bluuebunny/crossref_metadata_2025_split huggingface dataset:
High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation
Authors: Ren Dawei , Madsen Jonas S , Sørensen Søren J , Burmølle Mette 
Published: June 2014

Abstract
Biofilms that form on roots, litter and soil particles typically contain multiple bacterial species. Currently, little is known about multispecies biofilm interactions and few studies have been based on environmental isolates. Here, the prevalence of synergistic effects in biofilm formation among seven different soil isolates, cocultured in combinations of four species, was investigated. We observed greater biofilm biomass production in 63% of the four-species culture combinations tested than in biofilm formed by single-species cultures, demonstrating a high prevalence of synergism in multispecies biofilm formation. One four-species consortium, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, exhibited strong synergy in biofilm formation and was selected for further study. Of the four strains, X. retroflexus was the only one capable of forming abundant biofilm in isolation, under the in vitro conditions investigated. In accordance, strain-specific quantitative PCR revealed that X. retroflexus was predominant within the four-species consortium (&gt;97% of total biofilm cell number). Despite low relative abundance of all the remaining strains, all were indispensable for the strong synergistic effect to occur within the four-species biofilm. Moreover, absolute individual strain cell numbers were significantly enhanced when compared with those of single-species biofilms, indicating that all the individual strains benefit from inclusion in the multispecies community. Our results show a high prevalence of synergy in biofilm formation in multispecies consortia isolated from a natural bacterial habitat and suggest that interspecific cooperation occurs.
Role of the potassium channel KCa3.1 in diabetic nephropathy
Authors: Huang Chunling , Pollock Carol A. , Chen Xin-Ming 
Published: June 2014

There is an urgent need to identify novel interventions for mitigating the progression of diabetic nephropathy. Diabetic nephropathy is characterized by progressive renal fibrosis, in which tubulointerstitial fibrosis has been shown to be the final common pathway of all forms of chronic progressive renal disease, including diabetic nephropathy. Therefore targeting the possible mechanisms that drive this process may provide novel therapeutics which allow the prevention and potentially retardation of the functional decline in diabetic nephropathy. Recently, the Ca2+-activated K+ channel KCa3.1 (KCa3.1) has been suggested as a potential therapeutic target for nephropathy, based on its ability to regulate Ca2+ entry into cells and modulate Ca2+-signalling processes. In the present review, we focus on the physiological role of KCa3.1 in those cells involved in the tubulointerstitial fibrosis, including proximal tubular cells, fibroblasts, inflammatory cells (T-cells and macrophages) and endothelial cells. Collectively these studies support further investigation into KCa3.1 as a therapeutic target in diabetic nephropathy.
Organic chemicals jeopardize the health of freshwater ecosystems on the continental scale
Authors: Malaj Egina , von der Ohe Peter C. , Grote Matthias , Kühne Ralph , Mondy Cédric P. , Usseglio-Polatera Philippe , Brack Werner , Schäfer Ralf B. 
Published: June 2014

Significance
Protection of freshwater ecosystems from organic pollutants is important to preserve biodiversity and the goods they provide to society, such as clean drinking water and recreation. Organic chemicals have been shown to adversely impact freshwater ecosystems in local and regional studies. Nevertheless, due to paucity of studies on larger spatial scales, it remains unknown how widespread the risk from organic chemicals is. For the first time, to our knowledge, we provide strong evidence that chemicals threaten the ecological integrity and consequently the biodiversity of almost half of the water bodies on a continental scale, based on the analysis of governmental monitoring data from 4,000 European sites. Due to limitations associated with the monitoring programs, our results are likely to underestimate the actual risks.
RNF144A, an E3 ubiquitin ligase for DNA-PKcs, promotes apoptosis during DNA damage
Authors: Ho Shiuh-Rong , Mahanic Christina S. , Lee Yu-Ju , Lin Weei-Chin 
Published: June 2014

Significance
In response to DNA damage, a proper balance between DNA repair and apoptosis is very important for genomic integrity. DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) plays a key role in DNA repair. Many reports also indicate a prosurvival function for cytosolic DNA-PKcs. However, how this prosurvival activity of DNA-PKcs is regulated remains unknown. We identify Ring Finger protein 144A (RNF144A) as the first E3 ubiquitin ligase for cytosolic DNA-PKcs. RNF144A is induced in a p53-dependent manner during DNA damage and targets cytosolic DNA-PKcs for ubiquitination and degradation. The regulation of DNA-PKcs by RNF144A is important for proper apoptotic response during DNA damage, suggesting a tumor suppressor function for RNF144A.
Recapitulation of the forward nuclear auxin response pathway in yeast
Authors: Pierre-Jerome Edith , Jang Seunghee S. , Havens Kyle A. , Nemhauser Jennifer L. , Klavins Eric 
Published: June 2014

Significance
Auxin is a simple small molecule, yet it elicits an enormous variety of responses. How a single molecule can encode such diverse and context-specific information is a long-standing question. One hypothesis is that variation in auxin response components generates diversity in local auxin responses. To test this, we transplanted the forward nuclear auxin signal transduction pathway from plants into yeast. We found that auxin circuit composition can tune the dynamic response, and we identified which properties of auxin response components had the largest impact on circuit performance. Reconstitution of eukaryotic pathways in novel contexts can inform our understanding of the pathways themselves and can generate tools for engineering novel cellular behaviors.
Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ
Authors: Good-Jacobson Kim L. , Chen Yunshun , Voss Anne K. , Smyth Gordon K. , Thomas Tim , Tarlinton David 
Published: June 2014

SignificanceUnderstanding the intrinsic mechanisms underlying formation of humoral memory during infection and the ability of the humoral memory population to persist for long periods of time is important for identifying potential targets for improving the efficacy of vaccines. Here we demonstrate that the chromatin modifier MOZ regulates B-cell memory formation, controlling memory compartment composition. This activity of MOZ is B cell-intrinsic and is required for establishing the germinal center gene expression program. IgM memory B cells have been implicated in maintaining the memory B-cell population over time, whereas isotype-switched memory B cells rapidly differentiate into plasmablasts upon secondary infection. Therefore, identifying potential chromatin changes that may induce differentiation into one subset over another makes MOZ a viable target for clinical translation.
Cooperative binding of the outer arm-docking complex underlies the regular arrangement of outer arm dynein in the axoneme
Authors: Owa Mikito , Furuta Akane , Usukura Jiro , Arisaka Fumio , King Stephen M. , Witman George B. , Kamiya Ritsu , Wakabayashi Ken-ichi 
Published: June 2014

Significance
In eukaryotic cilia and flagella, outer arm dyneins (OADs) are bound to axonemal doublet microtubules every 24 nm; however, how this regular arrangement is produced remains unknown. To approach this problem, we studied the properties of the OAD-docking complex (ODA-DC), a three-subunit complex that functions as the OAD-docking site on the doublet. Using recombinant ODA-DC, we found that the ODA-DC has an ∼24-nm-long ellipsoidal shape and cooperatively binds to the axoneme in an end-to-end manner. These and other results indicate that cooperative association of the ODA-DC underlies the periodic OAD arrangement at specific positions on the doublets. These findings provide insight into how the regular axonemal repeat structure is produced.
Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles
Authors: Zwicker David , Decker Markus , Jaensch Steffen , Hyman Anthony A. , Jülicher Frank 
Published: June 2014

Significance
How cells position their proteins is still an open question. Here, we propose a physical description of centrosomes, which are membraneless organelles involved in cell division. In our model, centrosome material occurs in a soluble form and a form that tends to form droplets by phase separation. We find that an autocatalytic chemical transition between these forms quantitatively accounts for our experimental data. Importantly, a catalytic activity of the centrioles, which are located inside centrosomes, can control centrosome nucleation and suppress Ostwald ripening to allow for two equal-sized centrosomes to coexist in the cell. Consequently, our example shows how the combination of chemical reactions and phase separation can be used to control the formation of liquid-like compartments in cells.
China’s rise as a major contributor to science and technology
Authors: Xie Yu , Zhang Chunni , Lai Qing 
Published: June 2014

Significance
New data reveal that in the past three decades, China has become a major contributor to science and technology. Four factors favor China’s continuing rise in science: a large population and human capital base, a labor market favoring academic meritocracy, a large diaspora of Chinese-origin scientists, and a centralized government willing to invest in science. These factors may serve as an example to other nations aspiring to advance their standing in science. However, China’s science also faces potential difficulties due to political interference and scientific fraud.
Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan
Authors: Wang Yang , Yasuda Takashi , Sharmin Sultana , Kanao Tadayoshi , Kamimura Kazuo 
Published: June 2014

Abstract
Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51 mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.
Theory in the Public Eye
Authors: Piccini Angela 
Published: June 2014

Abstract
The high public profile of archaeology in television, film, and other media focuses on new discoveries and fieldwork, with little attention to the interpretive issues or theoretical debates that underpin the activities portrayed. The relationship between media and public expectations of archaeology and scholarly and professional archaeological practices is an important one. While a popular emphasis on discovery may undermine archaeology as a professional discipline requiring intellectual as well as physical labour, archaeology’s cultural position extends beyond specific factual knowledge and the role of the expert or public intellectual. Arguably, archaeology is a way of making knowledge about the world. The way in which this is enacted across media makes knowledge claims, claims that are at once aesthetic, affective, and political and which therefore invite critical analysis. Yet research into the relationship between archaeology and the media generated by archaeologists remains polarized and largely focused on Western European and North American formations. Critical voices focus largely on demystifying narrative and tend towards a monolithic construction of the public and its (in)abilities to distinguish archaeological fact from fiction. Those who seek to counter that criticality have expounded the democratizing and participatory nature of mediatized archaeologies. What is missing from these accounts, however, is an understanding of media theories, histories, and policies and how they impact on the future of archaeological practices. This chapter seeks to identify where archaeological theory and moving images intersect, and asks how the conversation between archaeological and media theories might contribute to wider debates. Where are there points of intersection and difference, and how might an understanding of these allow archaeologists to engage productively and critically with media making, with media making as a form of ‘working through’?
Emerging from Theoretical Anarchy in Anthropological Archaeology
Authors: Seymour Deni J. , Schiffer Michael Brian 
Published: June 2014

Abstract
Although the focus and underpinnings have adjusted through time, Americanist archaeology is founded on the notion that anthropology plays an important role in archaeology. Even now the nature of anthropological archaeology is transforming to incorporate modern developments and lessons from our predecessors. Anthropological archaeology remains vibrant, maintaining sensitivity to current trends and methodological, theoretical, and conceptual advances by updating and honing its direction, and gradually transforming itself through the ebbs and flows of current trends and renewed angles on long-established venerable issues. The discipline has passed through several phases that emphasized first an essentially historical focus, then staunch positivistic processualism, and then a refined socially relevant archaeology that incorporates process while contextualizing. Home-grown archaeological theory is among these more current approaches, which emphasizes method and theory developed by archaeologists to solve archaeological and anthropological problems. But fundamental to the approach, through all these adjustments, is the premise that archaeology is anthropological, taking its lead from anthropological understandings and theories of process, while at the same time incorporating what is relevant from history, geomorphology, psychology, and sociology. It is a compilation of approaches where generalizations have a role but are understood within the boundary conditions set by contextualized cases.
Time
Authors: Lucas Gavin 
Published: June 2014

Abstract
Archaeology is a discipline for which time is central, and although the methodological importance of the concept has been a constant source of interest (especially in relation to dating and chronology), theoretically it has only come under the spotlight in the last two decades. Rather than offer a summary of the literature and approaches, this contribution will explore time through a series of temporal concepts, drawing out paradoxes and problems in an attempt to map out a set of key issues. The chapter begins by exploring the idea of temporal succession and its basis in chronologies before moving onto the problem of contemporaneity: what does it mean to say two sites or two events are contemporary? The idea of temporal succession is then also explored in relation to a third concept, change. Both concepts—contemporaneity and change—raise critical problems with a successional view of time, and expose the limitations of a purely chronological view of the archaeological record. As an alternative, the chapter then explores the concept of memory in archaeology and how it has been deployed in studies of past people’s perceptions of time, although ultimately it is argued that archaeology itself should be regarded as a form of memory work in relation to the problem of forgetting.
Darwinism and its Influences
Authors: Jeffares Ben , Sterelny Kim 
Published: June 2014

Abstract
This chapter explores just what is, and is not, a Darwinian explanation in the archaeological context. It does this by reviewing attempts to use Darwinian explanations in the archaeological context, and showing ways in which they have been successful or otherwise. The chapter proceeds by working through historical case studies in archaeological theory, showing how these attempts to apply Darwinian ideas to archaeological data have run up against serious limitations. Typically, they have either assumed natural selection or failed to adequately specify the relevant selective environment. We then offer an alternative view of evolutionary processes—niche construction—that takes history and culture seriously. In so doing, the chapter demonstrates both Darwinism’s promise but, just as importantly, its limits as an explanatory framework in the social science context. In particular, we stress the need to show selection is in operation, rather than presuming it, and that at certain scales, and for certain purposes, Darwinian explanations may fail to capture the correct grain of analysis: Sometimes, archaeology is history, and as such, it is interested in explanations that are local, unique, and idiosyncratic to the culture concerned.
Taking Interdependence Seriously
Authors: Huckfeldt Robert 
Published: June 2014

Abstract
Networks of communication among interdependent citizens constitute the connecting tissue between citizens and electorates, revealing an electoral whole that is different from the sum of its citizen parts. These communication networks, in turn, reflect the social contexts within which an actor is imbedded, thereby bridging the micro-macro divide in our understanding of electoral politics. Belonging to a group and developing corresponding political loyalties is not simply a matter of individual characteristics and circumstance. Rather, it is a matter of being connected to the group through networks of communication and association. These patterns of interdependence produce profound implications that are not only substantive and theoretical but also methodological and profoundly dynamic. Indeed, new platforms for studying political communication continue to emerge, and they carry the potential for further transformations in the ways that we understand the consequences of political communication for individual voters as well as for electorates.
Popular and Academic Images of African American Islam, 1915–1945
Authors: Turner Richard Brent 
Published: June 2014

Abstract
This chapter looks at popular and academic images (descriptions and literary and visual representations) of African American Islam from 1915 to 1945. This time period is important because it is capped by two milestone events that influenced African American Muslim communities: the first, in 1915, was the beginning of the Great Migration and urbanization in black America, and the second, 1945, marked the end of World War II and the beginning of a powerful era in the African American civil rights movement. The chapter also examines the construction of African diasporic identities in the Moorish Science Temple of America, the Ahmadiyya movement in Islam, the Islamic Mission of America, and the Nation of Islam, as well as the impact of Marcus Garvey’s Universal Negro Improvement Association and the scholarship on African retentions in slavery as well as that on images of African American Islam.
Lactulose
Authors: Lee Gwenyth O. , Kosek Peter , Lima Aldo A.M. , Singh Ravinder , Yori Pablo P. , Olortegui Maribel P. , Lamsam Jesse L. , Oliveira Domingos B. , Guerrant Richard L. , Kosek Margaret 
Published: June 2014

ABSTRACTObjectives:The lactulose:mannitol (L:M) diagnostic test is frequently used in field studies of environmental enteropathy (EE); however, heterogeneity in test administration and disaccharide measurement has limited the comparison of results between studies and populations. We aim to assess the agreement between L:M measurement between high‐performance liquid chromatography with pulsed amperometric detection (HPLC‐PAD) and liquid chromatography‐tandem mass spectrometry (LC‐MSMS) platforms.Methods:The L:M test was administered in a cohort of Peruvian infants considered at risk for EE. A total of 100 samples were tested for lactulose and mannitol at 3 independent laboratories: 1 running an HPLC‐PAD platform and 2 running LC‐MSMS platforms. Agreement between the platforms was estimated.Results:The Spearman correlation between the 2 LC‐MSMS platforms was high (ρ ≥ 0.89) for mannitol, lactulose, and the L:M ratio. The correlation between the HPLC‐PAD platform and LC‐MSMS platform was ρ = 0.95 for mannitol, ρ = 0.70 for lactulose, and ρ = 0.43 for the L:M ratio. In addition, the HPLC‐PAD platform overestimated the lowest disaccharide concentrations to the greatest degree.Conclusions:Given the large analyte concentration range, the improved accuracy of LC‐MSMS has important consequences for the assessment of lactulose and mannitol following oral administration in populations at risk for EE. We recommend that researchers wishing to implement a dual‐sugar test as part of a study of EE use an LC‐MSMS platform to optimize the accuracy of results and increase comparability between studies.
Use of Cyproheptadine in Young Children With Feeding Difficulties and Poor Growth in a Pediatric Feeding Program
Authors: Sant'Anna Ana M.G.A. , Hammes Patricia S. , Porporino Mafalda , Martel Chantal , Zygmuntowicz Catherine , Ramsay Maria 
Published: June 2014

ABSTRACTObjective:The aim of this study was to assess the efficacy and safety of cyproheptadine (CY) use in infants and young children with poor growth treated at our multidisciplinary pediatric feeding program, and to describe changes in their weight and feeding behaviors.Methods:A retrospective chart review of children treated with CY from January 2007 to July 2011 was performed. Demographic data, medical diagnosis, adverse effects of the drug, and changes in mealtime behaviors were extracted from the patients' medical records. For each patient who received the CY, weight‐for‐age z scores (WtZ) were calculated before and during treatment. Repeated‐measures mixed model was used to analyze the pattern of change in WtZ over time and between groups. Differences in mean WtZ were tested between patients regularly receiving CY and a naturally conceived comparison group.Results:Of the 127 patients in treatment owing to poor weight gain who received the CY, 82 took the medication regularly as prescribed in combination with our interventional program. For these patients, the majority of the parents (96%) reported a positive change in mealtime and feeding behaviors. A significant improvement in mean WtZ was observed after starting CY when compared with the WtZ before treatment for those patients regularly receiving the medication. This effect was independent of patients' age and/or presence of an underline medical problem. No significant differences in mean WtZ were observed over time within the comparison group.Conclusions:In our experience, the use of CY in combination with a specialized multidisciplinary interventional program is a safe and effective therapy in infants and young children with low appetite and poor growth.