bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer‐associated missense mutations of caspase‐8 activate nuclear factor‐κB signaling
Authors: Ando Mizuo , Kawazu Masahito , Ueno Toshihide , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Yamashita Yoshihiro , Choi Young L. , Yamasoba Tatsuya , Mano Hiroyuki 
Published: May 2013

Head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer with a 5‐year survival rate of ~50%. With the use of a custom cDNA‐capture system coupled with massively parallel sequencing, we have now investigated transforming mechanisms for this malignancy. The cDNAs of cancer‐related genes (n = 906) were purified from a human HNSCC cell line (T3M‐1 Cl‐10) and subjected to high‐throughput resequencing, and the clinical relevance of non‐synonymous mutations thus identified was evaluated with luciferase‐based reporter assays. A CASP8 (procaspase‐8) cDNA with a novel G‐to‐C point mutation that results in the substitution of alanine for glycine at codon 325 was identified, and the mutant protein, CASP8 (G325A), was found to activate nuclear factor‐κB (NF‐κB) signaling to an extent far greater than that achieved with the wild‐type protein. Moreover, forced expression of wild‐type CASP8 suppressed the growth of T3M‐1 Cl‐10 cells without notable effects on apoptosis. We further found that most CASP8 mutations previously detected in various epithelial tumors also increase the ability of the protein to activate NF‐κB signaling. Such NF‐κB activation was shown to be mediated through the COOH‐terminal region of the second death effector domain of CASP8. Although CASP8 mutations associated with cancer have been thought to promote tumorigenesis as a result of attenuation of the proapoptotic function of the protein, our results now show that most such mutations, including the novel G325A identified here, separately confer a gain of function with regard to activation of NF‐κB signaling, indicating another role of CASP8 in the transformation of human malignancies including HNSCC.
Design, Synthesis, and Biological Evaluation of Novel 3,5‐Disubstituted‐1,2,6‐Thiadiazine‐1,1‐Dione Derivatives as HIV‐1 NNRTIs
Authors: Tian Ye , Rai Diwakar , Zhan Peng , Pannecouque Christophe , Balzarini Jan , De Clercq Erik , Liu Huiqing , Liu Xinyong 
Published: May 2013

On the basis of structural features, binding mode, and structure–activity relationship studies of two pyrimidine‐derived non‐nucleoside reverse‐transcriptase inhibitors, DABOs, and diaryl pyrimidines, a novel class of 1,2,6‐thiadiazine‐1,1‐dione derivatives were rationally designed using the strategies of bioisosterism and molecular hybridization, synthesized, and evaluated for their anti‐HIV activity in MT4 cell cultures. Three compounds were found to have moderate activity against HIV‐1 replication with EC50 values ranging from 23 to 32 μm. To further confirm the binding target, compound IIg was selected to conduct an HIV‐1 reverse‐transcriptase inhibitory assay. In addition, preliminary structure–activity relationship analysis among the newly synthesized compounds was discussed, and the binding mode of the active compound IIg was rationalized by molecular docking and physicochemical studies.
Radiographic outcomes of transcrestal sinus floor elevation performed with a minimally invasive technique in smoker and non‐smoker patients
Authors: Franceschetti Giovanni , Farina Roberto , Stacchi Claudio , Di Lenarda Roberto , Di Raimondo Rosario , Trombelli Leonardo 
Published: May 2013

AbstractObjectivesTo evaluate the association between smoking status and the outcomes of transcrestal sinus floor elevation (tSFE) performed with a minimally invasive technique (Smart Lift).MethodsForty‐five implants were placed in 25 non‐smoker (NS) and 20 smoker (S) patients in conjunction with the tSFE procedure. In all cases, an additional graft, chosen among different hydroxyapatite‐based or ß‐tricalcium phosphate‐based biomaterials, was pushed into the sinus by gradual increments. Immediately after surgery, residual bone height, implant penetration into the sinus, extent of sinus lift (SL) and the height of the graft apical to the implant apex (aGH) were assessed on periapical radiographs. At 6 months after surgery, SL and aGH were reassessed.Results(i) The Smart Lift procedure resulted in substantial 6‐month SL and aGH in both treatment groups; (ii) smoking status did not significantly affect the 6‐month radiographic outcomes; (iii) a similarly low incidence of intra‐ and postoperative complications was observed in NS and S patients.ConclusionsSmoking has a limited impact on the outcomes of tSFE performed with the Smart Lift technique.
Reproductive migration of fish and movement in a series of reservoirs in the Upper Parana River basin, Brazil
Authors: de C. Britto S. G. , Carvalho E. D. 
Published: May 2013

AbstractThis study evaluates the effectiveness of two fish passes at two hydropower dams (Canoas I and II) in the Upper Parana basin, which form part of a cascade of three reservoirs. Fish from 12 migratory species (3089 specimens) were captured during their ascending, reproductive migration and were tagged with hydrostatic tags. The recapture data (294 specimens over two consecutive years) showed that there is a strong tendency for the maintenance of ascending migration through reservoirs with fish passes but with differences in migratory activity within the same species. No eggs, larvae or juveniles of these species were found in samples collected over 5 years in the reservoirs above the fish passes. These data suggest that fish passes have contributed to the restoration of the migratory routes of adult fish but that in the absence of suitable spawning or nursery habitats for these species; they probably act as ecological traps and do not contribute to the recruitment of the species.
Hypoxic conditions enhance refuge effect of macrophyte zone for small prey fish from piscivorous predators
Authors: Yamanaka H. 
Published: May 2013

AbstractBody size dependency of the refuge effects of gape limitation and differences in hypoxia tolerance between the predator largemouth bass Micropterus salmoides (Lacépède) and the prey fish, nigorobuna carp Carassius buergeri grandoculis Temminck & Schlegel, were modelled to simulate the relative effect of size and physiological refuges for prey inhabiting the hypoxic macrophyte zone along a lakeshore. The model simulation suggested that a physiological refuge, maintained by the difference in hypoxia tolerance, could protect far smaller prey than a size refuge that is based solely on predator gape size and prey body depth. The dissolved oxygen gradient observed in the macrophyte zone located in Yamanoshita Bay, Lake Biwa, Japan, which was extremely low at the inner part and higher offshore, was determined to provide a physiological refuge that would be effective in terms of space.
Flow effects on periphyton patches and their ecological consequences in a New Zealand river
Authors: Hart David D. , Biggs Barry J. F. , Nikora Vladimir I. , Flinders Camille A. 
Published: May 2013

Summary

Proliferations of periphyton associated with the ecological degradation of streams have been linked to changes in flow regime, most frequently as a product of water abstraction and impoundment. We used descriptive and experimental studies to examine the relationship between water velocity and the distribution of two distinct, often high biomass, periphyton patch types and associated macroinvertebrate communities in the Waipara River, a meso‐eutrophic stream in Canterbury, New Zealand.

One patch type (‘Phormidium’) consisted mainly of two filamentous cyanobacterial taxa: a Phormidium/Lyngbya complex and Oscillatoria. The other type (‘filamentous greens’) consisted mainly of several filamentous chlorophyte taxa (Mougeotia sp.) along with various diatom epiphytes. Ash‐free dry mass, chlorophyll a and particulate N and P concentrations were significantly greater in the Phormidium than in the filamentous green patches.

There was a significant relationship between patch cover and water velocity, with filamentous greens negatively associated with velocity and dominant in areas with a velocity <∼0.20 m s−1, while Phormidium was dominant at velocities >∼0.40 m s−1. A 7‐day experimental reduction in velocity in Phormidium‐dominated habitats resulted in a significant reduction in% cover (84–21%) with a corresponding increase in filamentous greens (16–79%). There was a small but significant reduction in the % cover of filamentous greens (90–82%) with experimentally increased velocity, but no significant change in Phormidium cover (7–2%), perhaps due in part to the slow growth rate of taxa in this patch type.

Characterisation of macroinvertebrate assemblages collected from Phormidium and filamentous green patches and the substratum immediately below showed patch‐specific assemblages, although patch type was a less important determinant than vertical location, with 85% of the macroinvertebrates found in the substratum below algal mats.

The differential responses of Phormidium and filamentous green patches to velocity are considered in the context of a subsidy‐stress model that examines how trade‐offs between flow‐mediated biomass accrual and loss processes vary for different algal growth forms.

Collectively, these results indicated that key ecological characteristics of rivers can be quite sensitive to spatial and temporal variations in hydraulic conditions that are much smaller than those typical of floods and droughts.
Visiting the hyporheic zone: youngAtlantic salmon move through the substratum
Authors: Heggenes Jan , Bremset Gunnbjørn , Brabrand Åge 
Published: May 2013

SummaryThe hyporheic zone may be a habitat for fish, depending on habitat patch characteristics and interactions with fish behaviour, such as movements. Theory highlights the vertical connection and potentially significant functional role of the hyporheic zone, but actual use of the hyporheic zone by fish is understudied.In replicated factorial field experiments, we investigated movements of (i) young Atlantic salmon of various size (Salmo salar, mean total lengths, 28.3, 51.7, 52.1 and 84.6 mm) through substrata of (ii) different particle size (16–22, 24–60 mm) and (iii) thickness (20, 40, 60 cm), depending on (iv) current direction (horizontal up‐ to downstream, vertical ‘upwelling’) and (v) temperature/season (summer/autumn). In nine experiments, each with different treatments, three replicated 14‐cm‐diameter translucentPVCtubes were used as a proxy for the hyporheic zone and placed in parallel on the bottom in a natural salmon stream. Each tube consisted of five separable 20‐cm segments, with a no‐substratum segment in each end and three midsegments filled with substratum. Young salmon were placed in the upstream or/and downstream free segment, localised by a snorkeler every 15 min, and after 135 min, the segments were separated and the fish per segment counted.Results indicated that (i) a significant number of fish moved into the substratum, (ii) small Atlantic salmon (28 mm) in June rapidly moved into, and even 60 cm through, both substratum particle sizes regardless of flow direction, but fewer fish into the fine substratum, and (iii) significant numbers of larger fish (52 mm, 85 mm) in September and November also moved into the 24–60 mm substratum, but not so far and relatively fewer remained in the substratum. Horizontal or vertical flow did not affect results.We conclude that young Atlantic salmon can easily move into and through the interstitial spaces in the substratum, depending on fish size and substratum coarseness. The active use by Atlantic salmon of the substratum as part of their habitat remains to be studied, but is likely to be more prevalent than commonly assumed.
A projection of ozone‐induced wheat production loss in China and India for the years 2000 and 2020 with exposure‐based and flux‐based approaches
Authors: Tang Haoye , Takigawa Masayuki , Liu Gang , Zhu Jianguo , Kobayashi Kazuhiko 
Published: May 2013

AbstractUsing a high‐resolution (40 × 40 km) chemical transport model coupled with the Regional Emission inventory in Asia (REAS), we simulated surface ozone concentrations ([O3]) and evaluated O3‐induced wheat production loss in China and India for the years 2000 and 2020 using dose–response functions based on AOT40 (accumulated [O3] above 40 ppb) and PODY (phytotoxic O3 dose, accumulated stomatal flux of O3 above a threshold of Y nmol m−2 s−1). Two O3 dose metrics (90 days AOT40 and POD6) were derived from European experiments, and the other two (75 days AOT40 and POD12) were adapted from Asian studies. Relative yield loss (RYL) of wheat in 2000 was estimated to be 6.4–14.9% for China and 8.2–22.3% for India. POD6 predicted greater RYL, especially for the warm regions of India, whereas the 90 days AOT40 gave the lowest estimates. For the future projection, all the O3 dose metrics gave comparable estimates of an increase in RYL from 2000 to 2020 in the range 8.1–9.4% and 5.4–7.7% for China and India, respectively. The lower projected increase in RYL for India may be due to conservative estimation of the emission increase in 2020. Sensitivity tests of the model showed that the PODY‐based estimates of RYL are highly sensitive to perturbations in the meteorological inputs, but that the estimated increase in RYL from 2000 to 2020 is much more robust. The projected increase in wheat production loss in China and India in the near future is substantially larger than the uncertainties in the estimation and indicates an urgent need for curbing the rapid increase in surface [O3] in these regions.
A spatial model of climate change effects on yields and break‐even prices of switchgrass and miscanthus in Ontario, Canada
Authors: De Laporte Aaron V. , Weersink Alfons J. , McKenney Daniel W. 
Published: May 2013

AbstractConcerns over global climate change have led many jurisdictions to implement strategies aimed at reducing greenhouse gas levels. One example is the replacement of coal with dedicated energy crops, such as switchgrass and miscanthus. The yields and costs of these potentially valuable bio‐energy crops have been evaluated in only a few cases, and previous studies have not focused on climate change effects. This article assesses the potential yields and costs of growing switchgrass and miscanthus on the agricultural land base in Ontario, Canada, under different climate assumptions, using a GIS‐based integrated biophysical and economic simulation model. The model shows that miscanthus has a mean peak yield that is 88.5% (29.6 t ha−1 compared with 15.7 t ha−1) higher and a mean farm gate break‐even price that is 25.9% ($58.20 per tonne compared with $73.29 per tonne) lower than switchgrass. The impact of climate change on the yield and break‐even price of switchgrass and miscanthus is dependent upon the climate model. CGCM3.1 predicts that mean peak yields of switchgrass and miscanthus could drop by 17.8% and 14.9%, whereas CCSM3.0 predicts that mean yields could increase to 41.4% and 44.9%, from 2071 to 2100, in the A2 climate scenario respectively. Both crops show promise as biomass sources for bio‐energy production, but a changing global climate, along with cultivar and planting technology developments, could affect crop choices.
ORCHIDEE‐STICS, a process‐based model of sugarcane biomass production: calibration of model parameters governing phenology
Authors: Valade Aude , Vuichard Nicolas , Ciais Philippe , Ruget Françoise , Viovy Nicolas , Gabrielle Benoît , Huth Neil , Martiné Jean‐François 
Published: May 2013

AbstractAgro‐Land Surface Models (agro‐LSM) combine detailed crop models and large‐scale vegetation models (DGVMs) to model the spatial and temporal distribution of energy, water, and carbon fluxes within the soil–vegetation–atmosphere continuum worldwide. In this study, we identify and optimize parameters controlling leaf area index (LAI) in the agro‐LSM ORCHIDEE‐STICSdeveloped for sugarcane. Using the Morris method to identify the key parameters impactingLAI, at eight different sugarcane field trial sites, in Australia and La Reunion island, we determined that the three most important parameters for simulatingLAIare (i) the maximum predefined rate ofLAIincrease during the early crop development phase, a parameter that defines a plant density threshold below which individual plants do not compete for growing theirLAI, and a parameter defining a threshold for nitrogen stress onLAI. A multisite calibration of these three parameters is performed using three different scoring functions. The impact of the choice of a particular scoring function on the optimized parameter values is investigated by testing scoring functions defined from the model‐dataRMSE, the figure of merit and a Bayesian quadratic model‐data misfit function. The robustness of the calibration is evaluated for each of the three scoring functions with a systematic cross‐validation method to find the most satisfactory one. Our results show that the figure of merit scoring function is the most robust metric for establishing the best parameter values controlling theLAI. The multisite average figure of merit scoring function is improved from 67% of agreement to 79%. The residual error inLAIsimulation after the calibration is discussed.
THE LIMITS OF OTTOMAN PRAGMATISM
Authors: DAĞLI MURAT 
Published: May 2013

ABSTRACTIn this paper I reflect critically on the concept of pragmatism as it is used in Ottoman historiography. Pragmatism has gained increasing currency over the last ten to fifteen years as one of the defining features of the Ottoman polity. I argue that unless it is properly defined from a theoretical‐philosophical perspective, and carefully contextualized from a historical perspective, pragmatism cannot be used as an explanatory or comparative category. When used as a framework of explanation for historical change, pragmatism blurs more than it clarifies an essential aspect of the Ottoman polity that it seeks to define, namely, the political. It is essential to reflect on the difference between the political and politics because whereas the political refers to the configuration of the power relations that organize a society as a legitimate entity, politics refers to the strategies, practices, institutions, or discourses whose purpose is to construct and retain hegemony within a polity. Through an analysis of the concept of pragmatism in Ottoman historiography, I show that for most proponents of Ottoman pragmatism, pragmatism pertains to politics rather than to the political. From a perspective rigorously confined to political theory, I argue that much like the discourse of modern tolerance, pragmatism in Ottoman historiography posits a problematic periodization, relegates the political to the background, and depoliticizes essential power relations.
PINKER AND PROGRESS
Authors: Aronson Ronald 
Published: May 2013

ABSTRACTCondorcet's classical Enlightenment statement of human progress became an essential element of nineteenth‐ and twentieth‐century consciousness, but by the millennium grand narratives had fallen victim to a disillusioned cultural climate. Now Steven Pinker, like Condorcet drawing on a wide range of contemporary “knowledges,” has reasserted a sweeping narrative of human progress in The Better Angels of Our Nature: Why Violence Has Declined. Mapping a spectacular long‐term decline in person‐on‐person violence and reduction in deaths due to war, Pinker celebrates the spread of a cultural pattern of self‐restraint, sensitivity to human suffering, and recent regard for human rights, due to the modern state and gentle commerce capitalism.For Pinker the human condition has gotten steadily better, the decline of violence is an accomplishment we can savor and an impetus to cherish the forces of civilization and enlightenment that made it possible. Why then are so many so negative about modernity? Citing the psychology of temporal proximity to horrific events and the bad‐news predilection of the media, Pinker ignores the specifically modern and less directly brutal institutionalized forms of violence as well as the profound ambivalence of progress. He decisively demonstrates the drop in certain kinds of violence, but his account becomes strangely ideological, recapitulating key Cold‐War themes—the individual against totalitarianism, the Enlightenment against the counter‐Enlightenment, rationalism and freedom against murderous utopianism—distorting his study in the name of gentle commerce, Marxism, and anti‐Communism.
HISTORIOGRAPHY: A FIELD IN SEARCH OF A HISTORIAN?
Authors: Cheng Eileen Ka‐May 
Published: May 2013

ABSTRACTRichard Kirkendall's collection of essays, The Organization of American Historians and the Writing and Teaching of American History, examines the history of the Organization of American Historians (OAH) from its founding to the present, using that history to illuminate how the writing of American history has changed over the last hundred years. The book provides coverage of all the major dimensions of the Mississippi Valley Historical Association's (MVHA) and the OAH's activities, ranging from the work of its scholarly publications, the Mississippi Historical Valley Review and the Journal of American History, to its role in promoting the teaching of American history. Overall, the essays in the volume tell a story of the organization's progress toward greater inclusion and democracy, falling prey to a Whig interpretation of historiography. In doing so, the book is part of a larger tendency in the way that historians have approached historiography, which in turn reflects their ambivalence about their relationship to the historical process. Thus, even as the very enterprise of historiography is premised on the recognition of how historians are themselves the products of the historical process, historians have revealed the limits to that recognition in their approach to the subject. This essay shows how deeply rooted this duality has been in the study of American historiography and illuminates some of its sources by placing Kirkendall's book in the context of how the MVHA and the OAH have treated historiography over the course of the organization's history.
Courage and selflessness in professional actions: but are they enough?
Authors: Alder‐Collins J.K. 
Published: May 2013

BackgroundThe Great East Japan Earthquake on 11 March 2011 caused considerable loss of life, destruction of livelihood and infrastructure. Linked to this event but not its cause, was the meltdown and radioactive contamination of the environment from Fukishima Dai‐ichi power plant. This disaster, in turn, led to the enforced evacuation of populations at risk. Japanese nurses, physicians, paramedical staff and faculty from nearby universities all volunteered to staff decontamination centres for evacuees and survivors.AimThis commentary critically reflects on the insights provided in this issue by Noto, Kitamiya, Itaki, Urushizaka & Yamabe (pp. 196–200) on the role of nurses in the Fukishima Dai‐ichi disaster, extending that critique to evidence that has emerged through official and unofficial sources.DiscussionDisaster planning is not a popular subject for societies in general nor is it a finite art or process. Civil authorities often work under restricted or reducing budgets and resources while serving increasing demands. Disaster planning requires multidisciplinary skills sets to be able to work across the many different departments, agencies, interest groups and budgets. Planners need to think outside the box, allocate resources and training to a level that justifies known and/or projected threats in preparing first responders with the correct tools, training and time to practise skills they may never be called upon to use.ConclusionDisasters will always happen be they natural or man‐made. To rely on the courage and selflessness of professionals is not enough. Training and learning from previous disasters can help in responsible planning.