bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Evaluation of Uncertainty in Material Flow Analysis
Authors: Laner David , Rechberger Helmut , Astrup Thomas 
Published: May 2014

SummaryMaterial flow analysis (MFA) is a tool to investigate material flows and stocks in defined systems as a basis for resource management or environmental pollution control. Because of the diverse nature of sources and the varying quality and availability of data, MFA results are inherently uncertain. Uncertainty analyses have received increasing attention in recent MFA studies, but systematic approaches for selection of appropriate uncertainty tools are missing. This article reviews existing literature related to handling of uncertainty in MFA studies and evaluates current practice of uncertainty analysis in MFA. Based on this, recommendations for consideration of uncertainty in MFA are provided. A five‐step framework for uncertainty handling is outlined, reflecting aspects such as data quality and goal/scope of the MFA. We distinguish between descriptive (quantification of material turnover in a region) and exploratory MFA (identification of critical parameters and system behavior). Whereas mathematically simpler concepts focusing on data uncertainty characterization are appropriate for descriptive MFAs, statistical approaches enabling more‐rigorous evaluation of uncertainty and model sensitivity are needed for exploratory MFAs. Irrespective of the level of sophistication, lack of information about MFA data poses a major challenge for meaningful uncertainty analysis. The step‐wise framework suggested here provides a systematic way to consider available information and produce results as precise as the data warrant.
Cdk5/p35 is required for motor coordination and cerebellar plasticity
Authors: He Xiaojuan , Ishizeki Masato , Mita Naoki , Wada Seitaro , Araki Yoshifumi , Ogura Hiroo , Abe Manabu , Yamazaki Maya , Sakimura Kenji , Mikoshiba Katsuhiko , Inoue Takafumi , Ohshima Toshio 
Published: May 2014

AbstractPrevious studies have implicated the role of Purkinje cells in motor learning and the underlying mechanisms have also been identified in great detail during the last decades. Here we report that cyclin‐dependent kinase 5 (Cdk5)/p35 in Purkinje cell also contributes to synaptic plasticity. We previously showed that p35−/− (p35 KO) mice exhibited a subtle abnormality in brain structure and impaired spatial learning and memory. Further behavioral analysis showed that p35 KO mice had a motor coordination defect, suggesting that p35, one of the activators of Cdk5, together with Cdk5 may play an important role in cerebellar motor learning. Therefore, we created Purkinje cell‐specific conditional Cdk5/p35 knockout (L7‐p35 cKO) mice, analyzed the cerebellar histology and Purkinje cell morphology of these mice, evaluated their performance with balance beam and rota‐rod test, and performed electrophysiological recordings to assess long‐term synaptic plasticity. Our analyses showed that Purkinje cell‐specific deletion of Cdk5/p35 resulted in no changes in Purkinje cell morphology but severely impaired motor coordination. Furthermore, disrupted cerebellar long‐term synaptic plasticity was observed at the parallel fiber‐Purkinje cell synapse in L7‐p35 cKO mice. These results indicate that Cdk5/p35 is required for motor learning and involved in long‐term synaptic plasticity.
image
Purkinje cells play an important role in motor learning, the underlying mechanisms of which have been studied during the last two decades. We report here that the ablation of Cdk5/p35 in Purkinje cells impairs motor coordination, along with deficits in the cerebellar synaptic plasticity, which gives new insights into the mechanism of synaptic plasticity in Purkinje cells.
Serum Th1, Th2 and Th17 cytokine profiles and alpha‐enolase levels in recurrent aphthous stomatitis
Authors: Ozyurt Kemal , Çelik Ahmet , Sayarlıoglu Mehmet , Colgecen Emine , Incı Rahime , Karakas Tuba , Kelles Mehmet , Cetin Gozde Y. 
Published: May 2014

BackgroundAll aspects of aetiopathogenesis of recurrent aphthous stomatitis (RAS) have not been elucidated. RAS and Behçet's disease (BD) have clinical and immunological characteristics in common. Although T17 cytokines and alpha‐enolase have been shown to play effective roles in BD and many other autoinflammatory diseases recently, their roles in RAS have not been studied extensively. In the present study, we investigated levels of several Th1, Th2 and Th17 pathways related cytokines and alpha‐enolase to elucidate pathogenesis of RAS and to obtain data about possible treatment alternatives for the condition.MethodsSerum interleukin‐1, interleukin‐13, interleukin‐17, interleukin‐18, interferon gamma and alpha‐enolase levels in 24 patients with RAS, 30 patients with BD and 20 healthy controls were measured.ResultsSerum interleukin‐1, interleukin‐13, interleukin‐17, interleukin‐18, interferon gamma and alpha‐enolase levels were higher in patients with RAS and patients with BD than in healthy controls (P < 0.005).ConclusionLike Th1 and Th2 cells, Th17 cells were found to be effective in pathogenesis of RAS. In addition, alpha‐enolase, the levels of which were high, may play an important role in etio‐pathogenesis of RAS. Further studies to be designed in the light of these findings are required to shed light on pathogenesis and treatment of the condition.
THE DYNAMICS OF MICROINSURANCE DEMAND IN DEVELOPING COUNTRIES UNDER LIQUIDITY CONSTRAINTS AND INSURER DEFAULT RISK
Authors: Liu Yanyan , Myers Robert J. 
Published: May 2014

AbstractWe study the dynamics of microinsurance demand by risk‐averse agents who can borrow and lend subject to a liquidity constraint, and also perceive a risk of insurer default. Liquidity constraints and perceived insurer default both reduce the demand for insurance, possibly leading to nonparticipation. We also evaluate an alternative insurance design that allows agents to delay premium payment until the end of the insured period when income is realized and indemnities are paid. We show this alternative design increases insurance take‐up by relaxing the liquidity constraint and ameliorating concerns about insurer default. We also investigate the value of delayed premium payment, and the importance of the associated problem of reneging if the insured event does not occur, under a range of conditions.
SECTORAL CHANGE AND UNEMPLOYMENT DURING THE GREAT RECESSION, IN HISTORICAL PERSPECTIVE
Authors: Simon Curtis 
Published: May 2014

ABSTRACTI examine the effect of sectoral change on U.S. state unemployment during the Great Recession. Of the 4.1 percentage point increase in mean state unemployment between 2007 and 2009, increased structural change explains 0.6–1.18 percentage points, and increased estimated effects of structural change 0.8–2.7 percentage points. Despite the role of housing in the recession, neither construction nor any other one sector can account for the results. Although the pace and role of structural change had returned to normal levels after the Great Recession, their effects persisted, raising mean state unemployment by 0.9–2.3 percentage points in 2011.
Biodiversity of soil cyanobacteria in the hyper‐arid Atacama Desert, Chile
Authors: Patzelt Dominik J. , Hodač Ladislav , Friedl Thomas , Pietrasiak Nicole , Johansen Jeffrey R. 
Published: May 2014

The cyanobacterial diversity of soils of the Atacama Desert (Chile) was investigated using 16S rRNA gene cloning/sequencing directly from soil samples and 16S rRNA gene sequencing from unialgal cultures. Within the hyper‐arid Atacama Desert, one of the driest parts of the world, 10 sites with differing altitude and distance to the shore were sampled along a total air‐line distance (from south to north) of ~1,100 km. Filamentous cyanobacteria belonging to Nostocophycideae and Synechococcophycideae were present. Oscillatoriophycideae exhibited the highest species richness among the subclasses of cyanobacteria, and included mostly filamentous species along with some coccoids (e.g., Chroococcidiopsis). Thirty species‐level phylotypes could be recognized using a cut‐off of 99% 16S rRNA sequence similarity within the 22 genera defined at 97% 16S rRNA sequence similarity. Eight of the 30 taxa could be detected by both clonal and culture sequences. Five taxa were observed only in cultures, whereas the cloning approach revealed 17 additional taxa, which might be in the collection but unsequenced, hard‐to‐cultivate, or entirely unculturable species using standard cultivation media. The Atacama Desert soils have a high diversity of phylotypes, among which are likely both new genera and new species awaiting characterization and description.
Trichocytes in Lithophyllum kotschyanum and Lithophyllum spp. (Corallinales, Rhodophyta) from the NW Indian Ocean
Authors: Basso Daniela , Caragnano Annalisa , Rodondi Graziella 
Published: May 2014

The current diagnosis of the genus Lithophyllum includes absent or rare trichocyte occurrence. After examining holotype material, single trichocytes have been revealed to occur abundantly in Lithophyllum kotschyanum Unger, and in freshly collected specimens of Lithophyllum spp. from the Red Sea, Gulf of Aden and Socotra Island (Yemen). Trichocyte occurrence is not considered a diagnostic character at specific or supraspecific levels in the Lithophylloideae, and the ecological significance of trichocyte formation is discussed. The generitype species, L. incrustans Philippi, does not show trichocytes nor do many other Lithophyllum species from diverse geographic localities, but the presence of abundant trichocytes in other congeneric taxa requires emendation of the genus diagnosis. Therefore, the diagnosis of Lithophyllum is here emended by eliminating the adjective “rare” in the sentence concerning trichocyte occurrence, as follows: “Trichocytes present or absent, if present occurring singly.”
An attachment‐based model of therapeutic change processes in the treatment of personality disorder among male forensic inpatients
Authors: Willmot Phil , McMurran Mary 
Published: May 2014

PurposeThis study explores the processes of change during treatment among male forensic inpatients with primary diagnoses of personality disorder.MethodFifty patients in a high secure personality disorder treatment service completed a checklist about how they had changed during treatment and the factors that had caused that change.ResultsThe results support a limited reparenting attachment‐based model of therapeutic change. Self‐reported levels of change were highly correlated with measures of patient functioning, though significant levels of change did not occur until the later stages of treatment.ConclusionsThe behaviour of therapists was particularly important throughout treatment, though participants in the final stage of therapy reported that the behaviour of other staff was as important as that of therapists, suggesting that, by this stage of treatment they are able to extend their range of supportive and therapeutic relationships.
Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities
Authors: Paula Fabiana S. , Rodrigues Jorge L. M. , Zhou Jizhong , Wu Liyou , Mueller Rebecca C. , Mirza Babur S. , Bohannan Brendan J. M. , Nüsslein Klaus , Deng Ye , Tiedje James M. , Pellizari Vivian H. 
Published: May 2014

AbstractLand use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83 992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest‐to‐pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest‐to‐pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.
Replication fork inhibition in seqA mutants of Escherichia coli triggers replication fork breakage
Authors: Rotman Ella , Khan Sharik R. , Kouzminova Elena , Kuzminov Andrei 
Published: May 2014

SummarySeqA protein negatively regulates replication initiation in Escherichia coli and is also proposed to organize maturation and segregation of the newly replicated DNA. The seqA mutants suffer from chromosomal fragmentation; since this fragmentation is attributed to defective segregation or nucleoid compaction, two‐ended breaks are expected. Instead, we show that, in SeqA's absence, chromosomes mostly suffer one‐ended DNA breaks, indicating disintegration of replication forks. We further show that replication forks are unexpectedly slow in seqA mutants. Quantitative kinetics of origin and terminus replication from aligned chromosomes not only confirm origin overinitiation in seqA mutants, but also reveal terminus under‐replication, indicating inhibition of replication forks. Pre‐/post‐labelling studies of the chromosomal fragmentation in seqA mutants suggest events involving single forks, rather than pairs of forks from consecutive rounds rear‐ending into each other. We suggest that, in the absence of SeqA, the sister‐chromatid cohesion ‘safety spacer’ is destabilized and completely disappears if the replication fork is inhibited, leading to the segregation fork running into the inhibited replication fork and snapping the latter at single‐stranded DNA regions.
Adapting to new threats: the generation of memory by CRISPR‐Cas immune systems
Authors: Heler Robert , Marraffini Luciano A. , Bikard David 
Published: May 2014

SummaryClustered, regularly interspaced, short palindromic repeats (CRISPR) loci and their associated genes (cas) confer bacteria and archaea with adaptive immunity against phages and other invading genetic elements. A fundamental requirement of any immune system is the ability to build a memory of past infections in order to deal more efficiently with recurrent infections. The adaptive feature of CRISPR‐Cas immune systems relies on their ability to memorize DNA sequences of invading molecules and integrate them in between the repetitive sequences of the CRISPR array in the form of ‘spacers’. The transcription of a spacer generates a small antisense RNA that is used by RNA‐guided Cas nucleases to cleave the invading nucleic acid in order to protect the cell from infection. The acquisition of new spacers allows the CRISPR‐Cas immune system to rapidly adapt against new threats and is therefore termed ‘adaptation’. Recent studies have begun to elucidate the genetic requirements for adaptation and have demonstrated that rather than being a stochastic process, the selection of new spacers is influenced by several factors. We review here our current knowledge of the CRISPR adaptation mechanism.
Deletion of the cyclic di‐AMP phosphodiesterase gene (cnpB) in Mycobacterium tuberculosis leads to reduced virulence in a mouse model of infection
Authors: Yang Jun , Bai Yinlan , Zhang Yang , Gabrielle Vincent D. , Jin Lei , Bai Guangchun 
Published: May 2014

SummaryTuberculosis (TB) remains a major cause of morbidity and mortality worldwide. The pathogenesis by the causative agent, Mycobacterium tuberculosis, is still not fully understood. We have previously reported that M. tuberculosis Rv3586 (disA) encodes a diadenylate cyclase, which converts ATP to cyclic di‐AMP (c‐di‐AMP). In this study, we demonstrated that a protein encoded by Rv2837c (cnpB) possesses c‐di‐AMP phosphodiesterase activity and cleaves c‐di‐AMP exclusively to AMP. Our results showed that in M. tuberculosis, deletion of disA abolished bacterial c‐di‐AMP production, whereas deletion of cnpB significantly enhanced the bacterial c‐di‐AMP accumulation and secretion. The c‐di‐AMP levels in both mutants could be corrected by expressing the respective gene. We also found that macrophages infected with ΔcnpB secreted much higher levels of IFN‐β than those infected with the wild type (WT) or the complemented mutant. Interestingly, mice infected with M. tuberculosis ΔcnpB displayed significantly reduced inflammation, less bacterial burden in the lungs and spleens, and extended survival compared with those infected with the WT or the complemented mutant. These results indicate that deletion of cnpB results in attenuated virulence, which is correlated with elevated c‐di‐AMP levels.
Brassinosteroid nuclear signaling recruits HSP90 activity
Authors: Samakovli Despina , Margaritopoulou Theoni , Prassinos Constantinos , Milioni Dimitra , Hatzopoulos Polydefkis 
Published: May 2014

Summary

Heat shock protein 90 (HSP90) controls a number of developmental circuits, and serves a sophisticated and highly regulatory function in signaling pathways. Brassinosteroids (BRs) control many aspects of plant development.

Genetic, physiological, cytological, gene expression, live cell imaging, and pharmacological approaches provide conclusive evidence for HSP90 involvement in Arabidopsis thalianaBR signaling.

Nuclear‐localized HSP90s translocate to cytoplasm when their activity is blocked by the HSP90 inhibitor geldanamycin (GDA). GDA treatment promoted the export of BIN2, a regulator of BR signaling, from the nucleus into the cytoplasm, indicating that active HSP90 is required to sustain BIN2 in the nucleus. HSP90 nuclear localization was inhibited by brassinolide (BL). HSP90s interact with BIN2 in the nucleus of untreated cells and in the cytoplasm of BL‐treated cells, showing that the site‐specific action of HSP90 on BIN2 is controlled by BRs. GDA and BL treatments change the expression of a common set of previously identified BR‐responsive genes. This highlights the effect of active HSP90s on the regulation of BR‐responsive genes. Our observations reveal that HSP90s have a central role in sustaining BIN2 nuclear function.

We propose that BR signaling is mediated by HSP90 activity and via trafficking of BIN2–HSP90 complexes into the cytoplasm.
Effect of pH on elementary steps of dopachrome conversion from first‐principles calculation
Authors: Kishida Ryo , Ushijima Yohei , Saputro Adhitya G. , Kasai Hideaki 
Published: May 2014

SummaryDopachrome conversion, in which dopachrome is converted into 5,6‐dihydroxyindole (DHI) or 5,6‐dihydroxyindole‐2‐carboxylic acid (DHICA) upstream of eumelanogenesis, is a key step in determining the DHI/DHICA monomer ratio in eumelanin, which affects the antioxidant activity. Although the ratio of DHI/DHICA formed and the conversion rate can be regulated depending on pH, the mechanism is still unclear. To clarify the mechanism, we carried out first‐principles calculations. The results showed the kinetic preference of proton rearrangement to form quinone methide intermediate via β‐deprotonation. We also identified possible pathways to DHI/DHICA from the quinone methide. The DHI formation can be achieved by spontaneous decarboxylation after proton rearrangement from carboxyl group to 6‐oxygen. α‐Deprotonation, which leads to DHICA formation, can also proceed with a significantly reduced activation barrier compared with that of the initial dopachrome. Considering the rate of the proton rearrangements in a given pH, we conclude that the conversion is suppressed at acidic pH.
MC1R, the cAMP pathway, and the response to solar UV: extending the horizon beyond pigmentation
Authors: García‐Borrón Jose C. , Abdel‐Malek Zalfa , Jiménez‐Cervantes Celia 
Published: May 2014

SummaryThe melanocortin 1 receptor (MC1R) is a G protein‐coupled receptor crucial for the regulation of melanocyte proliferation and function. Upon binding melanocortins, MC1R activates several signaling cascades, notably the cAMP pathway leading to synthesis of photoprotective eumelanin. Polymorphisms in the MC1R gene are a major source of normal variation of human hair color and skin pigmentation, response to ultraviolet radiation (UVR), and skin cancer susceptibility. The identification of a surprisingly high number of MC1R natural variants strongly associated with pigmentary phenotypes and increased skin cancer risk has prompted research on the functional properties of the wild‐type receptor and frequent mutant alleles. We summarize current knowledge on MC1R structural and functional properties, as well as on its intracellular trafficking and signaling. We also review the current knowledge about the function of MC1R as a skin cancer, particularly melanoma, susceptibility gene and how it modulates the response of melanocytes to UVR.
Usefulness of the tri‐axial accelerometer for assessing balance function in children
Authors: Eguchi Ryota , Takada Satoshi 
Published: May 2014

AbstractBackgroundThe aim of this study was to verify whether the tri‐axial accelerometer can be used for quantitatively evaluating balance function in children.MethodsIn total, 198 participants, including 172 healthy children aged 3–11 years (87 boys, 85 girls) and 26 young adults aged 21–24 years (seven men, 19 women), were enrolled in this study. The participants undertook three types of balance tasks: quiet standing with eyes open and closed, one‐leg standing on the dominant leg and non‐dominant leg, and walking on the floor and a balance beam. We derived the root mean square from participants' accelerations measured by the tri‐axial accelerometer.ResultsWe found that for quiet standing, one‐leg standing, and walking tasks, postural sway decreased with age. Girls controlled their posture better than boys of the same age on all tasks. There was a significant sex difference in quiet standing for children aged 8–9 years. Furthermore, sex differences existed in one‐leg standing for children aged 5–11 years. A mild positive correlation was observed between static and dynamic balance.ConclusionsThe tri‐axial accelerometer is a useful quantitative tool for evaluating both static and dynamic balance function in children. Thus, it has the potential to be used clinically for diagnosis and rehabilitation.