bluuebunny/crossref_metadata_2025_split huggingface dataset:
Focus on the spectra that matter by clustering of quantification data in shotgun proteomics
Authors: The Matthew , Käll Lukas 
Published: December 2018

AbstractIn shotgun proteomics, the information extractable from label-free quantification experiments is typically limited by the identification rate and the noise level in the quantitative data. This generally causes a low sensitivity in differential expression analysis on protein level. Here, we propose a quantification-first approach for peptides that reverses the classical identification-first workflow. This prevents valuable information from being discarded prematurely in the identification stage and allows us to spend more effort on the identification process. Specifically, we introduce a method, Quandenser, that applies unsupervised clustering on both MS1 and MS2 level to summarize all analytes of interest without assigning identities. Not only does this eliminate the need for redoing the quantification for each new set of search parameters and engines, but it also reduces search time due to the data reduction by MS2 clustering. For a dataset of partially known composition, we could now employ open modification and de novo searches to identify analytes of interest that would have gone unnoticed in traditional pipelines. Moreover, Quandenser reports error rates for feature matching, which we integrated into our probabilistic protein quantification method, Triqler. This propagates error probabilities from feature to protein level and appropriately deals with the noise in quantitative signals caused by false positives and missing values. Quandenser+Triqler outperformed the state-of-the-art method MaxQuant+Perseus, consistently reporting more differentially abundant proteins at 5% FDR: 123 vs. 117 true positives with 2 vs. 25 false positives in a dataset of partially known composition; 62 vs. 3 proteins in a bladder cancer set; 8 vs. 0 proteins in a hepatic fibrosis set; and 872 vs. 661 proteins in a nanoscale type 1 diabetes set. Compellingly, in all three clinical datasets investigated, the differentially abundant proteins showed enrichment for functional annotation terms.The source code and binary packages for all major operating systems are available from https://github.com/statisticalbiotechnology/quandenser, under Apache 2.0 license.
Rhizosphere-enriched microbes as a pool to design synthetic communities for reproducible beneficial outputs
Authors: Tsolakidou Maria-Dimitra , Stringlis Ioannis A. , Fanega-Sleziak Natalia , Papageorgiou Stella , Tsalakou Antria , Pantelides Iakovos S. 
Published: December 2018

AbstractComposts represent a sustainable way to suppress diseases and improve plant growth. Identification of compost-derived microbial communities enriched in the rhizosphere of plants and characterization of their traits, could facilitate the design of microbial synthetic communities (SynComs) that upon soil inoculation could yield consistent beneficial effects towards plants. Here, we characterized a collection of compost-derived bacteria, previously isolated from tomato rhizosphere, forin vitroantifungal activity against soil-borne fungal pathogens and for their potential to change growth parameters inArabidopsis. We further assessed root-competitive traits in the dominant rhizospheric genusBacillus. Certain isolated rhizobacteria displayed antifungal activity against the tested pathogens and affected growth ofArabidopsis, and Bacilli members possessed several enzymatic activities. Subsequently, we designed two SynComs with different composition and tested their effect onArabidopsisand tomato growth and health. SynCom1, consisting of different bacterial genera, displayed negative effect onArabidopsis in vitro, but promoted tomato growth in pots. SynCom2, consisting of Bacilli, didn’t affectArabidopsisgrowth, enhanced tomato growth and suppressed Fusarium wilt symptoms. Overall, we found selection of compost-derived microbes with beneficial properties in the rhizosphere of tomato plants, and observed that application of SynComs on poor substrates can yield reproducible plant phenotypes.
Control of stem-cell niche establishment in Arabidopsis flowers by REVOLUTA and the LEAFY-RAX1 module
Authors: Grégoire Denay , Gabrielle Tichtinsky , Marie Le Masson , Hicham Chahtane , Sylvie Huguet , Irene Lopez-Vidriero , Christian Wenzl , Manuel Franco-Zorrilla José , Rüdiger Simon , Lohmann Jan U. , François Parcy 
Published: December 2018

AbstractPlants retain the ability to produce organs throughout their life by maintaining active stem cell niches called meristems. The shoot apical meristem (SAM) is responsible for the growth of aerial plant structures. InArabidopsis thaliana, the SAM initially produces leaves during the vegetative phase and later flowers during reproductive development. In the early stages of floral initiation, a group of cells first emerges from the SAM to form a stereotypically organized meristematic structure on its flank. However, the molecular mechanisms underlying the acquisition of this specific meristematic organization remain elusive. We show here that the transcription factors LEAFY (LFY) and REVOLUTA (REV) control two partially redundant pathways controlling meristematic organization in early flower primordia. We found that LFY acts through the transcription factor REGULATOR OF AXILLARY MERISTEM1 (RAX1) and we provide mechanistic insights in how RAX1 allows meristem identity establishment in young flowers. Our work provides a molecular link between the processes of meristem formation and floral identity acquisition in the nascent flower.
Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly
Authors: Cabrera Andrea A. , Hoekendijk Jeroen P. A. , Aguilar Alex , Barco Susan G. , Berrow Simon , Bloch Dorete , Borrell Asunción , Cunha Haydée A. , Rosa Luciano Dalla , Dias Carolina P. , Gauffier Pauline , Hao Wensi , Landry Scott , Larsen Finn , Martín Vidal , Mizroch Sally , Oosting Tom , Øien Nils , Pampoulie Christophe , Panigada Simone , Prieto Rui , Ramp Christian , Rivera-Léon Vania E. , Robbins Jooke , Ryan Conor , Schall Elena , Sears Richard , Silva Mónica A. , Urbán Jorge , Wenzel Frederick W. , Palsbøll Per J. , Bérubé Martine 
Published: December 2018

HighlightsMitochondrial monophyly is commonly employed to define evolutionary significant units.Monophyly may be caused by insufficient sampling or a recent common ancestor.Mitogenomic studies are generally based on few samples and prone to sampling issues.Expanded mitogenome sampling negates previous monophyly in fin whales.AbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales,Balaenoptera physalusspp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies,B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.
Retrieving High-Resolution Information from Disordered 2D Crystals by Single Particle Cryo-EM
Authors: Righetto Ricardo D. , Biyani Nikhil , Kowal Julia , Chami Mohamed , Stahlberg Henning 
Published: December 2018

AbstractElectron crystallography can reveal the structure of membrane proteins within 2D crystals under close-to-native conditions. High-resolution structural information can only be reached if crystals are perfectly flat and highly ordered. In practice, such crystals are difficult to obtain. Available image unbending algorithms correct for disorder, but only perform well on images of non-tilted, flat crystals, while out-of-plane distortions are not addressed. Here, we present an approach that employs single-particle refinement procedures to locally unbend crystals in 3D. With this method, density maps of the MloK1 potassium channel with a resolution of 4 Å were obtained from images of 2D crystals that do not diffract beyond 10 Å. Furthermore, 3D classification allowed multiple structures to be resolved, revealing a series of MloK1 conformations within a single 2D crystal. This conformational heterogeneity explains the poor diffraction observed and is related to channel function. The approach is implemented in the FOCUS package.
Adherence to referral guidelines
Authors: Lu Michel , Spigelman Allan D. 
Published: December 2018

Purpose
A significant subset of patients (12 per cent) with triple negative breast cancer (TNBC) is BRCA mutation carriers, which can be identified through genetic testing. The purpose of this paper is to evaluate the referral practice for TNBC patients with reference to New South Wales (NSW) referral guidelines at the time of diagnosis and to assess the effectiveness of such guidelines in identifying BRCA mutations. Robust health governance requires monitoring of adherence to evidence-based guidelines such as those that underpin referral for cancer genetic testing in this clinical scenario.

Design/methodology/approach
The authors conducted a retrospective clinical audit of identified TNBC patients at St Vincent’s Hospital (SVH) between 2006 and 2016 in NSW, comparing referral practice to guidelines extant at the time of diagnosis. Family history was considered for age guideline-inappropriate referrals to SVH while the results of BRCA gene testing were assessed for all referred.

Findings
Overall, of the 17 patients eligible for referral based on the age criterion, 10 (58.5 per cent) were referred appropriately; however, there were substantial improvements from 2012 with 100 per cent referred. Of note, 12 (33.4 per cent) of 36 patients referred to SVH were referred outside of guidelines, pointing to other reasons for referral, such as patient age (OR 0.945; 95% CI 0.914–0.978) and calendar year (OR: 1.332; 95% CI: 1.127–1.575) at TNBC diagnosis. Referral guidelines captured 66.67 per cent of identified deleterious BRCA mutations in those tested.

Originality/value
Substantial under-referral of guideline-eligible patients was identified, with evidence-based guidelines effective in identifying high-risk individuals for BRCA mutation testing. There was, however, a substantial proportion of guideline-inappropriate referrals.
A comparative study of tribological performance of helical gear pair with various types of tooth surface finishing
Authors: Gu Zonglin , Zhu Caichao , Liu Huaiju , Du Xuesong 
Published: December 2018

Purpose
This paper aims to compare the tribological performances of four different types of tooth surface finishing, namely, form grinding, generating grinding, super finishing and grinding and coating, and to reveal the details at dry contact nodes.

Design/methodology/approach
Real measured roughness is input to a finite line contact mixed elastohydrodynamic lubrication model developed for helical gear pairs. Their tribological performances are compared. The variation throughout one meshing period is analyzed. The influence of the root mean square (RMS) is studied. The textures are also scaled to the same RMS values to make comparisons while excluding the influence of roughness amplitude.

Findings
Roughness is directly reflected in pressure and film thickness. Average film thickness sees major changes while entering and leaving the single-tooth-contact region. The textures have different performances even under the same RMS. Roughness peaks incurring dry contact are those higher than the smooth-situation film thickness plus the sum of variation in normal approach and elastic deformation compared with the smooth situation. To lower dry contact severity, the surface finishing process should take care of both the overall amplitude and the portion of peaks with maximum height. When RMS value is the same, the latter plays a decisive role.

Originality/value
This paper interprets the differences between the tribological performances of four different types of tooth surface finishing from the aspect of roughness features and presents a way to analyze the details at dry contact nodes.
Simulation and experimental study on cavitation and noise of hydraulic cone valve
Authors: Wang Xiaojing , Liu Hao , Man Guojia 
Published: December 2018

PurposeAiming at the cavitations and noise problem of hydraulic cone valve and based on the radial force analysis of the valve core, the radial deviation of the spool is considered to obtain the changing rules of cavitations and noise.Design/methodology/approachThe solid model of the internal flow field of cone valve is established. The mesh models are divided using ICEM-CFD software. The numerical simulation of the liquid-gas two-phase flow is performed on the cavitation and noise of the flow field inside the cone valve based on FLUENT software. The visible experimental platform for cavitation and noise of hydraulic cone valve is built. According to the contrast of the experimental results, the correctness of the simulation results is verified.FindingsThe results show that the radial deviation causes the position of the cavitation accumulates in the valve cavity on the side of the upper cone. In addition, the strength of the cavitation changes slowly with the half cone angle of 45°, and the noise level is the smallest. Furthermore, appropriately increasing the opening degree within a reasonable range can effectively suppress cavitation and reduce the noise level.Originality/valueThe cavitation can be suppressed and the noise level can be reduced by means of changing the three factors, which lays the foundation for the design and theoretical research of the cone valve.
Appreciating vs venerating cultural outgroups
Authors: Cleveland Mark , Balakrishnan Anjana 
Published: December 2018

PurposeCosmopolitanism and xenocentrism denote distinct individual orientations toward cultural outgroups. The former considers an individual’s openness to cultural diversity and ability to navigate through intercultural environments, whereas the latter describes an individual’s feelings of admiration or preference for specific cultural outgroup(s), over his/her ingroup. Few studies have simultaneously examined these constructs and fewer still have considered these within a nomological framework of key predictors (i.e. basic psychological needs) and practical outcomes (e.g. influentialness and friendships across different groups). The paper aims to discuss these issues.Design/methodology/approachThe authors hypothesized a series of relationships of various antecedents and outcomes of cosmopolitanism and xenocentrism, and tested these conjectures using survey data from Canadians (n=238) and Americans (n=239).FindingsThe findings support the psychometric robustness of our tripartite operationalization of xenocentrism, and clearly distinguish this construct from cosmopolitanism. Beyond confirming earlier findings, the authors illuminate several novel relationships (e.g. between basic psychological needs, cosmopolitanism and xenocentrism), and elucidate the role played by a key personality dimension, neuroticism, in mediating the relationships between basic psychological needs and the two outgroup orientations.Research limitations/implicationsSamples of this study are drawn from North America and a cross-sectional research design is used.Originality/valueWhereas for xenocentric consumers admiration of one or more foreign culture(s) displaces customary preferences for one’s own cultural group, cosmopolitan consumers are able to embrace outside cultures without disaffection from their sociocultural ingroup. Given the obvious repercussions of these differences for targeting international consumer segments and for positioning brands across borders, our research has numerous practical applications as well as theoretical implications.
Country-of-origin effects on industrial purchase decision making: a systematic review of research
Authors: Dobrucalı Birce 
Published: December 2018

PurposeThis study aims to provide a contemporary, holistic and systematic review regarding the impact of country-of-origin on industrial purchase decision-making by ascertaining, synthesizing and evaluating theoretical, methodological and empirical dimensions of studies on the subject.Design/methodology/approachAfter the collection and refinement of 43 studies that appeared in marketing, business and management literatures during 1970-2017, systematic review was applied to discover the current situation and future research directions on the subject.FindingsThe vast majority of the existing studies obtained data from a single source even though industrial purchase decisions are mainly made by a large group of decision-makers. Moreover, the existing literature contains few over-studied theoretical perspectives while lacking integration of the subject with the more contemporary ones. Additionally, in the literature, combination of developing countries as source countries, and developed ones as target countries, is under-examined, and the differentiation between country-of-design and country-of-assembly is mainly avoided during operationalization. Finally, majority of the studies lack investigation of antecedents and mainly investigated few over-examined constructs as outcomes.Research limitations/implicationsThis study provides a conceptual synthesis of existing studies. A meta-analysis may be applied to empirical studies for providing a further detailed framework.Originality/valueThis study contributes to industrial marketing literature by providing a compiled and synthesized inventory of knowledge for scholars; deriving a comprehensive analysis of research designs, methodologies and findings addressed by researchers in the field; noticing various theoretical, methodological and other gaps to be examined; and providing future research directions.
The joys and sorrows of a start-up’s interactions with the public sphere: a case from medical technology
Authors: Wagrell Sofia , Baraldi Enrico 
Published: December 2018

PurposeThis paper aims to address the crucial interactions that a start-up enacts with actors from the public sphere in a context of medical technologies. The public actor commonly plays multiple roles, ranging from co-developers and financiers to large-scale users, which are all pivotal to the development and survival of the new venture. The paper investigates the possible “dark sides” of a start-up’s marriage with a public partner, departing from three specific roles the public sphere can assume in relation to a start-up: as a development partner, as a financer and as a customer.Design/methodology/approachThe study builds on an in-depth empirical case study of a Swedish med-tech startup company.FindingsThe authors find the financing role to be least problematic, whereas the customer role is the most problematic in that it provides numerous barriers to the possible development and growth of a start-up firm striving to get new customers in a public setting. Examples of the most prominent barriers found are regulations, complex decision-making processes and assessment elements of med-tech products that are outside the control of the startup firm, hence issues that cannot be handled within inter-organizational relationships.Originality/valueThe study builds on 27 in-depth interviews, which were undertaken during 2005-2013, thus contributing detailed data about a start-up’s many and crucial interactions with different public actors. Departing from three different roles, a public partner can adopt in relation to a start-up, (development, co-financer and customer) provides results with managerial implications for start-up’s and policy implications for health-care policy.
Ownership and leadership in building an innovation culture
Authors: Villaluz Vanessa C. , Hechanova Ma. Regina M. 
Published: December 2018

PurposeThe purpose of this paper is to test a culture-building model, CREATE, highlighting the central role of leadership in shaping the predictors of innovation culture. The authors hypothesize that leadership directly predicts innovation culture, as well, as indirectly impacts innovation culture through mediating variables. Also, the authors examine the impact of leadership on innovation by ownership type.Design/methodology/approachA total 631 survey responses were collected from employees of sole proprietorship, family-owned corporations, and non-family corporations. Parallel multiple mediator models were used to test the hypothesized relationships of the variables.FindingsThe findings show that a leadership variable, role modeling, and support for innovation, directly and indirectly predicts an innovation culture. However, it appears that in sole proprietorship and family-owned corporations, leaders impact on innovation culture are through mediating variables, while in non-family corporations, leaders influence innovation through strategy, evaluation, and rewards.Originality/valueThe study shows that the culture-building model, CREATE, can be used as a framework for building an innovation culture in organizations. The study also showed that leaders among sole proprietorships, family-owned corporations, and non-family corporations may need to employ different approaches in building an innovation culture in their organizations.
MNEs, FDI, inequality and growth
Authors: P. Doh Jonathan 
Published: December 2018

Purpose
The relationship among foreign direct investment, multinationals, inequality and growth is a vexing one that has occupied considerable scholarly and practical attention for many decades. To date, international business scholars have not fully concerned themselves with this issue (Buckley, Doh and Benischke, 2017, for an exception). This paper aims to briefly review this literature and report some of the insights of this work. The author draws from and integrates this literature, concluding that multinationals and the foreign investment that emanate from them have a generally positive impact on growth and a generally negative impact on income and wealth equality. The author then details some of the potential contributions MNEs can make to attenuate the negative relationship of foreign direct investment (FDI) on equality, concluding that governments and their policies are the primary vehicle for addressing wealth and income inequality.

Design/methodology/approach
This paper is an essay.

Findings
The relationship between inequality, growth and FDI is complex. On balance, FDI contributes to growth but may exacerbate inequality under some conditions. More research needs to be conducted, and policymakers need to carefully consider these nuanced relationships.

Originality/value
The paper provides review of the relationship of FDI, growth and inequality.