bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corynebacterium glutamicum promoters: a practical approach
Authors: Pátek Miroslav , Holátko Jiří , Busche Tobias , Kalinowski Jörn , Nešvera Jan 
Published: January 2013

SummaryTranscription initiation is the key step in gene expression in bacteria, and it is therefore studied for both theoretical and practical reasons. Promoters, the traffic lights of transcription initiation, are used as construction elements in biotechnological efforts to coordinate ‘green waves’ in the metabolic pathways leading to the desired metabolites. Detailed analyses of Corynebacterium glutamicum promoters have already provided large amounts of data on their structures, regulatory mechanisms and practical capabilities in metabolic engineering. In this minireview the main aspects of promoter studies, the methods developed for their analysis and their practical use in C. glutamicum are discussed. These include definitions of the consensus sequences of the distinct promoter classes, promoter localization and characterization, activity measurements, the functions of transcriptional regulators and examples of practical uses of constitutive, inducible and modified promoters in biotechnology. The implications of the introduction of novel techniques, such as in vitro transcription and RNA sequencing, to C. glutamicum promoter studies are outlined.
Glucagon: The renewal of an old hormone in the pathophysiology of diabetes (胰升糖素：一种老激素在糖尿病病理生理中的新作用)
Authors: Gosmain Yvan , Masson Mounia Heddad , Philippe Jacques 
Published: January 2013

AbstractType 2 diabetes (T2D) is one of the most common diseases, affecting 5–10% of the population in most countries; the progression of its prevalence has been constant over the past 50 years in all countries worldwide, creating a major public health problem in terms of disease management and financial burden. Although the pathophysiology of T2D has been attributed for decades to insulin resistance and decreased insulin secretion, particularly in response to glucose, the contributing role of glucagon in hyperglycemia has been highlighted since the early 1970s by demonstrating its glycogenolytic, gluconeogenic and ketogenic properties. More recently, the importance of glucagon in diabetes has been highlighted in a model of streptozotocin‐induced diabetic mice becoming euglycemic in the absence of glucagon receptors and without insulin treatment. Understanding the dysregulation of α‐cells in diabetes will be critical to better define the pathophysiology of diabetes and develop new antidiabetic treatment.
Habitat species pools for phylogenetic structure in microbes
Authors: Wang Jianjun , Soininen Janne , Shen Ji 
Published: January 2013

SummaryThe processes underlying the phylogenetic structure of the biotic communities are typically scale‐dependent and thus often poorly resolved. Illustrated by the study of macroorganisms, it is suggested that the relative influence of ecological processes on the phylogenetic structure of the communities can be inferred by the geographical definition of the species pools. However, given the high dispersal ability of microbes, the spatial delineation of the species pool may not be that practical for microbial taxa. This idea is supported by the observational data on bacteria along an elevational gradient. Significant negative values of standardized effect size of the mean nearest taxon distance were consistently observed for different sized species pools considered. Reviewing the reports on microbial phylogenetic structure so far, we suggested that the ‘habitat species pools’ are perhaps more important for microbes than spatial delineated ‘regional species pools’.
Scaling up predator–prey dynamics using spatial moment equations
Authors: Barraquand Frédéric , Murrell David J. 
Published: January 2013

Summary
Classical models of predator–prey dynamics, commonly used in community and evolutionary ecology to explain population cycles, species coexistence, the effects of enrichment, or predict the evolution of behavioural traits, are often based on the mass‐action assumption. This means encounter rates between predators and prey are expressed as a product of predator and prey landscape densities; as if the system was well‐mixed.
While mass‐action may occur at small spatial scales, spatial variances and covariances in prey and predator densities affect encounter rates at large spatial scales. In the context of host–parasitoid interactions, this has been incorporated into theory for some time, but for predators, well‐mixed or other ad hoc models are often used despite empirical evidence for intricate spatial variation in predator and prey numbers.
We review the classical models and concepts, their strengths and weaknesses, and we present two recent spatial moment approaches that scale up predator–prey population dynamics from the individual or patch level to large spatial scales. Both methods include descriptors of spatial structure as corrections to encounter rates, but differ in whether or not these descriptors have dynamics that are explicit functions of movements, births and deaths.
We describe how these spatial moment techniques work, what new results they have so far produced, and provide some suggestions to improve the connection of predator–prey theoretical models to empirical studies.
A hierarchical distance sampling approach to estimating mortality rates from opportunistic carcass surveillance data
Authors: Bellan Steve E. , Gimenez Olivier , Choquet Rémi , Getz Wayne M. 
Published: January 2013

SummaryDistance sampling is widely used to estimate the abundance or density of wildlife populations. Methods to estimate wildlife mortality rates have developed largely independently from distance sampling, despite the conceptual similarities between estimation of cumulative mortality and the population density of living animals. Conventional distance sampling analyses rely on the assumption that animals are distributed uniformly with respect to transects and thus require randomised placement of transects during survey design. Because mortality events are rare, however, it is often not possible to obtain precise estimates in this way without infeasible levels of effort. A great deal of wildlife data, including mortality data, are available via road‐based surveys. Interpreting these data in a distance sampling framework requires accounting for the non‐uniformity of sampling. In addition, analyses of opportunistic mortality data must account for the decline in carcass detectability through time. We develop several extensions to distance sampling theory to address these problems.We build mortality estimators in a hierarchical framework that integrates animal movement data, surveillance effort data and motion‐sensor camera trap data, respectively, to relax the uniformity assumption, account for spatiotemporal variation in surveillance effort and explicitly model carcass detection and disappearance as competing ongoing processes.Analysis of simulated data showed that our estimators were unbiased and that their confidence intervals had good coverage.We also illustrate our approach on opportunistic carcass surveillance data acquired in 2010 during an anthrax outbreak in the plains zebra of Etosha National Park, Namibia.The methods developed here will allow researchers and managers to infer mortality rates from opportunistic surveillance data.
Sociodemographic factors influence the risk for femur shaft fractures in children: a Swedish case–control study, 1997–2005
Authors: von Heideken Johan , Svensson Tobias , Iversen Maura , Blomqvist Paul , Haglund‐Åkerlind Yvonne , Janarv Per‐Mats 
Published: January 2013

AbstractAimTo investigate how sociodemographic factors relate to the risk of femur shaft fractures in children and how the relationship differs by gender and age.MethodsPopulation‐based case–control study. Swedish children (n = 1,874), 0–14 years of age, with a femur shaft fracture diagnostic code occurring between 1997 and 2005 were selected from the Swedish national inpatient register and compared with matched controls (n = 18,740). Demographic, socio‐economic and injury data were based on record linkage between six Swedish registers.ResultsThe risk of femur shaft fracture increased for children with younger parents or those living in low‐income households. Having a parent with a university education reduced the risk. Stratifying for gender and age group, the association between parents' age was evident only for older boys (7–14 years of age) (OR = 1.40; 95% CI 1.04–1.45), and the association between living in low‐income households and fracture rate was only seen in older girls (7–14 years) (OR = 1.50; 95% CI 1.01–2.22). Family composition, number of siblings, birth order or receiving social welfare did not influence the fracture risk.ConclusionSociodemographic variables influence the rate of femur shaft fractures, in older children the influence differs between boys and girls.
Differential effects of depression and mania symptoms on social adjustment: prospective study in bipolar disorder
Authors: Morriss Richard , Yang Min , Chopra Arun , Bentall Richard , Paykel Eugene , Scott Jan 
Published: January 2013

Morriss R, Yang M, Chopra A, Bentall R, Paykel E, Scott J. Differential effects of depression and mania symptoms on social adjustment: prospective study in bipolar disorder.  Bipolar Disord 2013: 15: 80–91. © 2013 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.Objectives:  Previous studies of social adjustment in bipolar disorder have been cross‐sectional and small in sample size, have examined a limited number of roles, or were not controlled for baseline mood and other clinical, social, or treatment confounders. We aimed to prospectively explore the strength and stability of correlations between depression and mania‐type symptoms and impairment in a broad range of social adjustment roles and domains.Methods:  Multilevel modeling analysis of correlation coefficients between depression and mania‐type symptoms with roles and domains of the modified social adjustment scale (overall, work, social/leisure, extended family, marital, parental social adjustment roles, performance, interpersonal behavior, friction, dependency, overactivity domains) was used. Interview assessments were made at eight‐week intervals beginning at eight weeks and continuing through 72 weeks after baseline in 253 patients in a multicenter randomized controlled trial.Results:  After controlling for baseline mood episodes, and other clinical, social, and treatment variables, depression symptoms showed strong and stable correlations over time with performance, overall social adjustment, and the work role; and a moderate but stable relationship with interpersonal behavior. The relationships of depression symptoms with the other roles were weak, non‐significant, or not stable. For mania‐type symptoms, only the correlation with interpersonal friction was moderately strong and reasonably stable over time. Mood episodes, substance use disorder, and borderline/antisocial personality disorder increased role impairment, while employment and marriage mildly decreased it.Conclusions:  Depression and mania‐type symptoms have specific effects on social adjustment in bipolar I disorder. Depression symptoms are correlated strongly with performance and moderately with interpersonal behavior, while mania‐type symptoms are correlated moderately with interpersonal friction.
Incorporating Uncertainty of Management Costs in Sensitivity Analyses of Matrix Population Models
Authors: SALOMON YACOV , M c CARTHY MICHAEL A. , TAYLOR PETER , WINTLE BRENDAN A. 
Published: January 2013

AbstractThe importance of accounting for economic costs when making environmental‐management decisions subject to resource constraints has been increasingly recognized in recent years. In contrast, uncertainty associated with such costs has often been ignored. We developed a method, on the basis of economic theory, that accounts for the uncertainty in population‐management decisions. We considered the case where, rather than taking fixed values, model parameters are random variables that represent the situation when parameters are not precisely known. Hence, the outcome is not precisely known either. Instead of maximizing the expected outcome, we maximized the probability of obtaining an outcome above a threshold of acceptability. We derived explicit analytical expressions for the optimal allocation and its associated probability, as a function of the threshold of acceptability, where the model parameters were distributed according to normal and uniform distributions. To illustrate our approach we revisited a previous study that incorporated cost‐efficiency analyses in management decisions that were based on perturbation analyses of matrix population models. Incorporating derivations from this study into our framework, we extended the model to address potential uncertainties. We then applied these results to 2 case studies: management of a Koala (Phascolarctos cinereus) population and conservation of an olive ridley sea turtle (Lepidochelys olivacea) population. For low aspirations, that is, when the threshold of acceptability is relatively low, the optimal strategy was obtained by diversifying the allocation of funds. Conversely, for high aspirations, the budget was directed toward management actions with the highest potential effect on the population. The exact optimal allocation was sensitive to the choice of uncertainty model. Our results highlight the importance of accounting for uncertainty when making decisions and suggest that more effort should be placed on understanding the distributional characteristics of such uncertainty. Our approach provides a tool to improve decision making.
The diagnostic value of fungal fluorescence in onychomycosis
Authors: Idriss Munir H. , Khalil Ahmed , Elston Dirk 
Published: January 2013

BackgroundFluorescence of pathogenic fungi has been previously shown when hematoxylin and eosin‐stained sections are examined under a fluorescent microscope. We hypothesize that this phenomenon could aid in the evaluation of nail specimens for onychomycosis.MethodsForty‐eight routinely stained nail sections of periodic acid‐Schiff (PAS)‐positive onychomycosis, along with 23 PAS‐negative control specimens with a clinical diagnosis of onychomycosis, were studied under a fluorescent microscope to determine the clinical usefulness of this technique.ResultsIn most cases, fluorescence of fungal organisms was noted. Fungi were identified by their tubular or annular shapes with fluorescence surrounding them. The sensitivity and specificity of the method were 96 and 90%, respectively. In some cases, it was difficult to identify the fungi because of the relative paucity of organisms, weak fluorescence and high background fluorescence of eosinophilic nail keratin.ConclusionsWe conclude that fluorescence microscopy can be used as a rapid screening tool for identification of fungi in nail specimens.
The hyperpolarization‐activated non‐specific cation current (Ih) adjusts the membrane properties, excitability, and activity pattern of the giant cells in the rat dorsal cochlear nucleus
Authors: Rusznák Zoltán , Pál Balázs , Kőszeghy Áron , Fu Yuhong , Szücs Géza , Paxinos George 
Published: January 2013

AbstractGiant cells of the cochlear nucleus are thought to integrate multimodal sensory inputs and participate in monaural sound source localization. Our aim was to explore the significance of a hyperpolarization‐activated current in determining the activity of giant neurones in slices prepared from 10 to 14‐day‐old rats. When subjected to hyperpolarizing stimuli, giant cells produced a 4‐(N‐ethyl‐N‐phenylamino)‐1,2‐dimethyl‐6‐(methylamino) pyridinium chloride (ZD7288)‐sensitive inward current with a reversal potential and half‐activation voltage of –36 and –88 mV, respectively. Consequently, the current was identified as the hyperpolarization‐activated non‐specific cationic current (Ih). At the resting membrane potential, 3.5% of the maximum Ih conductance was available. Immunohistochemistry experiments suggested that hyperpolarization‐activated, cyclic nucleotide‐gated, cation non‐selective (HCN)1, HCN2, and HCN4 subunits contribute to the assembly of the functional channels. Inhibition of Ih hyperpolarized the membrane by 6 mV and impeded spontaneous firing. The frequencies of spontaneous inhibitory and excitatory postsynaptic currents reaching the giant cell bodies were reduced but no significant change was observed when evoked postsynaptic currents were recorded. Giant cells are affected by biphasic postsynaptic currents consisting of an excitatory and a subsequent inhibitory component. Inhibition of Ih reduced the frequency of these biphasic events by 65% and increased the decay time constants of the inhibitory component. We conclude that Ih adjusts the resting membrane potential, contributes to spontaneous action potential firing, and may participate in the dendritic integration of the synaptic inputs of the giant neurones. Because its amplitude was higher in young than in adult rats, Ih of the giant cells may be especially important during the postnatal maturation of the auditory system.
Mapping China's freshwater fishes: diversity and biogeography
Authors: Kang Bin , Deng Junming , Wu Yunfei , Chen Liqiang , Zhang Jie , Qiu Haiyuan , Lu Yin , He Daming 
Published: January 2013

AbstractFreshwater fishes worldwide face an array of threats from dam construction, river fragmentation, pollution, over‐exploitation and interactions with introduced species. Such impacts are especially prevalent in densely populated countries undergoing rapid development, and their effects are felt most strongly where regional fish diversity is high. We reviewed studies of the distribution of freshwater fish species throughout China to map a biogeographical pattern and ascertain the environmental factors contributing to this distribution. We then linked this information to identify geographic areas to be recommended as the focus of conservation efforts. A total of 920 species in 302 genera, 54 families and 21 orders were recorded. Among the recorded species, 73% were Cypriniformes and 12% were Siluriformes. Cyprinidae was the most dominant family with 473 species, followed by Balitoridae with 157 species. The administrative division of the biogeography of China's freshwater fishes consisted of nine regions, including the Qinghai‐Tibetan Plateau Region, Oriental Region, Northwest Region, South Region, Loess Plateau Region, Heilongjiang Region, Upper Yangtze Region, 3H Plain Region and Middle‐Lower Yangtze Plain Region. The river system was the primary factor in determining China's freshwater fish biogeography. Under stepwise regression analysis, river discharge was found to be the most influential factor in determining richness, followed by population size and net primary productivity. The higher level of fish endemicity and sensitivity to environmental change led to the identification of Southwest China and the higher areas of Qinghai‐Tibetan Plateau as the primary areas to be considered for fish conservation and potential natural reserves.
Immunoarchitectural patterns in splenic marginal zone lymphoma: correlations with chromosomal aberrations, IGHV mutations, and survival. A study of 76 cases
Authors: Traverse‐Glehen Alexandra , Bachy Emmanuel , Baseggio Lucile , Callet‐Bauchu Evelyne , Gazzo Sophie , Verney Aurélie , Hayette Sandrine , Jallades Laurent , Ffrench Martine , Salles Gilles , Coiffier Bertrand , Felman Pascale , Berger Francoise 
Published: January 2013

AimsTo describe 76 cases of splenic marginal zone lymphoma (SMZL), including correlations with clinical and other characteristics.Methods and resultsPatients were predominantly female, with a median age of 62 years. The main clinical presentation was splenomegaly, except for eight cases presenting with evolution of autoimmune disorders or spontaneous splenic rupture. White pulp infiltration was nodular, with a monophasic (42%) or biphasic (53%) pattern, and associated diffuse or nodular infiltration of the red pulp, except for four cases which had atrophic white pulp. Plasmacytic differentiation and the MYD88 L265P mutation were observed in 18% and 5% of the cases, respectively. Histological progression was considered in cases with a significant association of large cells with Ki67 > 30% and macronodular architecture (P = 0.001). Other significant correlations were found between del7q (44%) and del6q (17%) (P = 0.018), IGHV1‐2*04 segment usage (35%) (P = 0.001) and unmutated IGHV (39%) (P = 0.019), and between CD5 expression (27%) and higher lymphocytosis (P = 0.002). Patients requiring intensive chemotherapy after splenectomy because of clinical and/or histological progression had significantly shorter overall survival (P = 0.012).ConclusionsWe report the histological spectrum of SMZL, and discuss the differential diagnosis and requirement for molecular and cytogenetic analysis in atypical cases.
Prevalence and impact on survival of positive surgical margins in partial nephrectomy for renal cell carcinoma: a population‐based study
Authors: Ani Ifeanyi , Finelli Antonio , Alibhai Shabbir M.H. , Timilshina Narhari , Fleshner Neil , Abouassaly Robert 
Published: January 2013

What's known on the subject? and What does the study add?
The increased detection of small renal masses (SRMs) with diagnostic imaging has highlighted the importance of preserving renal function, with many patients with SRMs being managed with nephron‐sparing procedures. The significance of positive surgical margins (PSMs) is debatable and various studies have looked at the risk factors for PSMs and recurrence. It has been suggested that tumour size may be a risk factor and the centrality of the tumour has been found to be an increased risk factor. The indication and location of the tumour has been found to be an independent predictive factor for recurrence.
Various studies have assessed the outcome of patients with PSMs with short‐ to intermediate‐term follow‐up. Our study has an intermediate‐term median follow‐up of 7.9 years, and found no significant difference in 5‐year disease‐specific and overall survival rates between patients with PSMs and negative surgical margins. We also found that tumour size was not significant, but pathological stage and fat invasion were found to be significant. These risk factors have not been published in previous studies.
Objectives
To determine the prevalence of positive surgical margins (PSMs) on a population level.
To identify the predictors of PSMs and assess their impact on survival.
Patients and Methods
Using the Ontario Cancer Registry, we reviewed pathology reports on 664 patients after partial nephrectomy for renal cell carcinoma between 1995 and 2004.
Demographic information and pathological characteristics were obtained and multivariable logistic regression analysis was performed to determine the predictors of PSMs.
Kaplan–Meier analysis was used to examine disease‐specific (DSS) and overall survival (OS) by margin status. A multivariable Cox proportional hazards model was used to determine the independent association between PSMs and survival.
Results
The mean patient age was 57.7 years and 61.6% were men. Tumour size was <2.0 cm in 25%, 2.0–3.9 cm in 59%, 4.0–6.9 cm in 13%, and ≥7.0 cm in 3% of patients.
Seventy‐one patients (10.7%) had PSMs on final pathology. Only stage (P = 0.02) and fat invasion (P = 0.04) were significantly associated with PSMs.
At a median follow‐up of 7.9 years, the unadjusted 5‐year DSS and OS rates were 91.8 and 88.3%, respectively.
Survival rates did not differ by surgical margin status, with 90.9 and 84.4% 5‐year DSS and OS rates for patients with PSMs compared with 91.9 and 88.6% for those with a negative surgical margin (P = 0.58, log rank test).
Using a Cox proportional hazards model, surgical margin status was not associated with time to all‐cause death (P = 0.67).
Conclusion
Our population‐level data suggest that, although PSMs are fairly prevalent, they appear to have little to no impact on 5‐year survival rates.