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.     

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.

     

Life-cycle assessment of the soybean-sunflower production system in the Brazilian Cerrado

Purpose

In the “Cerrado” (Brazilian savanna), sunflower comes mostly from a cropping system where its seeding follows soybean harvest. Soybean has a much higher economic value, but this association with sunflower reduces the environmental impacts from both crops by sharing resources. This study performed a life-cycle assessment (LCA) of the soybean-sunflower cropping system, identified its hotspots, and compared its environmental performance with two hypothetical monocultures, in order to corroborate its benefits.

Methods

Soybean-sunflower cropping system inventory used data from farms of the Parecis region, consolidated by experts. Inventories for soybean and sunflower monocultures were estimated from the cropping system inventory. LUC (land-use changes) were calculated from CONAB (2015), FAOSTAT (2012), and Macedo et al. (P Natl Acad Sci USA 109:1341–1346, 2012). Emissions estimation followed Nemecek and Schnetzer (2011), Milà i Canals (2003), and EC (2010). Land occupation, land-use changes, and liming were allocated by occupation time, but a sensitivity analysis was performed for yield and gross margin as allocation criteria. ReCiPe Midpoint (H) v1.12/World ReCiPe H was the impact assessment method, and some categories were disregarded as not relevant. We used pedigree matrix to estimate uncertainties for inventory and Monte Carlo method for impact uncertainty analysis as in Goedkoop et al. (2008). We used SimaPro 8.0.5.13.

Results and discussion

The soybean-sunflower cropping system generate relevant human toxicity, freshwater toxicity, freshwater eutrophication, climate change, and terrestrial acidification impacts, related to emissions derived from nitrogen and phosphate fertilizers and emissions generated by LUC. Sunflower-soybean cropping system has better environmental performance when compared to the combination of monocultures because of a number of synergies made possible by sharing land use and other resources. Changing the allocation criteria altered the relative performance of some categories, but in all categories the environmental impacts of the cropping system were lower than those of the corresponding monoculture impacts, regardless of the allocation criteria implemented.

Conclusions

We concluded that the environmental performance of the soybean-sunflower cropping system can be improved by optimizing the use of chemical fertilizers. Climate change impacts, which are mostly driven by LUC, could be reduced by production intensification, preventing the clearing of native vegetation for agricultural purposes. This study confirmed the environmental benefits of cropping systems when compared to monocultures and the advantages of association of nitrogen-fixing legumes with other plant species in a production system.

     

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.

     

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.     

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.

     

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.     

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).     

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).     

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.     

Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716–730, 2010; J Mol Biol 426:1109–1127, 2014; J Biol Chem 291:13098–13112, 2016; J Am Chem Soc 138:8538–8546, 2016; J Am Chem Soc 138:12029–12032, 2016; J Am Chem Soc 134:6455–6466, 2012; J Am Chem Soc 132:1976–1987, 2010; J Am Chem Soc 135:17793–17803, 2013; Proc Natl Acad Sci USA 112:14617–14622, 2015; J Am Chem Soc 138:14066–14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly ¹⁵N,¹³C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.     

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.

     

A perspective for reducing environmental impacts of mussel culture in Algeria

Purpose

In Algeria, the Ministry of Fisheries and Halieutic Resources has designed a strategic plan for the development of marine aquaculture for the years 2015–2025, which aims at expanding the annual production of Mediterranean mussel from less than 150 metric tonnes year^?1 in 2013 to 7600 metric tonnes year^?1 in 2025. We used Life Cycle Assessment (LCA) for evaluating the environmental impact of suspended mussel culture in Algeria and suggest management practices which could reduce it.

Methods

In order to estimate the current and perspective impact of this industry, we (1) applied LCA to one of the few farms currently operating in Algeria and (2) investigated two management scenarios for the farms to be established in the future in the same coastal area. The first scenario (Comp_S) represents the continuity with the current situation, in which each farm is competing with the other ones and is therefore managing the production cycle independently. In the second scenario (Coop_S), mussel farms are grouped in an aquaculture management area and shared the same facilities for post-processing harvested mussels before sending them to the market. The midpoint-based CML-IA method baseline 2000 V 3.01 was employed using SimaPro software. Furthermore, we carried out a Monte Carlo simulation, in order to assess the uncertainty in the results.

Results and discussion

The analysis focused on impact categories related to acidification and global warming potential. We took into account the energy consumptions (electricity and vessel fuel), the rearing infrastructure, including longlines, and a building for stabling, grading, and packing the mussel. Electricity contributes with 38.1 and 31.8 % respectively to global warming potential (GWP) and acidification, while fuel consumption contributes with 19.5 % to GWP and 31.8 % to acidification. Results of this work are compared with other LCA studies recently carried out in France (Aubin and Fontaine 2014) and in Spain (Iribarren et al. 2010c).

Conclusions

The LCA results show that important reductions in environmental impacts could be attained if the mussel farming activity would be operated according to the cooperative scenario here proposed. In this case, the environmental benefits will be a reduction of 3150 MJ and 156 kg CO₂ eq per metric tonne of mussel produced, compared with the alternative scenario. The results of this study suggest that LCA should be applied to the seafood production sector in Algeria, in order to identify best management practices.

     

A covalent antagonist for the human adenosine A<Subscript>2A</Subscript> receptor

The structure of the human A_2A adenosine receptor has been elucidated by X-ray crystallography with a high affinity non-xanthine antagonist, ZM241385, bound to it. This template molecule served as a starting point for the incorporation of reactive moieties that cause the ligand to covalently bind to the receptor. In particular, we incorporated a fluorosulfonyl moiety onto ZM241385, which yielded LUF7445 (4-((3-((7-amino-2-(furan-2-yl)-[1, 2, 4]triazolo[1,5-a][1, 3, 5]triazin-5-yl)amino)propyl)carbamoyl)benzene sulfonyl fluoride). In a radioligand binding assay, LUF7445 acted as a potent antagonist, with an apparent affinity for the hA_2A receptor in the nanomolar range. Its apparent affinity increased with longer incubation time, suggesting an increasing level of covalent binding over time. An in silico A_2A-structure-based docking model was used to study the binding mode of LUF7445. This led us to perform site-directed mutagenesis of the A_2A receptor to probe and validate the target lysine amino acid K153 for covalent binding. Meanwhile, a functional assay combined with wash-out experiments was set up to investigate the efficacy of covalent binding of LUF7445. All these experiments led us to conclude LUF7445 is a valuable molecular tool for further investigating covalent interactions at this receptor. It may also serve as a prototype for a therapeutic approach in which a covalent antagonist may be needed to counteract prolonged and persistent presence of the endogenous ligand adenosine.     

Strong Comma-Free Codes in Genetic Information

Comma-free codes constitute a class of circular codes, which has been widely studied, in particular by Golomb et al. (Biologiske Meddelelser, Kongelige Danske Videnskabernes Selskab 23:1–34, 1958a, Can J Math 10:202–209, 1958b), Michel et al. (Comput Math Appl 55:989–996, 2008a, Theor Comput Sci 401:17–26, 2008b, Inf Comput 212:55–63, 2012), Michel and Pirillo (Int J Comb 2011:659567, 2011), and Fimmel and Strüngmann (J Theor Biol 389:206–213, 2016). Based on a recent approach using graph theory to study circular codes Fimmel et al. (Philos Trans R Soc 374:20150058, 2016), a new class of circular codes, called strong comma-free codes, is identified. These codes detect a frameshift during the translation process immediately after a reading window of at most two nucleotides. We describe several combinatorial properties of strong comma-free codes: enumeration, maximality, self-complementarity and \(CF^3\)-property (comma-free property in all the three possible frames). These combinatorial results also highlight some new properties of the genetic code and its evolution. Each amino acid in the standard genetic code is coded by at least one strong comma-free code of size 1. There are 9 amino acids \(S=\{Asn,Asp,Gln,Gly,Lys,Met,Phe,Pro,Trp\}\) among 20 such that for each amino acid from S, its synonymous trinucleotide set (excluding the necessary periodic trinucleotides \(\{AAA,CCC,GGG,TTT\}\)) is a strong comma-free code. The primeval comma-free RNY code of Eigen and Schuster (Naturwissenschaften 65:341–369, 1978) is a self-complementary \(CF^3\)-code of size 16. Furthermore, it is the union of two strong comma-free codes of size 8 which are complementary to each other.     

Production of Estonian case-inflected nouns shows whole-word frequency and paradigmatic effects

Most psycholinguistic models of lexical processing assume that the comprehension and production of inflected forms is mediated by morphemic constituents. Several more recent studies, however, have challenged this assumption by providing empirical evidence that information about individual inflected forms and their paradigmatic relations is available in long-term memory (Baayen et al. 1997; Milin et al. 2009a, 2009b). Here, we investigate how whole-word frequency, inflectional paradigm size and morphological family size affect production latencies and articulation durations when subjects are asked to read aloud isolated Estonian case-inflected nouns. In Experiment 1, we observed that words with a larger morphological family elicited shorter speech onset latencies, and that forms with higher whole-word frequency had shorter acoustic durations. Experiment 2, for which we increased statistical power by using 2,800 words, revealed that higher whole-word frequency, inflectional paradigm size, and morphological family size reduced both speech onset times and acoustic durations. These results extend our knowledge of morphological processing in three ways. First, whole-word frequency effects of inflected forms in morphologically rich languages are not restricted to a small number of very high-frequency forms, contrary to previous claims (Niemi et al. 1994; Hankamer 1989; Yang 2016). Second, we replicated the morphological family size effect in a new domain, the acoustic durations of inflected forms. Third, we showed that a novel paradigmatic measure, inflectional paradigm size, predicts word naming latencies and acoustic durations. These results fit well with Word-and-Paradigm morphology (Blevins 2016) and argue against strictly (de)compositional models of lexical processing.     

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.

     

First record of <Emphasis Type="Italic">Pojetaia runnegari</Emphasis> Jell, 1980 and <Emphasis Type="Italic">Fordilla</Emphasis> Barrande, 1881 from the Middle East (Taurus Mountains,Turkey) and critical review of Cambrian bivalves

Cambrian bivalves from the Middle East are reported here for the first time. They come from early “Middle Cambrian” and latest “Early Cambrian” limestones of the lower Çal Tepe Formation at the type locality (near Seydi?ehir, western Taurides). The majority of the new findings consists of Pojetaia runnegari Jell, 1980, but a few specimens of Fordilla sp. represent the first report of this genus from “Middle Cambrian” strata. Based on a compilation of the hitherto reported, but mostly revised Cambrian bivalves, the today widely accepted taxa are discussed. The genera Pojetaia Jell, 1980 and Fordilla Barrande, 1881 are critically evaluated, and three valid species are included in Pojetaia: P. runnegari Jell, 1980, P. sarhroensis Geyer and Streng, 1998, and—with limitations—P. ostseensis Hinz-Schallreuter, 1995. Fordilla also includes three species: F. troyensis Barrande, 1881, F. sibirica Krasilova, 1977, and F. germanica Elicki, 1994. The Cambrian genera Tuarangia MacKinnon, 1982, Camya Hinz-Schallreuter, 1995, and Arhouriella Geyer and Streng, 1998 most probably belong to the class Bivalvia. Palaeoecologically, the Cambrian bivalves of the Western Perigondwanan shelf seem to occur in a relatively small window of low-energy, subtidal, open-marine, warm-water conditions on a muddy carbonate ramp or platform with reduced sedimentation rate. The frequently interpreted infaunal mode of life of Pojetaia and Fordilla is questioned by observations of similarly organized modern bivalves. The palaeogeographical distribution of Pojetaia and Fordilla is discussed with respect to their early ontogeny and to differences in the recent state of knowledge on shelly fossils from Cambrian carbonate successions of Perigondwana.