bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptochrome 1 in Retinal Cone Photoreceptors Suggests a Novel Functional Role in Mammals
Authors: Nießner Christine , Denzau Susanne , Malkemper Erich Pascal , Gross Julia Christina , Burda Hynek , Winklhofer Michael , Peichl Leo 
Published: February 2016

AbstractCryptochromes are a ubiquitous group of blue-light absorbing flavoproteins that in the mammalian retina have an important role in the circadian clock. In birds, cryptochrome 1a (Cry1a), localized in the UV/violet-sensitive S1 cone photoreceptors, is proposed to be the retinal receptor molecule of the light-dependent magnetic compass. The retinal localization of mammalian Cry1, homologue to avian Cry1a, is unknown and it is open whether mammalian Cry1 is also involved in magnetic field sensing. To constrain the possible role of retinal Cry1, we immunohistochemically analysed 90 mammalian species across 48 families in 16 orders, using an antiserum against the Cry1 C-terminus that in birds labels only the photo-activated conformation. In the Carnivora families Canidae, Mustelidae and Ursidae and in some Primates, Cry1 was consistently labeled in the outer segment of the shortwave-sensitive S1 cones. This finding would be compatible with a magnetoreceptive function of Cry1 in these taxa. In all other taxa, Cry1 was not detected by the antiserum that likely also in mammals labels the photo-activated conformation, although Western blots showed Cry1 in mouse retinal cell nuclei. We speculate that in the mouse and the other negative-tested mammals Cry1 is involved in circadian functions as a non-light-responsive protein.
Akt attenuates apoptotic death through phosphorylation of H2A under hydrogen peroxide-induced oxidative stress in PC12 cells and hippocampal neurons
Authors: Park Ji Hye , Kim Chung Kwon , Lee Sang Bae , Lee Kyung-Hoon , Cho Sung-Woo , Ahn Jee-Yin 
Published: February 2016

AbstractAlthough the essential role of protein kinase B (PKB)/Akt in cell survival signaling has been clearly established, the mechanism by which Akt mediates the cellular response to hydrogen peroxide (H2O2)-induced oxidative stress remains unclear. We demonstrated that Akt attenuated neuronal apoptosis through direct association with histone 2A (H2A) and phosphorylation of H2A at threonine 17. At early time points during H2O2 exposure of PC12 cells and primary hippocampal neurons, when the cells can tolerate the level of DNA damage, Akt was activated and phosphorylated H2A, leading to inhibition of apoptotic death. At later time points, Akt delivered the NAD+-dependent protein deacetylase Sirtuin 2 (Sirt 2) to the vicinity of phosphorylated H2A in response to irreversible DNA damage, thereby inducing H2A deacetylation and subsequently leading to apoptotic death. Ectopically expressed T17A-substituted H2A minimally interacted with Akt and failed to prevent apoptosis under oxidative stress. Thus Akt-mediated H2A phosphorylation has an anti-apoptotic function in conditions of H2O2-induced oxidative stress in neurons and PC12 cells.
Effect of ultrasonic irradiation on the preparation of Ag3PO4 particles
Authors: Yang Yang , Yang Hua , Li Ruishan , Wang Xiangxian 
Published: February 2016

Herein is investigated the effect of ultrasonic irradiation on the preparation of Ag3PO4 particles based on the ion‐exchange method. X‐ray diffraction, scanning electron microscope, diffuse reflectance spectrum and photoluminescence were used to characterise the products. It is found that the application of ultrasonic irradiation at a frequency of 40 kHz leads to the production of uniform spherical particles with an average size of ∼300 nm. However, at a higher ultrasonic frequency of 60 kHz, the prepared sample presents polyhedron‐shaped particles in the size range of 6–8 μm, which are constructed from small grains with a size of several hundred nanometres. Without the aid of ultrasonic irradiation, the samples prepared at room temperature or under 50 °C water‐bath condition are composed of spherical particles and large‐sized agglomerative particles. The photocatalytic activity of Ag3PO4 samples was evaluated by degrading rhodamine B (RhB) under simulated sunlight irradiation. Among these samples, the one prepared at 40 kHz exhibits the highest photocatalytic activity, where the degradation percentage of RhB reaches 96% after irradiation for 60 min.
Characterising visual context effects
Authors: Knoeferle Pia 
Published: February 2016

In this chapter, I will review recent research on visually situated language comprehension, and in doing so identify key characteristics of situated language comprehension. More specifically I will argue that both active visual context effects and the temporally coordinated interplay between visual attention and language comprehension are characteristic of situated comprehension, and are robust across a broad range of comprehension situations, spanning (a) different comprehension modalities (reading and spoken comprehension) and situations in which language is (versus isn’t) in accord with visual context; (b) different kinds of visual contexts (clipart depictions, photographs, and real-world objects and events); (c) speaker-based information such as eye-gaze and gestures; and (d) both concrete and abstract language. Because of their broad coverage ((a)–(d)), situated language comprehension paradigms are, in principle, well suited for developing a relatively comprehensive theory of situated language comprehension. One challenge in further specifying model predictions is the development of more detailed linking hypotheses between comprehension processes and one of the key measures used to examine situated comprehension (visual attention to objects across time).
In-silico analysis of MHC genes in hereditary colorectal cancer shows identical by state SNP sharing affecting HLA-DQB1 binding groove
Authors: Koko Mahmoud E. , Suleiman Suleiman H. , Abdallah Mohammed O.E. , Saad Muhallab , Ibrahim Muntaser E. 
Published: February 2016

ABSTRACTBackgroundThe role of Human Leukocyte Antigen (HLA) alleles in colorectal cancer susceptibility, development and progression is the focus of ongoing scrutiny. MHC polymorphisms in a Sudanese family with hereditary colorectal cancer were studied using anin silicoapproach and the results were verified using The Cancer Genome Atlas (TCGA). In this family study, we tested for sharing of nucleotide polymorphisms identified by whole exome capture inmajor histocompatibility complexregion and carried outin-silicoprediction of their effects in tumor and control samples. SNPs were analyzed to highlight identical by state sharing, to identify runs of homozygosity, as well as to predict structural and functional effects using homology modeling, damaging effect predictions, and regulatory changes prediction.ResultsMHC II area showed significantly high degree of homozygosity in tumor samples. Non-synonymous SNPs sharedidentical by state(IBS) between tumor samples were predicted to affect HLA-DQB1 binding groove. A similar haplotype of these SNPs was identified in a TCGA colonic adenocarcinoma tumor sample. No significant regulatory effects (in the form of transcription factor or miRNA binding site variants) were predicted.ConclusionsThe results demonstrate IBS SNP sharing of markers affecting HLA-DQB1 binding specificity and probable loss of heterozygosity in MHC II region in colorectal cancer. The significance of this sharing in cancer pathogenesis remains to be established.
The evolution of labile traits in sex‐ and age‐structured populations
Authors: Childs Dylan Z. , Sheldon Ben C. , Rees Mark 
Published: February 2016

Summary

Many quantitative traits are labile (e.g. somatic growth rate, reproductive timing and investment), varying over the life cycle as a result of behavioural adaptation, developmental processes and plastic responses to the environment. At the population level, selection can alter the distribution of such traits across age classes and among generations. Despite a growing body of theoretical research exploring the evolutionary dynamics of labile traits, a data‐driven framework for incorporating such traits into demographic models has not yet been developed.

Integral projection models (IPMs) are increasingly being used to understand the interplay between changes in labile characters, life histories and population dynamics. One limitation of the IPM approach is that it relies on phenotypic associations between parents and offspring traits to capture inheritance. However, it is well‐established that many different processes may drive these associations, and currently, no clear consensus has emerged on how to model micro‐evolutionary dynamics in an IPM framework.

We show how to embed quantitative genetic models of inheritance of labile traits into age‐structured, two‐sex models that resemble standard IPMs. Commonly used statistical tools such as GLMs and their mixed model counterparts can then be used for model parameterization. We illustrate the methodology through development of a simple model of egg‐laying date evolution, parameterized using data from a population of Great tits (Parus major).

We demonstrate how our framework can be used to project the joint dynamics of species' traits and population density. We then develop a simple extension of the age‐structured Price equation (ASPE) for two‐sex populations, and apply this to examine the age‐specific contributions of different processes to change in the mean phenotype and breeding value.

The data‐driven framework we outline here has the potential to facilitate greater insight into the nature of selection and its consequences in settings where focal traits vary over the lifetime through ontogeny, behavioural adaptation and phenotypic plasticity, as well as providing a potential bridge between theoretical and empirical studies of labile trait variation.
Demography beyond the population
Authors: Griffith Alden B. , Salguero‐Gómez Roberto , Merow Cory , McMahon Sean 
Published: February 2016

SummaryPopulation ecology, the discipline that studies the dynamics of species’ populations and how they interact with the environment, has been one of the most prolific fields of ecology and evolution. Demographic research is central to quantifying population‐level processes and their underlying mechanisms and has provided critical contributions to a diversity of research fields. Examples include the spread of infectious diseases, eco‐evolutionary dynamics and rapid evolution, mechanisms underlying invasions and extinctions, and forest productivity. As the fates of individual organisms are influenced by, and subsequently underlie, many other patterns and processes, we suggest that connecting demographybeyondthe population level offers promising avenues of innovation in ecology and evolution.Under the premise that population‐level processes are an ideal common currency within ecology and evolution, we organized the British Ecological Society Symposium,Demography Beyond the Population. This event attracted international researchers who are applying demographic theory and approaches to a broad range of questions. This special feature builds off of the symposium and illustrates the ability of demography to connect across diverse research areas in ecology and evolution, including functional traits, transient dynamics, quantitative genetics, environmental drivers and feedbacks, land management and other topics. In addition to highlighting the contributed manuscripts, this editorial provides a brief background on the development of the discipline and suggests how demographic tools may be used in novel ways to study more thanjustpopulations.Synthesis. This special feature integrates novel lines of research in the vast field of demography that directly interact with other ecological and evolutionary disciplines. The cross‐disciplinary potential of demography is further emphasized by the fact that its 20 manuscripts are spread across all six journals of the British Ecological Society. Together, these articles highlight that there is much to be gained by linking demography to other disciplines and scales in ecology and evolution.
l‐Cysteine enhances nutrient absorption via a cystathionine‐β‐synthase‐derived H2S pathway in rodent jejunum
Authors: Xiao Ailin , Li Jing , Liu Tianjian , Liu Zhuxi , Wei Chuanfei , Xu Xiaomeng , Li Qin , Li Jingxin 
Published: February 2016

SummaryHydrogen sulphide (H2S) is generated endogenously from l‐cysteine (l‐Cys) by the enzymes cystathionine‐β‐synthase (CBS) and cystathionine‐γ‐lyase (CSE). In addition, l‐Cys is commonly used as a precursor in the food and pharmaceutical industries. The aim of the present study is to determine whether l‐Cys regulates intestinal nutrient transport. To that end, the presence of CBS and CSE in the jejunum epithelium was assessed by immunohistochemistry, Western blotting and the methylene blue assay. In addition, in vivo l‐Cys (100 mg/kg, administered immediately after the glucose load) significantly increased blood glucose levels 30 min after the oral administration of glucose to mice. This effect of l‐Cys was completely blocked by amino‐oxyacetic acid (AOA; 50 mg/kg; administered at the same time as l‐Cys) an inhibitor of CBS. Measurements of the short‐circuit current (Isc) in the rat jejunum epithelium revealed that l‐Cys (1 mmol/L; 6 min before the administration of l‐alanine) enhances Na+‐coupled l‐alanine or glucose transport, and that this effect is inhibited by AOA (1 mmol/L;10 min before the administration of l‐Cys), but not d,l‐propargylglycine (PAG;1 mmol/L; 10 min before the administration of l‐Cys), a CSE inhibitor. Notably, l‐Cys‐evoked enhancement of nutrient transport was alleviated by glibenclamide (Gli;0.1 mmol/L; 10 min before the administration of l‐Cys), a K+ channel blocker. Together, the data indicate that l‐Cys enhances jejunal nutrient transport, suggesting a new approach to future treatment of nutrition‐related maladies, including a range of serious health consequences linked to undernutrition.
Before theory comes theorizing or how to make social science more interesting
Authors: Swedberg Richard 
Published: February 2016

AbstractThe basic argument in this article is that sociology and social science more generally are today severely hampered by the lack of attention being paid to theory. Methods – qualitative as well as quantitative methods – have proven to be very useful in practical research (as opposed to theory); and as a result they dominate modern social science. They do not, however, do the job that belongs to theory. One way to redress the current imbalance between methods and theory, it is suggested, would be to pay more attention to theorizing, that is, to the actual process that precedes the final formulation of a theory; and in this way improve theory. Students of social science are today primarily exposed to finished theories and are not aware of the process that goes into the production and design of a theory. Students need to be taught how to construct a theory in practical terms (‘theorizing’); and one good way to do so is through exercises. This is the way that methods are being taught by tradition; and it helps the students to get a hands‐on knowledge, as opposed to just a reading knowledge of what a theory is all about. Students more generally need to learn how to construct a theory while drawing on empirical material. The article contains a suggestion for the steps that need to be taken when you theorize. Being trained in what sociology and social science are all about – an important precondition! – students may proceed as follows. You start out by observing, in an attempt to get a good empirical grip on the topic before any theory is introduced. Once this has been done, it may be time to name the phenomenon; and either turn the name into a concept as the next step or bring in some existing concepts in an attempt to get a handle on the topic. At this stage one can also try to make use of analogies, metaphors and perhaps a typology, in an attempt to both give body to the theory and to invest it with some process. The last element in theorizing is to come up with an explanation; and at this point it may be helpful to draw on some ideas by Charles Peirce, especially his notion of abduction. Before having been properly tested against empirical material, according to the rules of the scientific community, the theory should be considered unproven. Students who are interested in learning more about theorizing may want to consult the works of such people as Everett C. Hughes, C. Wright Mills, Ludwig Wittgenstein and James G. March. Many of the issues that are central to theorizing are today also being studied in cognitive science; and for those who are interested in pursuing this type of literature, handbooks represent a good starting point. The article ends by arguing that more theorizing will not only redress the balance between theory and methods; it will also make sociology and social science more interesting.
Inflammation in central nervous system diseases
Authors: Shichita Takashi , Yoshimura Akihiko 
Published: February 2016

AbstractInflammation is implicated in the pathogenesis of various central nervous system diseases. The brain is a sterile organ; therefore, inflammation is triggered by endogenous molecules. Pattern recognition receptors recognize specific endogenous molecules, and activate resident glial cells and peripheral immune cells. Inflammasome complex formation is also important for neuroinflammation in brain tissue injury, epilepsy and neurodegenerative diseases. Although inflammation exaggerates the pathology and neurological deficits in neurological disorders, triggering the pro‐resolution process and neuronal repair is a beneficial side of inflammation. We introduce recent accumulating evidence about the relationship between neuroinflammation by innate immunity and the process of pathogenesis in central nervous system diseases.
Preschoolers' Acquisition of Novel Verbs in the Double Object Dative
Authors: Arunachalam Sudha 
Published: February 2016

AbstractChildren have difficulty comprehending novel verbs in the double object dative (e.g., Fred blicked the dog a stick) as compared to the prepositional dative (e.g., Fred blicked a stick to the dog). We explored this pattern with 3 and 4 year olds (N = 60). In Experiment 1, we replicated the documented difficulty with the double object frame, even though we provided more contextual support. In Experiment 2, we tested a novel hypothesis that children would comprehend novel verbs in, and generalize them to, the double object frame if they were first familiarized to the verbs in the prepositional frame. They did, suggesting that part of their difficulty with the double object frame is due to uncertainty about a new verb's semantic/syntactic properties, information that the easy‐to‐comprehend prepositional frame provides. The benefits of training were short‐lived, however; children again struggled after a 2‐h delay. The results are discussed in the context of mechanisms underlying verb acquisition.
Environmental heterogeneity among lakes promotes hyper β‐diversity across phytoplankton communities
Authors: Maloufi Selma , Catherine Arnaud , Mouillot David , Louvard Clarisse , Couté Alain , Bernard Cécile , Troussellier Marc 
Published: February 2016

Summary

The extent to which stochastic and deterministic processes influence variations in species communities across space and time remains a central question in theoretical and applied ecology. Despite their high dispersal ability, the composition of phytoplankton communities displays striking spatial variations among lakes even at small spatial scale.

To investigate the mechanisms underlying the distribution of phytoplankton species, we evaluate the contribution of stochastic, spatial and environmental processes in determining β‐diversity patterns of phytoplankton at a regional scale. Phytoplankton communities were surveyed in 50 different lakes from north‐central France, a region characterised by strong environmental heterogeneity.

The regional species pool was characterised by extremely high β‐diversity levels, which were mainly explained by species replacement (i.e. turnover) rather than by differences in species richness (i.e. nestedness). Null models of random species distribution and spatial processes failed to explain observed β‐diversity patterns. At the opposite, local environmental conditions strongly influenced the degree of uniqueness of local phytoplankton communities, with the most contrasted environments, including human‐dominated areas, promoting highly distinct phytoplankton communities.

Our results suggest that species‐sorting mechanisms that arise from variations in local environmental conditions drive high species turnover at the region scale. Thus, in a landscape strongly impacted by cultural eutrophication, further anthropogenic impacts on aquatic ecosystems would likely induce regional homogenisation of phytoplankton communities. Overall, our study supports the fact that the management of lakes and reservoirs in anthropic landscapes should aim at maintaining environmental heterogeneity while preventing further eutrophication in order to favour the maintenance of high phytoplankton β‐ and γ‐diversity.
Simeprevir or telaprevir with peginterferon and ribavirin for recurrent hepatitis C after living‐donor liver transplantation: A Japanese multicenter experience
Authors: Ueda Yoshihide , Ikegami Toru , Soyama Akihiko , Akamatsu Nobuhisa , Shinoda Masahiro , Ishiyama Kohei , Honda Masaki , Marubashi Shigeru , Okajima Hideaki , Yoshizumi Tomoharu , Eguchi Susumu , Kokudo Norihiro , Kitagawa Yuko , Ohdan Hideki , Inomata Yukihiro , Nagano Hiroaki , Shirabe Ken , Uemoto Shinji , Maehara Yoshihiko 
Published: February 2016

AimThis study aimed to clarify the efficacy and safety of simeprevir, a second‐generation NS3/4A inhibitor, with peginterferon and ribavirin for recurrent hepatitis C after liver transplantation.MethodsA retrospective cohort study of living‐donor liver transplant recipients with recurrent hepatitis C with the hepatitis C virus genotype 1 treated with either simeprevir‐ or telaprevir‐based triple therapy was carried out at eight Japanese liver transplant centers.ResultsSimeprevir‐ and telaprevir‐based triple therapies were given to 79 and 36 patients, respectively. Of the 79 patients treated with simeprevir‐based triple therapy, 44 (56%) achieved sustained virological response 12 weeks (SVR12) after treatment ended, and there was no significant difference in the SVR12 between the simeprevir‐ and telaprevir‐based triple therapy groups (69%). The rates of adverse events were not significantly different between the simeprevir‐ and telaprevir‐based triple therapy groups, although the rate of patients who received blood cell transfusion and erythropoietin due to anemia and had renal insufficiency were significantly higher in the telaprevir group than in the simeprevir group. Three baseline factors, the presence of prior dual therapy with peginterferon and ribavirin (P = 0.001), a non‐responder to the prior dual therapy (P < 0.001), and male sex (P = 0.040), were identified as significant predictive factors for non‐SVR with simeprevir‐based triple therapy.ConclusionSimeprevir‐based triple therapy for recurrent hepatitis C after living‐donor liver transplantation resulted in a high SVR rate and good tolerability, especially in treatment‐naïve patients.