of major destination markets
Authors: Varma Poornima , Issar Akash 
Published: December 2015

AbstractThe pricing behaviour of India's high value agricultural and food exporters in their major destination markets is examined using a pricing‐to‐market (PTM) model for noncompetitive and exchange rate related pricing behaviour. The analysis was undertaken in a context where India is showing high commodity concentration in agricultural trade. The econometric analysis employed is panel corrected standard errors (PCSE) estimation technique. The results indicated evidence of a greater degree of imperfect competition either through price discrimination across destinations or through imperfect exchange rate pass‐through. The analysis of exchange rate effects showed that the local currency price stabilization by the Indian exporters were more prominent than the amplification of exchange rates. The analysis of the asymmetric effects of exchange rates on export prices showed that in most cases the depreciation of Indian rupee had a greater impact than the appreciation. Moreover the results showed that the exchange rate pass‐through is sensitive to the kind of exchange rate index utilised. In our analysis we found that the commodity specific exchange rate better predicts the pricing to market behaviour in most cases.
Spectrum of EGFR gene mutations in Vietnamese patients with non–small cell lung cancer
Authors: Vu Hoang Anh , Xinh Phan Thi , Ha Hua Thi Ngoc , Hanh Ngo Thi Tuyet , Bach Nguyen Duc , Thao Doan Thi Phuong , Dat Ngo Quoc , Trung Nguyen Sao 
Published: December 2015

AbstractAimEpidermal growth factor receptor (EGFR) mutational status is a crucial biomarker for prediction of response to tyrosine kinase inhibitors in patients with non–small cell lung cancer (NSCLC). Although these mutations have been well characterized in other countries, little is known about the frequency or spectrum of EGFR mutations in Vietnamese NSCLC patients.MethodsUsing Sanger DNA sequencing, we investigated mutations in EGFR exons 18–21 from 332 patients diagnosed with NSCLC at University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam. DNA was extracted from formalin‐fixed, paraffin‐embedded tissues, followed by PCR amplification and sequencing.ResultsEGFR mutations were detected in 135 samples (40.7%), of which eight samples carried double mutations. In total, 46 different types of EGFR mutations were found, including six novel mutations (p.K713E, p.K714R, p.P794S, p.R803W, p.P848S, and p.K867E). Among the four exons investigated, exon 19 was most frequently mutated (63 out of 332 patients, 19%), with the p.E746_A750del appearing in 43 samples. Exon 21 was mutated in 56 samples (16.9%), of which 47 were p.L858R. Each of exons 18 and 20 was mutated in 12 samples (3.6%). The frequency of EGFR mutations was higher in females than in males (48.9% vs 35%, P = 0.012), but not statistically different between adenocarcinomas and other histological types of NSCLC (41.3% vs 34.5%, P = 0.478).ConclusionDNA sequencing detected EGFR mutations with high frequency and revealed a broad spectrum of mutation type in Vietnamese patients with NSCLC.
Measuring action understanding: Relations between goal prediction and imitation
Authors: Gampe Anja , Prinz Wolfgang , Daum Moritz M. 
Published: December 2015

We explored the developmental course of goal prediction and imitation as two commonly used measures of action understanding. In particular, we investigated the relationships between the measures in two complex multistep actions (hammering and pulling action) in children between 12 and 30 months (n = 64) in a between‐subjects design. The results showed that the prediction of an action goal was related to the imitation in the hammering action, but not in the pulling action. The results are discussed in the light of current theories on goal prediction and imitation.
The effect of colour on children's cognitive performance
Authors: Brooker Alice , Franklin Anna 
Published: December 2015

BackgroundThe presence of red appears to hamper adults’ cognitive performance relative to other colours (see Elliot & Maier, 2014, Ann. Rev. Psychol. 65, 95).Aims and sampleHere, we investigate whether colour affects cognitive performance in 8‐ and 9‐year‐olds.MethodChildren completed a battery of tasks once in the presence of a coloured screen that was one of eight colours and once in the presence of a grey screen. Performance was assessed for each colour relative to the grey baseline, and differences across colours were compared.ResultsWe find a significant difference in performance across colours, with significantly worse performance in the presence of red than grey. The effect of colour did not significantly interact with task.ConclusionThe findings suggest that colour can affect children's cognitive performance and that there is a detrimental effect of red. Findings are related to the adult literature and implications for educational contexts are discussed.
Involvement of Rac1 signalling pathway in the development and maintenance of acute inflammatory pain induced by bee venom injection
Authors: Wang Yan , Lu Yun‐Fei , Li Chun‐Li , Sun Wei , Li Zhen , Wang Rui‐Rui , He Ting , Yang Fan , Yang Yan , Wang Xiao‐Liang , Guan Su‐Min , Chen Jun 
Published: December 2015

Background and PurposeThe Rho GTPase, Rac1, is involved in the pathogenesis of neuropathic pain induced by malformation of dendritic spines in the spinal dorsal horn (sDH) neurons. In the present study, the contribution of spinal Rac1 to peripheral inflammatory pain was studied.Experimental ApproachEffects of s.c. bee venom (BV) injection on cellular localization of Rac1 in the rat sDH was determined with double labelling immunofluorescence. Activation of Rac1 and its downstream effector p21‐activated kinase (PAK), ERKs and p38 MAPK in inflammatory pain states was evaluated with a pull‐down assay and Western blotting. The preventive and therapeutic analgesic effects of intrathecal administration of NSC23766, a selective inhibitor of Rac1, on BV‐induced spontaneous nociception and pain hypersensitivity were investigated.Key ResultsRac1 labelling was mainly localized within neurons in both the superficial and deep layers of the sDH in rats of naïve, vehicle‐treated and inflamed (BV injected) groups. GTP‐Rac1‐PAK and ERKs/p38 were activated following s.c. BV injection. Post‐treatment with intrathecal NSC23766 significantly inhibited GTP‐Rac1 activity and phosphorylation of Rac1‐PAK, ERKs and p38 MAPK in the sDH. Both pre‐treatment and post‐treatment with intrathecal NSC23766 dose‐dependently attenuated the paw flinches, primary thermal and mechanical hyperalgesia and the mirror‐image thermal hyperalgesia induced by BV injection, but without affecting the baseline pain sensitivity and motor coordination.Conclusions and ImplicationsThe spinal GTP‐Rac1‐PAK‐ERK/p38MAPK signalling pathway is involved in both the development and maintenance of peripheral inflammatory pain and can be used as a potential molecular target for developing a novel therapeutic strategy for clinical pain.
Pathways to Third‐Grade Calculation Versus Word‐Reading Competence: Are They More Alike or Different?
Authors: Fuchs Lynn S. , Geary David C. , Fuchs Douglas , Compton Donald L. , Hamlett Carol L. 
Published: December 2015

Children (n = 747; 6.5 years) were assessed on domain‐general processes and mathematics and reading‐related competencies (start of first grade), addition retrieval (end of second grade), and calculations and word reading (end of third grade). Attentive behavior, reasoning, visuospatial memory, and rapid automatized naming (RAN) indirectly contributed to both outcomes, via retrieval. However, there was no overlap in domain‐general direct effects on calculations (attentive behavior, reasoning, working memory) versus word reading (language, phonological memory, RAN). Results suggest ease of forming associative relations and abilities engaged during the formation of these long‐term memories are common to both outcomes and can be indexed by addition‐fact retrieval, but further growth in calculations and word reading is driven by different constellations of domain‐general abilities.
Distinct expression of interleukin (IL)-36α, β and γ, their antagonist IL-36Ra and IL-38 in psoriasis, rheumatoid arthritis and Crohn's disease
Authors: Boutet M-A , Bart G , Penhoat M , Amiaud J , Brulin B , Charrier C , Morel F , Lecron J-C , Rolli-Derkinderen M , Bourreille A , Vigne S , Gabay C , Palmer G , Le Goff B , Blanchard F 
Published: December 2015

Summary
Interleukin (IL)-36α, IL-36β and IL-36γ are expressed highly in skin and are involved in the pathogenesis of psoriasis, while the antagonists IL-36Ra or IL-38, another potential IL-36 inhibitor, limit uncontrolled inflammation. The expression and role of IL-36 cytokines in rheumatoid arthritis (RA) and Crohn's disease (CD) is currently debated. Here, we observed that during imiquimod-induced mouse skin inflammation and in human psoriasis, expression of IL-36α, γ and IL-36Ra, but not IL-36β and IL-38 mRNA, was induced and correlated with IL-1β and T helper type 17 (Th17) cytokines (IL-17A, IL-22, IL-23, CCL20). In mice with collagen-induced arthritis and in the synovium of patients with RA, IL-36α, β, γ, IL-36Ra and IL-38 were all elevated and correlated with IL-1β, CCL3, CCL4 and macrophage colony-stimulating factor (M-CSF), but not with Th17 cytokines. In the colon of mice with dextran sulphate sodium-induced colitis and in patients with CD, only IL-36α, γ and IL-38 were induced at relatively low levels and correlated with IL-1β and IL-17A. We suggest that only a minor subgroup of patients with RA (17–29%) or CD (25%) had an elevated IL-36 agonists/antagonists ratio, versus 93% of patients with psoriasis. By immunohistochemistry, IL-36 cytokines were produced by various cell types in skin, synovium and colonic mucosa such as keratinocytes, CD68+ macrophages, dendritic/Langerhans cells and CD79α+ plasma cells. In primary cultures of monocytes or inflammatory macrophages (M1), IL-36β and IL-36Ra were produced constitutively, but IL-36α, γ and IL-38 were produced after lipopolysaccharide stimulation. These distinct expression profiles may help to explain why only subgroups of RA and CD patients have a potentially elevated IL-36 agonists/antagonists ratio.
Activation of the lectin pathway of complement by cardiopulmonary bypass contributes to the development of systemic inflammatory response syndrome after paediatric cardiac surgery
Authors: Pągowska-Klimek I , Świerzko A S , Michalski M , Głowacka E , Szala-Poździej A , Sokołowska A , Moll M , Krajewski W R , Romak J , Cedzyński M 
Published: December 2015

Summary
The systemic inflammatory response is a challenge in the management of paediatric patients undergoing cardiac surgery. Although multi-factorial, a contribution by the lectin pathway of complement activation has been postulated. We therefore investigated the changes in serum levels of mannose binding lectin (MBL) and activities of MBL–MBL-associated serine protease (MASP)-1 and MBL–MASP-2 complexes immediately before and during surgery, throughout the first postoperative day and at discharge from the hospital. These changes were analysed in relation to postoperative complications. Blood samples were obtained from 185 children with congenital heart disease undergoing surgical correction with the use of cardiopulmonary bypass: preoperatively (MBL-1), 15 min after initiation of cardiopulmonary bypass (CPB) (MBL-E), 30 min (MBL-2), 4 h (MBL-3), 12 h (MBL-4) and 24 h (MBL-5) post-CPB and at discharge from hospital (MBL-K). Alterations in serum MBL levels were calculated as a ratio of its serum level at subsequent time-points (MBL-2, -3, -4, -5) to the preoperative (MBL-1) value. Decreases in MBL and MBL–MASP complexes were observed in all samples, correlating with a decrease in C4 and increase in C4a, confirming activation of the lectin pathway. Changes in MBL levels between children with an uncomplicated postoperative course and those suffering from infection or low cardiac output syndrome did not differ significantly, but significant differences were observed between the SIRS and non-SIRS groups. Paediatric cardiac surgery with the use of cardiopulmonary bypass activates the complement system via the lectin pathway and the latter contributes to the development of the post-bypass systemic inflammatory response.
Evaluation of autogenous PRGF+β‐TCP with or without a collagen membrane on bone formation and implant osseointegration in large size bone defects. A preclinical in vivo study
Authors: Batas Leonidas , Stavropoulos Andreas , Papadimitriou Serafim , Nyengaard Jens R. , Konstantinidis Antonios 
Published: December 2015

AbstractObjectivesThe aim of this study was to evaluate whether the adjunctive use of a collagen membrane enhances bone formation and implant osseointegration in non‐contained defects grafted with chair‐side prepared autologous platelet‐rich growth factor (PRGF) adsorbed on a β‐TCP particulate carrier.Materials and methodsLarge box‐type defects (10 × 6 mm; W × D) were prepared in the edentulated and completely healed mandibles of six Beagles dogs. An implant with moderately rough surface was placed in the center of each defect leaving the coronal 6 mm of the implant not covered with bone. The remaining defect space was then filled out with chair‐side prepared autologous PRGF adsorbed on β‐TCP particles and either covered with a collagen membrane (PRGF/β‐TCP+CM) (6 defects) or left without a membrane (PRGF/β‐TCP) (5 defects).ResultsHistology 4 months post‐op showed new lamellar and woven bone formation encompassing almost entirely the defect and limited residual β‐TCP particles. Extent of osseointegration of the previously exposed portion of the implants varied, but in general was limited. Within the defect, new mineralized bone (%) averaged 43.2 ± 9.86 vs. 39.9 ± 13.7 in the PRGF/β‐TCP+CM and PRGF/β‐TCP group (P = 0.22) and relative mineralized bone‐to‐implant contact (%) averaged 26.2 ± 16.45 vs. 35.91 ± 24.45, respectively (P = 0.5). First, bone‐to‐implant contact from the implant top was 4.1 ± 1.5 and 3.2 ± 2.3 (P = 0.9), in the PRGF/β‐TCP+CM and PRGF/β‐TCP group, respectively.ConclusionsImplantation of chair‐side prepared autologous PRGF adsorbed on a β‐TCP carrier in non‐contained peri‐implant defects resulted in large amounts of bone regeneration, but osseointegration was limited. Provisions for GBR with a collagen membrane did not significantly enhance bone regeneration or implant osseointegration.