bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonautonomous contact guidance signaling during collective cell migration
Authors: Londono Camila , Loureiro M. Jimena , Slater Benjamin , Lücker Petra B. , Soleas John , Sathananthan Suthamathy , Aitchison J. Stewart , Kabla Alexandre J. , McGuigan Alison P. 
Published: January 2014

Significance
Group cell migration in response to guidance signals is a critical process in determining tissue organization. Here we explore the response of groups of cells to topographic guidance signals and reveal that guidance information can be transmitted between cells within the group. Significantly, we show that guidance information transmission is not dependent on cell–cell junctions or tensional forces within cells. Instead, we propose that signal transmission arises from a volume exclusion-type mechanism and is an emergent property that can arise in dense cell populations.
TAp73 is required for spermatogenesis and the maintenance of male fertility
Authors: Inoue Satoshi , Tomasini Richard , Rufini Alessandro , Elia Andrew J. , Agostini Massimiliano , Amelio Ivano , Cescon Dave , Dinsdale David , Zhou Lily , Harris Isaac S. , Lac Sophie , Silvester Jennifer , Li Wanda Y. , Sasaki Masato , Haight Jillian , Brüstle Anne , Wakeham Andrew , Mckerlie Colin , Jurisicova Andrea , Melino Gerry , Mak Tak W. 
Published: January 2014

Significance
Defects in spermatogenesis, many of which are unexplained, underlie the infertility problems of ∼20% of couples. Although specific roles for the p53 family members in female fertility have been described, their involvement in spermatogenesis is largely unexpected. Using gene-targeted mice, we have demonstrated that deficiency of TAp73, but not p53 or ∆Np73, leads to male infertility caused by severely impaired germ cell differentiation and maturation to viable sperms in the testes. Importantly, our work has established that TAp73, but not p53, regulates many genes involved in spermatogenesis. Thus, our results provide previously unidentified in vivo evidence that TAp73 is a “guardian” of male germ cells and may point toward a novel avenue for the diagnosis and management of male infertility.
Differential expression of estrogen receptor α, β1, and β2 in lobular and ductal breast cancer
Authors: Huang Bo , Omoto Yoko , Iwase Hirotaka , Yamashita Hiroko , Toyama Tatsuya , Coombes Raoul Charles , Filipovic Aleksandra , Warner Margaret , Gustafsson Jan-Åke 
Published: January 2014

Significance
Whether breast cancer will respond to the antiestrogen tamoxifen is determined by whether cellular proliferation is estrogen receptor (ER) α-mediated. As opposed to early ductal cancer, which is an ERα-rich, proliferating disease, in early lobular cancer both ERα and ERβ are abundantly expressed and proliferation is rare. In advanced lobular cancer, ERβ is lost, ERα is retained, and proliferation is high. Thus, tamoxifen may be an effective pharmaceutical in late but not early lobular cancer.
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
Authors: Cheng Ryan R. , Morcos Faruck , Levine Herbert , Onuchic José N. 
Published: January 2014

Significance
Our study uses amino acid coevolutionary information to better understand how bacterial two-component signaling (TCS) proteins preferentially interact with their correct partners while avoiding interactions with nonpartners. We extract coevolutionary couplings from sequences of TCS partners and study how coevolution is necessary to maintain their ability to transfer signals with high specificity. We use these coevolving couplings to devise a metric, which can predict the effects of mutations in the quality of signal transmission observed in vitro and provide support to the hypothesis that hybrid TCS proteins have reduced specificity. Our metric can potentially be used to redesign a TCS protein to preferentially interact with a nonpartner. Furthermore, our study can potentially be extended to networks of interacting proteins.
Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass
Authors: Lee Young-Sam , Gregory Mark T. , Yang Wei 
Published: January 2014

Significance
Although human DNA polymerase ζ (Pol ζ) is essential for DNA replication and cell proliferation, difficulties purifying active Pol ζ have hindered its biochemical characterization. We report here the first purification of an active form of human Pol ζ holoenzyme composed of Rev3, Rev7, PolD2, and PolD3, which opens up the possibility for detailed biochemical and structural studies of this essential enzyme. Based on genetic data, it has been postulated that two specialized DNA polymerases are needed for successful translesion synthesis. We show here that human Pol η inserts a nucleotide opposite the lesion, followed by Pol ζ extending the DNA primer; thus, the two complement each other to fully bypass the cisplatin cross-link.
The Evolving Institutional Structure of Public and Private Agricultural Research
Authors: Fuglie Keith O. , Toole Andrew A. 
Published: January 2014

AbstractOver the past several decades, the private sector has assumed a larger role in developing improved technology for food and agriculture. Private companies fund nearly all food processing research and development (R&D) and perform a growing share of production‐oriented R&D for agriculture. In addition, institutional partnerships for public–private research collaboration are growing in the United States and other countries. This article outlines the major forces driving these changes and offers an interpretive framework to explore some of the implications for the volume and nature of research performed by the public and private sectors. One of the critical issues is whether public agricultural research complements and thereby stimulates additional private agricultural R&D investments. Another important issue concerns the role and contribution of alternative public–private partnership arrangements. To date, changes in the institutional structure of public and private agricultural research have outpaced systematic investigation, and new theoretical and empirical research is needed to help guide policy and address key societal challenges, such as climate change, clean energy, water scarcity, food safety, and health.
Morphological, Structural, and Thermal Properties of Starch Nanocrystals Affected by Different Botanic Origins
Authors: Xu Yixiang , Sismour Edward N. , Grizzard Cory , Thomas Melissa , Pestov Dmitry , Huba Zachary , Wang Tongwen , Bhardwaj Harbans L. 
Published: January 2014

ABSTRACTSix types of starch nanocrystals were prepared from corn, barley, potato, tapioca, chickpea, and mungbean starches with an acid hydrolysis method. The yields and morphological, structural, and thermal properties of starch nanocrystals were characterized. Starch nanocrystals had yields ranging from 8.8 to 35.7%, depending on botanical origin. During acid hydrolysis, amylose was effectively degraded, and no amylose was detected in any starch nanocrystal. Shape and size of native starch granules varied between starches, whereas there was no obvious difference in shape among different types of starch nanocrystals. The average particle size of starch nanocrystals was mainly related to crystalline type of native starches. Compared with their native starch counterparts, changes in crystalline diffraction patterns of starch nanocrystals depended on the original botanical source and crystalline structure. Degree of crystallinity, melting temperature, and enthalpy of starch nanocrystals increased, whereas their thermal decomposition temperature decreased. Of six produced starch nanocrystals, potato starch nanocrystal had the lowest yield, degree of crystallinity, and onset and melting temperatures, the largest particle size, and obvious changes in crystalline diffraction pattern.
Complex behavioral manipulation drives mismatch between host and parasite diversity
Authors: Baccaro Fabricio B. , de Araújo João P. M. , Evans Harry C. , Souza Jorge L. P. , Magnusson William E. , Hughes David P. 
Published: January 2014

AbstractParasites and hosts are intimately associated such that changes in the diversity of one partner are thought to lead to changes in the other. We investigated this linked diversity hypothesis in a specialized ant-Ophiocordycepssystem in three forests across 750 km in Central Amazonia. All species belonging to the fungal genusOphiocordycepsassociated with ants have evolved some degree of behavioral control to increase their own transmission, but the leaf-biting behavior is the most complex form of host manipulation. Such a system requires control of the mandibular muscles and a distinct shift in behavior, from climbing vegetation to walking on leaves to rasping leaf veins in the seconds before death. The need to induce complex behavior may limit host availability and represent a constraint on parasite diversity. The consequence for community structure is that complex behavioral manipulation leads to a mismatch between ant hosts and the diversity of their fungal parasites.
An E4 Ligase Facilitates Polyubiquitination of Plant Immune Receptor Resistance Proteins in Arabidopsis
Authors: Huang Yan , Minaker Sean , Roth Charlotte , Huang Shuai , Hieter Philip , Lipka Volker , Wiermer Marcel , Li Xin 
Published: January 2014

Abstract
Proteins with nucleotide binding and leucine-rich repeat domains (NLRs) serve as immune receptors in animals and plants that recognize pathogens and activate downstream defense responses. As high accumulation of NLRs can result in unwarranted autoimmune responses, their cellular concentrations must be tightly regulated. However, the molecular mechanisms of this process are poorly detailed. The F-box protein Constitutive expressor of PR genes 1 (CPR1) was previously identified as a component of a Skp1, Cullin1, F-box protein E3 complex that targets NLRs, including Suppressor of NPR1, Constitutive 1 (SNC1) and Resistance to Pseudomonas syringae 2 (RPS2), for ubiquitination and further protein degradation. From a forward genetic screen, we identified Mutant, snc1-enhancing 3 (MUSE3), an E4 ubiquitin ligase involved in polyubiquitination of its protein targets. Knocking out MUSE3 in Arabidopsis thaliana results in increased levels of NLRs, including SNC1 and RPS2, whereas overexpressing MUSE3 together with CPR1 enhances polyubiquitination and protein degradation of these immune receptors. This report on the functional role of an E4 ligase in plants provides insight into the scarcely understood NLR degradation pathway.
Social capital and accountability in grass‐roots NGOs
Authors: Awio Godwin , Northcott Deryl , Lawrence Stewart 
Published: January 2014

PurposeThis paper aims to examine how small, grass‐roots non‐governmental organisations (NGOs) account for their actions and expenditures and how this accountability is discharged to, and benefits, the citizens they serve.Design/methodology/approachThe paper draws on social capital theory to inform an interpretive analysis of documentary and interview evidence. The empirical material is derived from CHAI policy and project documents, coupled with interviews with 75 participants at the national, district and community levels of the CHAI programme. An illustrative case study is presented of an NGO that delivers welfare services to a Ugandan community affected by the HIV/AIDS pandemic.FindingsThe research finds that, by harnessing the attributes of social capital, grass‐roots NGOs can supplement formal accountability obligations to funders with effective “bottom‐up” accountability to an often overlooked NGO stakeholder group – the service beneficiaries, with positive outcomes for social services delivery.Research limitations/implicationsThe research examines a single community‐led public welfare initiative (the Ugandan CHAI), with a particular focus on one illustrative grass‐roots NGO within that programme. Nevertheless, it offers insights into how accountability mechanisms can be reconceptualised to suit the context of developing countries where smaller NGOs increasingly operate.Practical implicationsThe potential for less formal, “bottom‐up” accountability mechanisms is illustrated using the case of the Ugandan community‐led HIV/AIDS initiative (CHAI), a programme for delivering social services to communities ravaged by the effects of the HIV/AIDS pandemic.Originality/valueThis research addresses the lack of empirical studies of smaller, grass‐roots NGOs in the accounting literature. It also contributes to the under‐researched area of how NGOs can appropriately discharge their accountability obligations to beneficiaries. The use of social capital theory to inform the study is also a novel contribution of this paper.
Open innovation and SMEs
Authors: Vega Arturo , Brown David , Chiasson Mike 
Published: January 2014

PurposeThe purpose of this paper is to explore, through the use of a multidisciplinary lens, the policy context and the scope for improvements in university‐based public programmes focused on improving innovation in small and medium enterprises (SMEs).Design/methodology/approachThe authors use the street‐level bureaucracy (SLB), combined with the systems of innovation approach (SIA) and diagnostic analysis (DA) to understand the context components that impact on public programme services. The study is part of a research programme oriented to the diffusion of information systems in SMEs and which used original interview‐based programme support case studies, interviews with regional policy managers, and documentation relating to the policy system and different public programmes. Although the empirical work was UK and European Union centric the results of the research have wide applicability.FindingsThe paper establishes the importance of programme contexts for diagnosing and providing a basis for public programme improvements. It further demonstrates the robustness of the context analysis framework to provide insights into proposed policy changes. The responsibility of improving programme contexts relies on actors that operate outside programme organisations, for instance EU funding bodies, government departments in charge of SME policies, public‐private partnerships, and private evaluators. Given this complexity it is suggested that SME associations have a potentially important role in increasing participation by SMEs in the public programme for innovation and knowledge support policy. Despite possible policy changes the requirement for public programme support for innovation and hence the role of universities as programme providers is confirmed and expanded.Research limitations/implicationsThe results demonstrate the value of a multidisciplinary framework to analyse programme interventions at both macro and micro levels and provide a basis for programme policy and policy implementation improvements.Originality/valueThis research is a novel attempt to use the SLB, SIA and DA to public programme university‐based interventions in SMEs and SME policies in general. It complements extant research on open innovation and knowledge exchange by extending the concept of public programme contexts. Beneficiaries of the findings include policy makers, programme organisations, universities, SME associations, and researchers.
Restoration of a megaherbivore: landscape‐level impacts of white rhinoceros in Kruger National Park, South Africa
Authors: Cromsigt Joris P. G. M. , te Beest Mariska 
Published: January 2014

Summary

Megaherbivores have been lost from most ecosystems world‐wide, and current increases in poaching of rhino and elephant spp. threaten their status in the systems where they still occur. Although megaherbivores are said to be key drivers of ecosystem structure and functioning, empirical evidence is strongly biased to studies on African elephant. We urgently need a better understanding of the impact of other megaherbivore species to predict the consequences of megaherbivore loss.

We used a unique ‘recolonization experiment’ to test how a megagrazer, white rhinoceros, is affecting the structure of savanna grasslands in Kruger National Park (KNP).

With a 30‐year record of rhinoceros distribution, we quantified how they recolonized KNP following their re‐introduction. This allowed us to identify landscapes with high rhino densities and long time since recolonization versus landscapes with low rhino densities that were recolonized more recently but were otherwise biophysically similar. We recorded grassland heterogeneity on 40 transects covering a total of 30 km distributed across both landscapes. We used two proxies of grassland heterogeneity: % short grass cover and number of grazing lawn patches. Grazing lawns are patches with specific communities of prostrate‐growing stoloniferous short grass species.

Short grass cover was clearly higher in the high rhino impact (17.5%) than low rhino impact landscape (10.7%). Moreover, we encountered ~20 times more grazing lawns in the high rhino impact landscape. The effect of rhino on number of lawns and on short grass cover was similar to the two dominant geologies in KNP, basalt‐derived versus granite‐derived soils.

Synthesis. We provide empirical evidence that white rhinoceros may have started to change the structure and composition of KNP's savanna grasslands. It remains to be tested if these changes lead to other ecological cascading effects. However, our results highlight that the current rhino poaching crisis may not only affect the species, but also threaten the potential key role of this megaherbivore as a driver of savanna functioning.
Phylogenomic reconstruction of archaeal fatty acid metabolism
Authors: Dibrova Daria V. , Galperin Michael Y. , Mulkidjanian Armen Y. 
Published: January 2014

SummaryWhile certain archaea appear to synthesize and/or metabolize fatty acids, the respective pathways still remain obscure. By analysing the genomic distribution of the key lipid‐related enzymes, we were able to identify the likely components of the archaeal pathway of fatty acid metabolism, namely, a combination of the enzymes of bacterial‐type β‐oxidation of fatty acids [acyl‐coenzyme A (CoA) dehydrogenase, enoyl‐CoA hydratase and 3‐hydroxyacyl‐CoA dehydrogenase] with paralogs of the archaeal acetyl‐CoA C‐acetyltransferase, an enzyme of the mevalonate biosynthesis pathway. These three β‐oxidation enzymes working in the reverse direction could potentially catalyse biosynthesis of fatty acids, with paralogs of acetyl‐CoA C‐acetyltransferase performing addition of C2 fragments. The presence in archaea of the genes for energy‐transducing membrane enzyme complexes, such as cytochrome bc complex, cytochrome c oxidase and diverse rhodopsins, was found to correlate with the presence of the proposed system of fatty acid biosynthesis. We speculate that because these membrane complexes functionally depend on fatty acid chains, their genes could have been acquired via lateral gene transfer from bacteria only by those archaea that already possessed a system of fatty acid biosynthesis. The proposed pathway of archaeal fatty acid metabolism operates in extreme conditions and therefore might be of interest in the context of biofuel production and other industrial applications.
Association study of human leukocyte antigen‐DRB1 alleles with rheumatoid arthritis in Algerian patients
Authors: Djidjik Réda , Allam Ines , Douaoui Sanaa , Meddour Yanis , Cherguelaîne Khaled , Tahiat Azzedine , Raaf Nabil , Abdessemed Amina , Khaldoun Naouel , Bahaz Naima , Chaib Samia , Ladjouze‐Rezig Aicha , Ghaffor Mohamed 
Published: January 2014

AbstractIntroductionRheumatoid arthritis (RA) is a chronic, systemic, inflammatory and multifactorial disease. Genetic predisposition seems to play an important role. The aim of this study is to explore the relationship between human leukocyte antigen (HLA)‐DRB1 alleles and susceptibility, clinical and biological features ofRAin an Algerian patient population.MethodsUsing polymerase chain reaction – sequence specific primers (SSP), 134RApatients and 132 healthy controls were genotyped forHLA‐DRB1 andHLA‐DRB1*04 subtypes.ResultsHLA‐DRB1*04 was found to have increased frequency in theRAgroup compared to controls (P < 0.001,OR = 3.14), and was associated with anti‐citrullinated protein antibodies positivity (ACPA) (P = 0.01,OR = 2.35). In contrast,HLA‐DRB1*07 was found to have a decreased frequency in patients compared to controls (P = 0.003,OR = 0.44) and significant decrease was observed in patients with the rheumatoid factor (RF) positivity subgroup (P = 0.009,OR = 0.29).HLA‐DRB1*04:05 was associated withRA(P = 0.005,OR = 3.41), whereas,HLA‐DRB1*04:02 showed a protective effect againstRA(P = 0.003,OR = 0.20).ConclusionsHLA‐DRB1*04 was associated with increased risk forRAandACPApositivity, whileHLA‐DRB1*07 was associated with reduced risk forRAandRFsynthesis in Algerian patients.
The fourth‐corner solution – using predictive models to understand how species traits interact with the environment
Authors: Brown Alexandra M. , Warton David I. , Andrew Nigel R. , Binns Matthew , Cassis Gerasimos , Gibb Heloise 
Published: January 2014

Summary

An important problem encountered by ecologists in species distribution modelling (SDM) and in multivariate analysis is that of understanding why environmental responses differ across species, and how differences are mediated by functional traits.

We describe a simple, generic approach to this problem – the core idea being to fit a predictive model for species abundance (or presence/absence) as a function of environmental variables, species traits and their interaction.

We show that this method can be understood as a model‐based approach to the fourth‐corner problem – the problem of studying the environment–trait association using matrices of abundance or presence/absence data across species, environmental data across sites and trait data across species. The matrix of environment–trait interaction coefficients is the fourth corner.

We illustrate that compared with existing approaches to the fourth‐corner problem, the proposed model‐based approach has advantages in interpretability and its capacity to perform model selection and make predictions.

To illustrate the method we used a generalized linear model with a LASSO penalty, fitted to data sets from four different studies requiring different models, illustrating the flexibility of the proposed approach.

Predictive performance of the model is compared with that of fitting SDMs separately to each species, and in each case, it is shown that the trait model, despite being much simpler, had comparable predictive performance, even significantly outperforming separate SDMs in some cases.