Analysis of gene copy number changes in tumor phylogenetics

Backgound

Evolution of cancer cells is characterized by large scale and rapid changes in the chromosomal  landscape. The fluorescence in situ hybridization (FISH) technique provides a way to measure the copy numbers of preselected genes in a group of cells and has been found to be a reliable source of data to model the evolution of tumor cells. Chowdhury et al. (Bioinformatics 29(13):189–98, 23; PLoS Comput Biol 10(7):1003740, 24) recently develop a computational model for tumor progression driven by gains and losses in cell count patterns obtained by FISH probes. Their model aims to find the rectilinear Steiner minimum tree (RSMT) (Chowdhury et al. in Bioinformatics 29(13):189–98, 23) and the duplication Steiner minimum tree (DSMT) (Chowdhury et al. in PLoS Comput Biol 10(7):1003740, 24) that describe the progression of FISH cell count patterns over its branches in a parsimonious manner. Both the RSMT and DSMT problems are NP-hard and heuristics are required to solve the problems efficiently.

Methods

In this paper we propose two approaches to solve the RSMT problem, one inspired by iterative methods to address the “small phylogeny” problem (Sankoff et al. in J Mol Evol 7(2):133–49, 27; Blanchette et al. in Genome Inform 8:25–34, 28), and the other based on maximum parsimony phylogeny inference. We further show how to extend these heuristics to obtain solutions to the DSMT problem, that models large scale duplication events.

Results

Experimental results from both simulated and real tumor data show that our methods outperform previous heuristics (Chowdhury et al. in Bioinformatics 29(13):189–98, 23; Chowdhury et al. in PLoS Comput Biol 10(7):1003740, 24) in obtaining solutions to both RSMT and DSMT problems.

Conclusion

The methods introduced here are able to provide more parsimony phylogenies compared to earlier ones which are consider better choices.

     

Small bowel Gastrointestinal Stromal Tumors can physiologically alter gut motility before causing mechanical obstruction

Background

Gastro Intestinal Stromal Tumors (GISTs) are rare stromal neoplasms that represent the most common mesenchymal tumor of the G.I. tract, accounting for 5% of all sarcomas [1, 2]. Originating from interstitial cells of Cajal, which are regulators of gut peristalsis, they are preferentially located in the stomach and the small intestine [3] and clinical presentation is variable, ranging from vague complaints to major G.I. bleeding. Surgical resection is the mainstay of treatment for patients with resectable GIST and 5-year survival ranges from 21% to 88% in different series depending on risk grading and completeness of surgical resection [4, 5]. Imatinib mesylate, a tyrosine kinase inhibitor, provides an encouraging option for treating high risk GISTs.

Case presentation

We report the case of a 62-year-old lady who had been diagnosed and being treated unsuccessfully for Irritable bowel syndrome for 11 years and eventually found to have an obstructing small bowel GIST.

Conclusion

The symptoms from GIST may mimic those of irritable bowel syndrome. A physiological alteration in gut peristalsis resulting from neoplastic transformation of the interstitial cells of Cajal, is a hypothesis that could explain this presentation. An alternative diagnosis should be considered when treating patients with irritable bowel syndrome who fail to respond for a prolonged period.

     

Using the product environmental footprint for supply chain management: lessons learned from a case study on pork

Purpose

The purpose of this study was to test the chain-organization environmental footprint (chain-OEF) approach by applying it to part of a pork production chain in Belgium. The approach is supposed to provide insight into the environmental impact of a specific production chain in an efficient manner by applying pragmatic data collection throughout the chain. This is achieved by allocating the environmental impact of each of the production sites to the product of interest using straightforward allocation rules.

Methods

The cradle-to-gate (up to retail) environmental impact of pork was determined by life cycle assessment (LCA), in line with the product and organisation environmental footprint guidelines (PEF and OEF; European Commission 2013b). Foreground data was gathered at a feed production site, two farmers, a slaughterhouse and a meat processing site. All foreground operations are part of the same pork production chain in Belgium. The chain was completed using background data from Ecoinvent v3.01 (Wernet et al. 2016), Agri-Footprint v1.0 (Blonk 2014), European Life Cycle Database v3.0, LCA Food Database (Nielsen et al. 2003) and OEF Sector Rules Retail (Humbert et al. 2015b). The impact was quantified using the international reference life cycle data system (ILCD) midpoint method for 14 impact categories, but focussing on climate change.

Results and discussion

The total carbon footprint of the cradle-to-gate pork production system equals 0.46 kg CO₂-eq. (100 g pork)^?1. This result is quite similar to that of earlier studies analysing the pork production chain: 0.58 and 0.57 kg CO₂-eq. (100 g pork)^?1 (Bracquené et al. 2011, Agri-Footprint 2014). Most of the carbon footprint was caused by feed production and more specifically, by the feed ingredients and their transport. Grains, soy and palm oil have the largest impact contributions. The farms are responsible for most of the remaining impact. N₂O and CH₄ emissions are the largest cause of greenhouse gas emissions at the farms. Also, in the other 13 considered impact categories, feed production and farming are responsible for more than half of the total impact, mostly followed by meat processing.

Conclusions

Applying the chain-OEF approach in this study has shown that a chain LCA can be performed successfully and pragmatic data collection allows obtaining LCA results relatively fast, especially for small or medium-sized enterprises (SMEs). Whereas data availability was not such an issue, the main bottlenecks identified are data management and the link of LCA to other disciplines such as engineering, policy, etc. which could increase the added value of LCA studies.

     

Preclinical models for interrogating drug action in human cancers using Stable Isotope Resolved Metabolomics (SIRM)

Objectives

In this review we compare the advantages and disadvantages of different model biological systems for determining the metabolic functions of cells in complex environments, how they may change in different disease states, and respond to therapeutic interventions.

Introduction

All preclinical drug-testing models have advantages and drawbacks. We compare and contrast established cell, organoid and animal models with ex vivo organ or tissue culture and in vivo human experiments in the context of metabolic readout of drug efficacy. As metabolism reports directly on the biochemical state of cells and tissues, it can be very sensitive to drugs and/or other environmental changes. This is especially so when metabolic activities are probed by stable isotope tracing methods, which can also provide detailed mechanistic information on drug action. We have developed and been applying Stable Isotope-Resolved Metabolomics to examine metabolic reprogramming of human lung cancer cells in monoculture, in mouse xenograft/explant models, and in lung cancer patients in situ (Lane et al. in Omics 15:173–182, 2011; Fan et al. in Metabolomics 7(2):257–269, 2011a, in Pharmacol Ther 133:366–391, 2012a, in Metabolomics 8(3):517–527, b; Xie et al. in Cell Metab 19:795–809, 2014; Ren et al. in Sci Rep 4:5414, 2014; Sellers et al. in J Clin Investig 125(2):687–698, 2015). We are able to determine the influence of the tumor microenvironment using these models. We have now extended the range of models to fresh human tissue slices, similar to those originally described by Warburg (Biochem Z 142:317–333, 1923), which retain the native tissue architecture and heterogeneity with a paired benign versus cancer design under defined cell culture conditions. This platform offers an unprecedented human tissue model for preclinical studies on metabolic reprogramming of human cancer cells in their tissue context, and response to drug treatment (Xie et al. 2014). As the microenvironment of the target human tissue is retained and individual patient’s response to drugs is obtained, this platform promises to transcend current limitations of drug selection for clinical trials or treatments

Conclusions

Development of ex vivo human tissue and animal models with humanized organs including bone marrow and liver show considerable promise for analyzing drug responses that are more relevant to humans. Similarly using stable isotope tracer methods with these improved models in advanced stages of the drug development pipeline, in conjunction with tissue biopsy is expected significantly to reduce the high failure rate of experimental drugs in Phase II and III clinical trials.

     

Positive impacts in social life cycle assessment: state of the art and the way forward

Purpose

Social life cycle assessment (SLCA) is a methodology under continuous development, which may be applied at different scales: from products to economic sectors up to systems at region (meso) and country (macro) scales. Traditionally, SLCA has been focusing on the assessment of negative social externalities, whereas also positive social impacts could be associated to human interventions. The purpose of the present study is to understand how positive impacts are defined in published literature and how they could be assessed through indicators. The aim is to clarify the concept among scholars and to support decision making in business and policy context.

Methods

The study uses a systematic review approach in order to analyse the types of indicators adopted. In the field of SLCA and according to Paragahawewa et al. (2009), “[I]ndicators are ‘pointers’ to the state of the impact categories (and/or subcategories) being evaluated by the SLCA”. Indicators can be quantitative, semi-quantitative or qualitative (UNEP/SETAC 2009). This review was carried out in order to identify and analyse positive impacts and indicators. After careful scrutiny, 47 papers containing theoretical frameworks were considered, as well as 46 papers presenting case studies.

Results and discussion

Compared to environmental life cycle assessment (E-LCA), where the presence of positive impacts is lower, evaluating benefits or positive impacts can still play a major role in SLCA (Benoît et al. 2010). A quarter of the analysed papers on theoretical frameworks take into account the topic of positive impacts and indicators. Results from case study analysis highlight as “workers”, was the most considered stakeholder (in 100 % of the analysed papers), and as the majority of positive indicators used in the case study analysed are recorded in relation to “other value chain actors”. Within the concept of “positive impacts”, no reference should be made merely to the utility of a product or service. In a broader sense, we could refer to solutions improving the conditions of one or various stakeholders involved. In other words, these are solutions that carry a positive contribution to one or more stakeholders without harming others.

Conclusions

So far, positive impacts are barely covered in literature. There is a clear need of streamlining definition and indicators, especially if they should be applied in a policy context complementing traditional—and often monetary-based, cost-benefit analysis (CBA).

     

Extending the geopolitical supply risk method: material “substitutability” indicators applied to electric vehicles and dental X-ray equipment

Purpose

While environmental LCA is relatively well developed, impact assessment methods for the “natural resources” AoP are weak. In particular, resource “criticality” is not addressed in conventional environmental impact assessment methods, though it could be captured within life cycle sustainability assessment. In that regard, the present article extends the previously developed geopolitical supply risk (GPSR) method by demonstrating the connection of criticality to a functional unit while incorporating measures of material substitutability to reflect the “vulnerability” dimension of criticality.

Methods

The GPSR method developed by Gemechu et al. (J Ind Ecol 20:154–165, 2015a) and subsequently extended by Helbig et al. (J Clean Prod 137:1170–1178, 2016a), and Cimprich et al. (J Clean Prod, 2017) is integrated into an LCIA characterization model. Further, semi-quantitative material substitutability indicator values based on a study by Graedel et al. (PNAS 112:6295–6300, 2015) are incorporated to represent the vulnerability dimension of criticality. The method is demonstrated with an update of a previously published case study of a European-manufactured electric vehicle by Gemechu et al. (Int J Life Cycle Assess 22:31–39, 2015b), along with a new case study of dental X-ray equipment. Due to novel aspects of the GPSR method, the latter case involves constructing an unusually comprehensive bill of materials by tracing unit processes to input commodities with identification codes for collecting commodity trade data.

Results and discussion

Supply risk “hotspots” are often associated with “minor” commodities such as neodymium in an electric vehicle and cesium iodide in a dental X-ray system. Though difficult to measure, material substitutability can mitigate supply risk. Environmental loads of a dental X-ray system are dominated by production of relatively small specialized functional components like capacitors and printed circuit boards, which are far more environmentally intensive per unit of mass than common structural and mechanical components. Thus, small components comprised of minor materials can “pack a punch” from a supply risk and environmental perspective.

Conclusions

The GPSR method presented in the present article brings resource criticality assessment to a product-level while addressing a gap in conventional LCIA methods regarding short-run, socioeconomic availability of natural resources. Further, the case studies illustrate the significance of material substitutability in supply risk assessment. Several complications and limitations of the GPSR method offer directions for future research. Nonetheless, the GPSR method complements environmental LCA to better inform design and management decisions on a product-level.

     

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Background

Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes, i.e. the number of nucleotides between consecutive genes, although it was recently shown decisive for the accuracy of inference methods (Biller et al. in Genome Biol Evol 8:1427–39, 2016; Biller et al. in Beckmann A, Bienvenu L, Jonoska N, editors. Proceedings of Pursuit of the Universal-12th conference on computability in Europe, CiE 2016, Lecture notes in computer science, vol 9709, Paris, France, June 27–July 1, 2016. Berlin: Springer, p. 35–44, 2016). In this line, we define a new genome rearrangement model called wDCJ, a generalization of the well-known double cut and join (or DCJ) operation that modifies both the gene order and the intergene size distribution of a genome.

Results

We first provide a generic formula for the wDCJ distance between two genomes, and show that computing this distance is strongly NP-complete. We then propose an approximation algorithm of ratio 4/3, and two exact ones: a fixed-parameter tractable (FPT) algorithm and an integer linear programming (ILP) formulation.

Conclusions

We provide theoretical and empirical bounds on the expected growth of the parameter at the center of our FPT and ILP algorithms, assuming a probabilistic model of evolution under wDCJ, which shows that both these algorithms should run reasonably fast in practice.

     

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Background

Recently, Marcus et al. (Bioinformatics 30:3476–83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an \(O(n\log g)\) time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome. Baier et al. (Bioinformatics 32:497–504, 2016) improved their result.

Results

In this paper, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele—a variant form of a gene) within the pan-genome. The ability to search within the pan-genome graph is of utmost importance and is a design goal of pan-genome data structures.

     

IFN-γ production in response to <Emphasis Type="Italic">in vitro</Emphasis> stimulation with collagen type II in rheumatoid arthritis is associated with HLA-DRB1<Superscript>*</Superscript>0401 and HLA-DQ8

Introduction

Despite much work over past decades, whether antigen-specific immune reactions occur in rheumatoid arthritis (RA) and to what extent such reactions are directed towards joint-specific autoantigens is still questionable. One strong indicator for antigenic involvement in RA is the fact that certain major histocompatibility complex (MHC) class II genotypes [human leucocyte antigen (HLA)-DR4 and HLA-DR1] predispose for the development of the disease [1]. In the present report, collagen type II (CII) was studied as a putative autoantigen on the basis of both clinical and experimental data that show an increased frequency of antibodies to CII in RA patients [2,3,4] and that show that CII can induce experimental arthritis [5].It is evident from the literature that RA peripheral blood mononuclear cells (PBMCs) respond poorly to antigenic stimulation [6,7,8], and in particular evidence for a partial tolerization to CII has been presented [9]. The strategy of the present work has accordingly been to reinvestigate T-cell reactivity to CII in RA patients, to relate it to the response to commonly used recall antigens and to analyze IFN-γ responses as an alternative to proliferative responses.     

Superbubbles revisited

Background

Superbubbles are distinctive subgraphs in direct graphs that play an important role in assembly algorithms for high-throughput sequencing (HTS) data. Their practical importance derives from the fact they are connected to their host graph by a single entrance and a single exit vertex, thus allowing them to be handled independently. Efficient algorithms for the enumeration of superbubbles are therefore of important for the processing of HTS data. Superbubbles can be identified within the strongly connected components of the input digraph after transforming them into directed acyclic graphs. The algorithm by Sung et al. (IEEE ACM Trans Comput Biol Bioinform 12:770–777, 2015) achieves this task in \(\mathcal {O}(m~log(m))\)-time. The extraction of superbubbles from the transformed components was later improved to by Brankovic et al. (Theor Comput Sci 609:374–383, 2016) resulting in an overall \(\mathcal {O}(m+n)\)-time algorithm.

Results

A re-analysis of the mathematical structure of superbubbles showed that the construction of auxiliary DAGs from the strongly connected components in the work of Sung et al. missed some details that can lead to the reporting of false positive superbubbles. We propose an alternative, even simpler auxiliary graph that solved the problem and retains the linear running time for general digraph. Furthermore, we describe a simpler, space-efficient \(\mathcal {O}(m+n)\)-time algorithm for detecting superbubbles in DAGs that uses only simple data structures.

Implementation

We present a reference implementation of the algorithm that accepts many commonly used formats for the input graph and provides convenient access to the improved algorithm. https://github.com/Fabianexe/Superbubble.

     

Independent information modules—a powerful approach for life cycle management

Background, aim, and scope

The term “information module” has been initially introduced by ISO 14025 (ISO 14025 2006) which specifies Type III environmental declarations. It comprises a set of predetermined parameters (PDPs) assigned to a process. Such a process can be part of a product system, i.e., a unit process or a combination of unit processes as, e.g., the production processes of a company. Independent information modules (IIMs) of processes within a system are modeled in a way that the predetermined parameters of the information modules related to these processes are identical and sufficiently independent so they can be added up to the predetermined parameters of such a system, typically after multiplication with specific factors based on the reference flow of the system.

Materials and methods

This paper shows how IIMs can be used as powerful approach in life cycle management and how operations, goods, and services of a company can be modeled efficiently with the help of IIMs. To define environmental objectives of their operations, organizations typically assess their foreground processes but do not apply system expansion for each of the foreground processes to include background processes. With the help of IIMs, background processes can be easily included, and the PDPs, therefore, also include both direct and indirect elementary flows, i.e., emissions and resources. In a “plant ecobalance” the PDPs of the different (foreground and background) processes of an organization can be determined and added up. This provides each process owner with important information about the environmental aspects which he or she can control and shows options for setting and implementing environmental objectives. For specific purposes, the number of PDPs can be restricted or even limited to one parameter, e.g., the carbon footprint. This paper illustrates the method with one example of the aluminum industry (carbon footprint of an automotive bumper beam) and shows how PDPs of product systems can be built up from IIMs which represent the different stages of a life cycle; how such results can show the influence of these stages in a transparent way, as required as a part of the life cycle interpretation phase.

Results and discussion

Life cycle assessments (LCAs) based on IIMs follow the principles and requirements of ISO 14040 (2006) and ISO 14044 (2006), as applicable. However, as a specific approach of life cycle management, they can obtain the required information with less effort than “conventional” LCAs where, following the guidance of ISO 14044, indicator results are calculated after the inventory data have been aggregated for the whole product system. Future efforts in ISO standardization should strengthen the role of LCA as a tool of environmental management.

     

Plant individuality: a solution to the demographer’s dilemma

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800; Braun and Stone 1853; Münch 1938) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977; Cook 1985; Ariew and Lewontin 2004), a lively debate conducted mostly in Scandinavian journals proves that the issues are far from being resolved (Tuomi and Vuorisalo 1989b; Fagerström 1992; Pan and Price 2001). In this paper I settle the matter once and for all, by showing which elements of each side are correct.     

Use of CD40L immunoconjugates to overcome the defective immune response to vaccines for infections and cancer in the aged

Multiple investigators have reported thepresence of defects in the immune response of the elderly [Castle In: Clin Infect Dis 31:578, 2000; Ortqvist et al. In: Eur Respir J 30:414–422, 2007; Saurwein-Teissl et al. In: J Immunol 168:5893, 2002; Haynes et al. In: Proc Natl Acad Sci USA 100:15053–15058, 2003]. These defects reduce the magnitude of the immune response to infection and to vaccination. In individuals greater than 55 years of age, the probability of developing a fully protective neutralizing antibody response to the yearly multivalent particle inactivated influenza vaccine is less than 20% [Jefferson et al. In: Lancet 264:1165–1174, 2005; Goodwin et al. In: Vaccine 24:1159–1169, 2006; Jackson et al. In: Lancet 372:398–405, 2008; Simonsen and Taylor In: Lancet 7:658–666, 2007]. The defects in the aged immune system that are responsible for this limited response to vaccination in the older age groups include functional defects of the antigen presenting cells, functional defects in CD4 helper CD4 T cells and monocytes, and an altered microenvironment [Eaton et al. In: J Exp Med 200:1613–1622, 2004; Dong et al. In: J Gen Virol 84:1623–1628, 2003; Deng et al. In: Immunology 172:3437–3446, 2004; Cella et al. In: J Exp Med 184:747–752, 1996]. Starting at puberty, the involution of the thymus and the consequent reduction of the export of naïve T cells specific to neo-antigens leads to the reduction of the ratio of antigen naïve to memory cells as chronological age advances [Prelog In: AutoimmunRev 5:136–139, 2006; McElhaney et al. In: J Immunology 176:6333–6339, 2006]. Changes in glycosylation of T cells and target antigens acquired during the aging process and the antibodies to these new glycopeptides and glycoproteins may also contribute to a reduction in the functioning of the adaptive immune response [Ishii et al. In: J Clin Neurosci 14:110–115, 2007; Shirai et al. In: Clin Exp Immunol 12:455–464, 1972; Adkins and Riley In: Mech AgeingDev 103:147–164, 1998; Ben-Yehuda and Weksler In: Cancer Investigation 10:525–531, 1992]. One of the more interesting examples of the functional defects in the cells of the adaptive immune response is a reduced level of expression in the surface cytoadhesion and activation receptor molecules on CD4 helper T cells undergoing activation during vaccination. Upon infection or vaccination, CD40L is typically increased on the surface of CD4 helper T cells during activation, and this increased expression is absolutely essential to the CD40L promotion of expansion of antigen-specific B cells and CD 8 effector T cells in response to infection or vaccination [Singh et al. In: Protein Sci 7:1124–1135, 1998; Grewal and Flavell In: Immunol Res 16: 59–70, 1997; Kornbluth In: J Hematother Stem Cell Res 11:787–801, 2002; Garcia de Vinuesa et al. In: Eur J Immunol 29:3216–3224, 1999]. In aged human beings and mice, the reduced levels of expression of CD40 ligand (CD40L) in activated CD4 helper T cells is dramatically reduced [Eaton et al. In: J Exp Med 200:1613–1622, 2004; Dong et al. In: J Gen Virol 84:1623–1628, 2003]. To circumvent the reduction in CD40L expression and the subsequent reduction in immune response in the elderly, we have developed a chimeric vaccine comprised of the CD40L linked to the target antigen, in a replication incompetent adenoviral vector and in booster protein. This review will discuss the implementation the potential use of this approach for the vaccination of the older populations for cancer and infection.     

Using human case studies to teach evolution in high school A.P. biology classrooms

Background

While recent research indicates that using human examples can be an engaging way to teach core evolutionary concepts such as natural selection and phylogenetic thinking, teachers still face potential conflicts and challenges that arise from cultural barriers to teaching and learning about evolution. The “Teaching Evolution through Human Examples” (TEtHE) project developed (1) a set of four curriculum mini-units for advanced placement (A.P.) biology that use human examples to teach evolutionary principles (Adaptation to Altitude, Evolution of Human Skin Color, Malaria, and What Does It Mean To Be Human?), and (2) a cultural and religious sensitivity (CRS) teaching strategies resource that includes background materials and two in-class activities to help teachers create a classroom environment to increase student willingness to engage the topic.

Methods

This paper reports on the development and field test of the TEtHE materials in A.P. biology classes in 10 schools in 8 states during the 2012–2013 school year using a design-based research framework (cf. Anderson and Shattuck in Educ Res 41:16–25, 2012). We chose A.P. classrooms to study the potential impacts of the materials in a “best case scenario” and analyzed data about understanding and acceptance of evolution from pre-post assessments in the 10 classrooms separately to mitigate potential validity concerns arising from the design (Anderson and Shattuck in Educ Res 41:16–25, 2012; Shadish et al. in Experimental and quasi-experimental designs for generalized causal inference. Houghton Mifflin, Boston, 2002). These data were treated as a secondary source of formative data to add additional perspective to teacher self-reports, observations, student and teacher questionnaires, teacher interviews, and student focus groups.

Results

Results indicate that the use of the three curriculum mini-units which focus on natural selection and the CRS classroom activities generally increased A.P. biology students’ understanding and acceptance of evolution. Students whose teachers used one of the CRS activities showed generally larger increases in understanding of evolution than those whose teachers did not use one of the CRS activities.

Conclusions

Although the utility of using human examples to teach evolution in college-level classes has been demonstrated in a few previous studies, this is the first national project of which we are aware to systematically explore the effect of a similar approach in high school biology classes. While we recognize that the results may be mitigated by the limitations of design-based research, particularly the absence of a comparison or control group, the general effectiveness of this approach suggested by qualitative and quantitative data in increasing student understanding and acceptance of evolution suggests that using human examples and explicitly creating a classroom environment to help students engage the topic of evolution are worth considering for further development and more robust testing.

     

Soil under nurse plants is always better than outside: a survey on soil amelioration by a complete guild of nurse plants across a long environmental gradient

Aims

Soil under nurse plants is more fertile than in the harsh surroundings. This is a primary mechanism involved in plant to plant facilitation and it is critical in structuring plant communities under stressful conditions. However we do not know how this soil enrichment process varies along complex environmental gradients and among coexisting nurse plants.

Methods

Soil properties related to structure, resource stocks and microbial activity, were compared among up to ten nurse plant species and adjacent barren soil areas, along a 1600 m elevation gradient above the treeline in central Chilean Andes. Shifts in Relative Interaction Index (RII) sensu Armas (Ecology 85: 2682–2686, 2004) and in coefficient of variation on soil properties were also modelled.

Results

Soil under nurse plants was always richer than on barren areas irrespective of altitude, except in the case of texture with more small particles in the intermediate altitude. β-glucosidase activity was higher under cushion plants than under nurse plants with other growth habit. Besides β-glucosidase and phosphatase activities were more variable at higher altitudes. Nitrogen was more variable under nurse plants than in barren areas and its RII values were lower at intermediate altitudes.

Conclusions

Soil amelioration by nurse plants occurred all along the studied environmental gradient promoting islands of fertility and a general increase on soil niches heterogeneity.

     

Lexical splits within periphrasis: mixed perfective auxiliation systems in Italo-Romance

This paper addresses the phenomenon of mixed paradigms, i.e. mixed perfective auxiliation systems, attested in a wide range of Italo-Romance varieties (cf. Loporcaro 2001, 2007a, 2014; Manzini and Savoia 2005, among others). In these varieties, two auxiliary verbs, esse and habere, alternate within one and the same (sub)paradigm, displaying various patterns which can range from morphosyntactically motivated to apparently unmotivated distributions (here termed ‘morphomic’). I propose that, in these varieties, auxiliary selection is no longer a syntactically driven phenomenon, but becomes morphologized. I draw on the notion of ‘lexical split’ (cf. Corbett 2013, 2015, 2016) and describe the attested splits induced by intraparadigmatic auxiliary alternation. Following Bonami (2015), I put forward a typology of such splits. It is shown that, apart from motivated distributions, some morphomic patterns can also be found. The typology becomes more complex insofar as patterns with free variation between both auxiliaries are taken into account, as well as patently morphomic patterns which also seem to display external syntactic relevance (cf. Corbett 2013: 174–176). The phenomena reviewed and discussed in this paper are of major interest because they demonstrate the existence of competing exponence strategies within periphrasis, thus enriching the notion of ‘possible lexeme’ (cf. Corbett 2015: 146).     

From possessive suffix to affective demonstrative suffix in Hungarian: a grammaticalization analysis

The non-possessive uses of possessive morphology in Uralic languages have been a topic of intense debate (Fraurud 2001; Nikolaeva 2003; Gerland 2014; Janda 2015; É. Kiss and Tánczos to appear). In this paper, I focus on a special use of the poss.3sg suffix in Hungarian constructions such as a hülyéje (the stupid-poss.3sg): lit. ‘its stupid’, meaning ‘that total idiot’. My main claim is that this suffix is an affective demonstrative suffix (Lakoff 1974; Liberman 2008; Potts and Schwarz 2010), and that it has developed as a result of grammaticalization from a full-fledged possessive construction of the form a világ hülyéje (the world stupid-poss.3sg): lit. ‘the world’s stupid’, meaning: ‘the biggest idiot in the world’. I will show that this gradual process can be reconstructed fairly accurately using historical and contemporary corpora. I also claim that this grammaticalization pathway is very natural as it is based on a set-element relationship which is often expressed by possessive constructions cross-linguistically. I also identify two parameters which facilitate this grammaticalization process: the availability of (silent) pro possessors and the lack of gender agreement on the possessive suffix. Since Uralic languages in general have these parameters, I will argue that this grammaticalization pathway should at least be considered as one of the possible sources of the demonstrative (and definiteness marking) uses of poss.3sg suffixes in Uralic languages. Finally, my results are also an important contribution to the debate on whether demonstratives can be derived from other functional elements through grammaticalization (Plank 1979; Traugott 1982; Himmelmann 1997).     

First-principle investigation on growth patterns and properties of cobalt-doped lithium nanoclusters

A systematic theoretical investigation on cobalt lithium clusters Li_nCo [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] was performed with a DFT approach. The location of global minima and structural evolution were carried out using the partical swarm optimization method. Li₆Co is the transition structure in going from low-coordinated structures to three-dimensional torispherical structures with a cobalt atom enclosed by lithium atoms. Maxima of ?₂ E and E _b for Li_nCo were found at n?=?3, 6, 8, 10, indicating that these clusters possess higher relative stability than their neighbors. In comparison with small clusters, n?=?1–6, the greater electron transfer from Li-2s to Co-3d within cage-like clusters Li_nCo (n?=?7–12) strengthens the bonding effect between Li_n and Co, which is reflected in the Wiberg bond index of Co and atomic binding energy analysis. AdNDP analysis verified the presence of both Lewis bonding elements (1c–2e objects) and delocalized bonding elements (6c–2e, 9c–2e and 10c–2e bonds). It is hoped that this theoretical work will provide favorable information to help understand the influence of dopant transition metal atoms on the properties of lithium-based materials.