bluuebunny/crossref_metadata_2025 huggingface dataset:
Alzheimer’s disease cerebrospinal fluid biomarkers are not influenced by gravity drip or aspiration extraction methodology
Authors: Rembach Alan , Evered Lisbeth A. , Li Qiao-Xin , Nash Tabitha , Vidaurre Lesley , Fowler Christopher J. , Pertile Kelly K. , Rumble Rebecca L. , Trounson Brett O. , Maher Sarah , Mooney Francis , Farrow Maree , Taddei Kevin , Rainey-Smith Stephanie , Laws Simon M. , Macaulay S. Lance , Wilson William , Darby David G. , Martins Ralph N. , Ames David , Collins Steven , Silbert Brendan , Masters Colin L. , Doecke James D. ,   the AIBL Research Group
Published: November 2015

Introduction

Cerebrospinal fluid (CSF) biomarkers, although of established utility in the diagnostic evaluation of Alzheimer’s disease (AD), are known to be sensitive to variation based on pre-analytical sample processing. We assessed whether gravity droplet collection versus syringe aspiration was another factor influencing CSF biomarker analyte concentrations and reproducibility.

Methods

Standardized lumbar puncture using small calibre atraumatic spinal needles and CSF collection using gravity fed collection followed by syringe aspirated extraction was performed in a sample of elderly individuals participating in a large long-term observational research trial. Analyte assay concentrations were compared.

Results

For the 44 total paired samples of gravity collection and aspiration, reproducibility was high for biomarker CSF analyte assay concentrations (concordance correlation [95%CI]: beta-amyloid1-42 (Aβ42) 0.83 [0.71 - 0.90]), t-tau 0.99 [0.98 - 0.99], and phosphorylated tau (p-tau) 0.82 [95 % CI 0.71 - 0.89]) and Bonferroni corrected paired sample t-tests showed no significant differences (group means (SD): Aβ42 366.5 (86.8) vs 354.3 (82.6), p = 0.10; t-tau 83.9 (46.6) vs 84.7 (47.4) p = 0.49; p-tau 43.5 (22.8) vs 40.0 (17.7), p = 0.05). The mean duration of collection was 10.9 minutes for gravity collection and <1 minute for aspiration.

Conclusions

Our results demonstrate that aspiration of CSF is comparable to gravity droplet collection for AD biomarker analyses but could considerably accelerate throughput and improve the procedural tolerability for assessment of CSF biomarkers.
Fixed point theorems on cone 2-metric spaces over Banach algebras and an application
Authors: Wang Tao , Yin Jiandong , Yan Qi
Published: November 2015

In this paper, the concept of cone 2-metric spaces over Banach algebras is introduced and some existence and uniqueness theorems of fixed points for some mappings satisfying certain contractive conditions are established. As an application of one of the main results, an example is given at the end of the paper.
Removal of multiple-tip artifacts from scanning tunneling microscope images by crystallographic averaging
Authors: Straton Jack C. , Moon Bill , Bilyeu Taylor T. , Moeck Peter
Published: November 2015

Crystallographic image processing (CIP) techniques may be utilized in scanning probe microscopy (SPM) to glean information that has been obscured by signals from multiple probe tips. This may be of particular importance for scanning tunneling microscopy (STM) and requires images from samples that are periodic in two dimensions (2D). The image-forming current for double-tips in STM is derived with a slight modification of the independent-orbital approximation (IOA) to allow for two or more tips. Our analysis clarifies why crystallographic averaging works well in removing the effects of a blunt STM tip (that consists of multiple mini-tips) from recorded 2D periodic images and also outlines the limitations of this image-processing technique for certain spatial separations of STM double-tips. Simulations of multiple mini-tip effects in STM images (that ignore electron interference effects) may be understood as modeling multiple mini-tip (or tip shape) effects in images that were recorded with other types of SPMs as long as the lateral sample feature sizes to be imaged are much larger than the effective scanning probe tip sizes.
Benefits of a Transfer Clinic in Adolescent and Young Adult Kidney Transplant Patients
Authors: McQuillan Rory F. , Toulany Alene , Kaufman Miriam , Schiff Jeffrey R.
Published: November 2015

Background:

Adolescent and young adult kidney transplant recipients have worse graft outcomes than older and younger age groups. Difficulties in the process of transition, defined as the purposeful, planned movement of adolescents with chronic health conditions from child to adult-centered health care systems, may contribute to this. Improving the process of transition may improve adherence post-transfer to adult care services.

Objective:

The purpose of this study is to investigate whether a kidney transplant transfer clinic for adolescent and young adult kidney transplant recipients transitioning from pediatric to adult care improves adherence post-transfer.

Methods:

We developed a joint kidney transplant transfer clinic between a pediatric kidney transplant program, adult kidney transplant program, and adolescent medicine at two academic health centers. The transfer clinic facilitated communication between the adult and pediatric transplant teams, a face-to-face meeting of the patient with the adult team, and a meeting with the adolescent medicine physician. We compared the outcomes of 16 kidney transplant recipients transferred before the clinic was established with 16 patients who attended the clinic. The primary outcome was a composite measure of non-adherence. Non-adherence was defined as either self-reported medication non-adherence or displaying two of the following three characteristics: non-attendance at clinic, non-attendance for blood work appointments, or undetectable calcineurin inhibitor levels within 1 year post-transfer.

Results:

The two groups were similar at baseline, with non-adherence identified in 43.75 % of patients. Non-adherent behavior in the year post-transfer, which included missing clinic visits, missing regular blood tests, and undetectable calcineurin inhibitor levels, was significantly lower in the cohort which attended the transfer clinic (18.8 versus 62.5 %, p = 0.03). The median change in estimated glomerular filtration rate (eGFR) in the year following transfer was smaller in the group that attended the transition clinic (–0.9 ± 13.2 ml/min/1.73 m2) compared to those who did not (–12.29 ± 14.9 ml/min/1.73 m2), p = 0.045.

Conclusions:

Attendance at a single kidney transplant transfer clinic was associated with improved adherence and renal function in the year following transfer to adult care. If these changes are sustained, they may improve long-term graft outcomes for adolescent kidney transplant recipients.
Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
Authors: Uchino Yoshihito , Miura Takamasa , Hosoyama Akira , Ohji Shoko , Yamazoe Atsushi , Ito Masako , Takahata Yoh , Suzuki Ken-ichiro , Fujita Nobuyuki
Published: November 2015

A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.
Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22T
Authors: Lee Kevin C. Y. , Morgan Xochitl C. , Power Jean F. , Dunfield Peter F. , Huttenhower Curtis , Stott Matthew B.
Published: November 2015

Strain K22T is the type species of the recently- described genus Pyrinomonas, in subdivision 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014; 64(1):220–7). It was isolated from geothermally-heated soil from Mt. Ngauruhoe, New Zealand, using low-nutrient medium. P. methylaliphatogenes K22T has a chemoheterotrophic metabolism; it can hydrolyze a limited range of simple carbohydrates and polypeptides. Its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether lipids. It is obligately aerobic, thermophilic, moderately acidophilic, and non-spore-forming. The 3,788,560 bp genome of P. methylaliphatogenes K22T has a G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding RNA genes. Genomic analysis was consistent with nutritional requirements; in particular, the identified transporter classes reflect the oligotrophic nature of this strain.
Comparing Breast Cancer Outcomes Between Medicaid and the Ohio Breast and Cervical Cancer Early Detection Program
Authors: Koroukian Siran M. , Bakaki Paul M. , Schluchter Mark , Owusu Cynthia , Cooper Gregory S. , Flocke Susan A.
Published: November 2015

Compared with women who did not participate in the Breast and Cervical Cancer Program (BCCEDP), BCCEDP participants experienced earlier breast cancer stage at diagnosis, shorter time to treatment initiation, and increased survival benefits.
Screening for Pain in the Ambulatory Cancer Setting: Is 0-10 Enough?
Authors: LeBaron Virginia T. , Blonquist Traci M. , Hong Fangxin , Halpenny Barbara , Berry Donna L.
Published: November 2015

Asking about pain frequency and intensity and reconsidering threshold values on pain intensity scales may be practical strategies to better identify patients with cancer who have relevant pain.
Clinical Trial Participants With Metastatic Renal Cell Carcinoma Differ From Patients Treated in Real-World Practice
Authors: Mitchell Aaron P. , Harrison Michael R. , Walker Mark S. , George Daniel J. , Abernethy Amy P. , Hirsch Bradford R.
Published: November 2015

Patients with mRCC treated with tyrosine kinase inhibitors in real-world clinical practice are sicker than those enrolled onto pivotal clinical trials, and more than one third are trial ineligible.
Common Sense or Gun Control? Political Communication and News Media Framing of Firearm Sale Background Checks After Newtown
Authors: McGinty Emma E. , Wolfson Julia A. , Sell Tara Kirk , Webster Daniel W.
Published: November 2015

Gun violence is a critical public health problem in the United States, but it is rarely at the top of the public policy agenda. The 2012 mass shooting in Newtown, Connecticut, opened a rare window of opportunity to strengthen firearm policies in the United States. In this study, we examine the American public's exposure to competing arguments for and against federal- and state-level universal background check laws, which would require a background check prior to every firearm sale, in a large sample of national and regional news stories (n = 486) published in the year following the Newtown shooting. Competing messages about background check laws could influence the outcome of policy debates by shifting support and political engagement among key constituencies such as gun owners and conservatives. We found that news media messages in support of universal background checks were fact-based and used rational arguments, and opposing messages often used rights-based frames designed to activate the core values of politically engaged gun owners. Reframing supportive messages about background check policies to align with gun owners' and conservatives' core values could be a promising strategy to increase these groups' willingness to vocalize their support for expanding background checks for firearm sales.
The Politics of Native American Health Care and the Affordable Care Act
Authors: Skinner Daniel
Published: November 2015

This article examines an important but largely overlooked dimension of the Patient Protection and Affordable Care Act (ACA), namely, its significance for Native American health care. The author maintains that reading the ACA against the politics of Native American health care policy shows that, depending on their regional needs and particular contexts, many Native Americans are well-placed to benefit from recent Obama-era reforms. At the same time, the kinds of options made available by the ACA constitute a departure from the service-based (as opposed to insurance-based) Indian Health Service (IHS). Accordingly, the author argues that ACA reforms—private marketplaces, Medicaid expansion, and accommodations for Native Americans—are best read as potential “supplements” to an underfunded IHS. Whether or not Native Americans opt to explore options under the ACA will depend in the long run on the quality of the IHS in the post-ACA era. Beyond understanding the ACA in relation to IHS funding, the author explores how Native American politics interacts with the key tenets of Obama-era health care reform—especially “affordability”—which is critical for understanding what is required from and appropriate to future Native American health care policy making.
What Health Care Reform Means for Immigrants: Comparing the Affordable Care Act and Massachusetts Health Reforms
Authors: Joseph Tiffany D.
Published: November 2015

The 2010 Patient Protection and Affordable Care Act (ACA) was passed to provide more affordable health coverage to Americans beginning in 2014. Modeled after the 2006 Massachusetts health care reform, the ACA includes an individual mandate, Medicaid expansion, and health exchanges through which middle-income individuals can purchase coverage from private insurance companies. However, while the ACA provisions exclude all undocumented and some documented immigrants, Massachusetts uses state and hospital funds to extend coverage to these groups. This article examines the ACA reform using the Massachusetts reform as a comparative case study to outline how citizenship status influences individuals' coverage options under both policies. The article then briefly discusses other states that provide coverage to ACA-ineligible immigrants and the implications of uneven ACA implementation for immigrants and citizens nationwide.
Longitudinal micro-CT provides biomarkers of lung disease that can be used to assess the effect of therapy in preclinical mouse models, and reveal compensatory changes in lung volume
Authors: Vande Velde Greetje , Poelmans Jennifer , De Langhe Ellen , Hillen Amy , Vanoirbeek Jeroen , Himmelreich Uwe , Lories Rik J.
Published: November 2015

In vivo lung micro-computed tomography (micro-CT) is being increasingly embraced in pulmonary research because it provides longitudinal information on dynamic disease processes in a field in which ex vivo assessment of experimental disease models is still the gold standard. To optimize the quantitative monitoring of progression and therapy of lung diseases, we evaluated longitudinal changes in four different micro-CT-derived biomarkers [aerated lung volume, lung tissue (including lesions) volume, total lung volume and mean lung density], describing normal development, lung infections, inflammation, fibrosis and therapy. Free-breathing mice underwent micro-CT before and repeatedly after induction of lung disease (bleomycin-induced fibrosis, invasive pulmonary aspergillosis, pulmonary cryptococcosis) and therapy (imatinib). The four lung biomarkers were quantified. After the last time point, we performed pulmonary function tests and isolated the lungs for histology. None of the biomarkers remained stable during longitudinal follow-up of adult healthy mouse lungs, implying that biomarkers should be compared with age-matched controls upon intervention. Early inflammation and progressive fibrosis led to a substantial increase in total lung volume, which affects the interpretation of aerated lung volume, tissue volume and mean lung density measures. Upon treatment of fibrotic lung disease, the improvement in aerated lung volume and function was not accompanied by a normalization of the increased total lung volume. Significantly enlarged lungs were also present in models of rapidly and slowly progressing lung infections. The data suggest that total lung volume changes could partly reflect a compensatory mechanism that occurs during disease progression in mice. Our findings underscore the importance of quantifying total lung volume in addition to aerated lung or lesion volumes to accurately document growth and potential compensatory mechanisms in mouse models of lung disease, in order to fully describe and understand dynamic processes during lung disease onset, progression and therapy. This is highly relevant for the translation of therapy evaluation results from preclinical studies to human patients.
The NF-κB-modulated microRNAs miR-195 and miR-497 inhibit myoblast proliferation by targeting Igf1r, Insr and cyclin genes
Authors: Wei Wei , Zhang Wei-Ya , Bai Jian-Bo , Zhang Hai-Xin , Zhao Yuan-Yuan , Li Xin-Yun , Zhao Shu-Hong
Published: November 2015

MicroRNAs (miRNAs) play important roles in the development of skeletal muscle. In our previous study, expression of miR-195 and miR-497 were shown to be upregulated during muscle development in pigs. In this study, we investigated the roles of these two miRNAs in myogenesis and analyzed their transcriptional regulation. Our results showed that miR-195 and miR-497 were upregulated during muscle development and myoblast differentiation. Moreover, miR-195 and miR-497 inhibited proliferation but not differentiation in C2C12 cells. Further investigation revealed that Igf1r, Insr, Ccnd2 and Ccne1 were directly targeted by miR-195 and miR-497 in myoblasts. In addition, we confirmed that miR-195 and miR-497, which shared the similar expression profiling, were negatively regulated by nuclear factor κB (NF-κB) in both myoblasts and skeletal muscle tissue. Our data illustrate that the signaling pathway NF-κB–miR-195/497–Igf1r/Insr-Ccnd2/Ccne1 plays important roles in myogenesis. Our study provides novel evidence for the roles of miR-195 and miR-497 in muscle development.
Drosophila Rabex-5 restricts Notch activity in hematopoietic cells and maintains hematopoietic homeostasis
Authors: Reimels Theresa A. , Pfleger Cathie M.
Published: November 2015

Hematopoietic homeostasis requires the maintenance of a reservoir of undifferentiated blood cell progenitors and the ability to replace or expand differentiated blood cell lineages when necessary. Multiple signaling pathways function in these processes, but how their spatiotemporal control is established and their activity is coordinated in the context of the entire hematopoietic network are still poorly understood. We report here that loss of the gene Rabex-5 in Drosophila causes several hematopoietic abnormalities, including blood cell (hemocyte) overproliferation, increased size of the hematopoietic organ (the lymph gland), lamellocyte differentiation and melanotic mass formation. Hemocyte-specific Rabex-5 knockdown was sufficient to increase hemocyte populations, increase lymph gland size and induce melanotic masses. Rabex-5 negatively regulates Ras, and we show that Ras activity is responsible for specific Rabex-5 hematopoietic phenotypes. Surprisingly, Ras-independent Notch protein accumulation and transcriptional activity in the lymph gland underlie multiple distinct hematopoietic phenotypes of Rabex-5 loss. Thus, Rabex-5 plays an important role in Drosophila hematopoiesis and might serve as an axis coordinating Ras and Notch signaling in the lymph gland.
Activated microglia cause reversible apoptosis of pheochromocytoma cells, inducing their cell death by phagocytosis
Authors: Hornik Tamara C. , Vilalta Anna , Brown Guy C.
Published: November 2015

Some apoptotic processes, such as phosphatidylserine exposure, are potentially reversible and do not necessarily lead to cell death. However, phosphatidylserine exposure can induce phagocytosis of a cell, resulting in cell death by phagocytosis: phagoptosis. Phagoptosis of neurons by microglia might contribute to neuropathology, whereas phagoptosis of tumour cells by macrophages might limit cancer. Here, we examined the mechanisms by which BV-2 microglia killed co-cultured pheochromocytoma (PC12) cells that were either undifferentiated or differentiated into neuronal cells. We found that microglia activated by lipopolysaccharide rapidly phagocytosed PC12 cells. Activated microglia caused reversible phosphatidylserine exposure on and reversible caspase activation in PC12 cells, and caspase inhibition prevented phosphatidylserine exposur and decreased subsequent phagocytosis. Nitric oxide was necessary and sufficient to induce the reversible phosphatidylserine exposure and phagocytosis. The PC12 cells were not dead at the time they were phagocytised, and inhibition of their phagocytosis left viable cells. Cell loss was inhibited by blocking phagocytosis mediated by phosphatidylserine, MFG-E8, vitronectin receptors or P2Y6 receptors. Thus, activated microglia can induce reversible apoptosis of target cells, which is insufficient to cause apoptotic cell death, but sufficient to induce their phagocytosis and therefore cell death by phagoptosis.
N-linked glycosylation plays a crucial role in the secretion of HMGB1
Authors: Kim Young Hun , Kwak Man Sup , Park Jun Bae , Lee Shin-Ae , Choi Ji Eun , Cho Hyun-Soo , Shin Jeon-Soo
Published: November 2015

HMGB1 protein is a delayed mediator of sepsis that is secreted to the extracellular milieu in response to various stimulants, inducing a pro-inflammatory response. HMGB1 is devoid of an endoplasmic reticulum (ER)-targeting signal peptide; hence, the mechanism of extracellular secretion is not completely understood, although HMGB1 is secreted after being subjected to post-translational modifications. Here, we identified the role of N-glycosylation of HMGB1 in extracellular secretion. We found two consensus (N37 and N134) and one non-consensus (N135) residues that were N-glycosylated in HMGB1 by performing liquid chromatography tandem mass spectrometry (LC-MS/MS) and analyzing for N-glycan composition and structure. Inhibition of N-glycosylation with tunicamycin resulted in a molecular shift of HMGB1 as assessed by gel electrophoresis. Non-glycosylated double mutant (N→Q) HMGB1 proteins (HMGB1N37Q/N134Q and HMGB1N37Q/N135Q) showed localization to the nuclei, strong binding to DNA, weak binding to the nuclear export protein CRM1 and rapid degradation by ubiquitylation. These mutant proteins had reduced secretion even after acetylation, phosphorylation, oxidation and exposure to pro-inflammatory stimuli. Taken together, we propose that HMGB1 is N-glycosylated, and that this is important for its DNA interaction and is a prerequisite for its nucleocytoplasmic transport and extracellular secretion.
The Ccl1–Kin28 kinase complex regulates autophagy under nitrogen starvation
Authors: Zhu Jing , Deng Shuangsheng , Lu Puzhong , Bu Wenting , Li Tian , Yu Li , Xie Zhiping
Published: November 2015

Starvation triggers global alterations in the synthesis and turnover of proteins. Under such conditions, the recycling of essential nutrients by using autophagy is indispensable for survival. By screening known kinases in the yeast genome, we newly identified a regulator of autophagy, the Ccl1–Kin28 kinase complex (the equivalent of the mammalian cyclin-H–Cdk7 complex), which is known to play key roles in RNA-polymerase-II-mediated transcription. We show that inactivation of Ccl1 caused complete block of autophagy. Interestingly, Ccl1 itself was subject to proteasomal degradation, limiting the level of autophagy during prolonged starvation. We present further evidence that the Ccl1–Kin28 complex regulates the expression of Atg29 and Atg31, which is crucial in the assembly of the Atg1 kinase complex. The identification of this previously unknown regulatory pathway sheds new light on the complex signaling network that governs autophagy activity.
Reciprocal regulation of alternative lineages by Rgs18 and its transcriptional repressor Gfi1b
Authors: Sengupta Ananya , Upadhyay Ghanshyam , Sen Sayani , Saleque Shireen
Published: November 2015

Appropriate diversification of cellular lineages from multi-potent progenitors is essential for normal development and homeostasis. The specification of erythroid and megakaryocytic lineages represents an especially vital developmental event whose molecular regulation remains incompletely defined. We now demonstrate the role of Rgs18, a GTPase-activating protein and transcriptional target of the repressor Gfi1b, in regulating these processes in mouse and human cells. Gfi1b stringently represses Rgs18 expression in erythroid cells, whereas, during megakaryocytic differentiation, declining Gfi1b levels facilitate a robust induction of Rgs18. Concordantly, alterations in Rgs18 expression produce disparate outcomes by augmenting megakaryocytic and potently suppressing erythroid differentiation and vice versa. These phenotypes reflect the differential impact of Rgs18 on signaling through p38 MAPK family proteins, and ERK1 and ERK2 (also known as MAPK3 and MAPK1, respectively) in the two lineages, which in turn alter the balance between the mutually antagonistic transcription factors Fli1 and Klf1. Overall, these results identify Rgs18 as a new and crucial effector of Gfi1b that regulates downstream signaling and gene expression programs to orchestrate erythro-megakaryocytic lineage choices. This dual role of Rgs18 in reciprocally regulating divergent lineages could exemplify generic mechanisms characteristic of multiple family members in different contexts.
BAR-SH3 sorting nexins are conserved interacting proteins of Nervous wreck that organize synapses and promote neurotransmission
Authors: Ukken Fiona P. , Bruckner Joseph J. , Weir Kurt L. , Hope Sarah J. , Sison Samantha L. , Birschbach Ryan M. , Hicks Lawrence , Taylor Kendra L. , Dent Erik W. , Gonsalvez Graydon B. , O'Connor-Giles Kate M.
Published: November 2015

Nervous wreck (Nwk) is a conserved F-BAR protein that attenuates synaptic growth and promotes synaptic function in Drosophila. In an effort to understand how Nwk carries out its dual roles, we isolated interacting proteins using mass spectrometry. We report a conserved interaction between Nwk proteins and BAR-SH3 sorting nexins, a family of membrane-binding proteins implicated in diverse intracellular trafficking processes. In mammalian cells, BAR-SH3 sorting nexins induce plasma membrane tubules that localize NWK2, consistent with a possible functional interaction during the early stages of endocytic trafficking. To study the role of BAR-SH3 sorting nexins in vivo, we took advantage of the lack of genetic redundancy in Drosophila and employed CRISPR-based genome engineering to generate null and endogenously tagged alleles of SH3PX1. SH3PX1 localizes to neuromuscular junctions where it regulates synaptic ultrastructure, but not synapse number. Consistently, neurotransmitter release was significantly diminished in SH3PX1 mutants. Double-mutant and tissue-specific-rescue experiments indicate that SH3PX1 promotes neurotransmitter release presynaptically, at least in part through functional interactions with Nwk, and might act to distinguish the roles of Nwk in regulating synaptic growth and function.
Feast or flee: bioelectrical regulation of feeding and predator evasion behaviors in the planktonic alveolateFavellasp. (Spirotrichia)
Authors: Echevarria Michael L. , Wolfe Gordon V. , Taylor Alison R.
Published: November 2015

Alveolate (ciliates and dinoflagellates) grazers are integral components of the marine food web and must therefore be able to sense a range of mechanical and chemical signals produced by prey and predators, integrating them via signal transduction mechanisms to respond with effective prey capture and predator evasion behaviors. However, the sensory biology of alveolate grazers is poorly understood. Using novel techniques that combine electrophysiological measurements and high-speed videomicroscopy we investigated the sensory biology of Favella sp., a model alveolate grazer, in the context of its trophic ecology. Favella sp. produced frequent rhythmic depolarizations (∼500 ms long) that caused backward swimming and are responsible for endogenous swimming patterns relevant to foraging. Contact of both prey cells and non-prey polystyrene microspheres at the cilia produced immediate mechano-stimulated depolarizations (∼500 ms long) that caused backward swimming, and likely underlie aggregative swimming patterns of Favella sp. in response to patches of prey. Contact of particles at the peristomal cavity that were not suitable for ingestion resulted in MSDs after a lag of ∼600 ms, allowing time for particles to be processed before rejection. Ingestion of preferred prey particles was accompanied by transient hyperpolarizations (∼1 s) that likely regulate this step of the feeding process. Predation attempts by the copepod Acartia tonsa elicited fast (∼20 ms) animal-like action potentials accompanied by rapid contraction of the cell to avoid predation. We have shown that the sensory mechanisms of Favella sp. are finely tuned to the type, location, and intensity of stimuli from prey and predators.
Differences in electrosensory anatomy and social behavior in an area of sympatry between two species of mormyrid electric fishes
Authors: Carlson Bruce A.
Published: November 2015

Sensory systems play a key role in social behavior by mediating the detection and analysis of communication signals. In mormyrid fishes, electric signals are processed within a dedicated sensory pathway, providing a unique opportunity to relate sensory biology to social behavior. Evolutionary changes within this pathway led to new perceptual abilities that have been linked to increased rates of signal evolution and species diversification in a lineage called ‘clade A’. Previous field observations suggest that clade-A species tend to be solitary and territorial, whereas non-clade-A species tend to be clustered in high densities suggestive of schooling or shoaling. To explore behavioral differences between species in these lineages in greater detail, I studied population densities, social interactions, and electric signaling in two mormyrid species, Gnathonemus victoriae (clade A) and Petrocephalus degeni (non-clade A), from Lwamunda Swamp, Uganda. P. degeni was found at higher population densities, but intraspecific diversity in electric signal waveform was greater in G. victoriae. In the laboratory, G. victoriae exhibited strong shelter-seeking behavior and competition for shelter, whereas P. degeni were more likely to abandon shelter in the presence of conspecifics as well as electric mimics of signaling conspecifics. In other words, P. degeni exhibited social affiliation whereas G. victoriae exhibited social competition. Further, P. degeni showed correlated electric signaling behavior whereas G. victoriae showed anti-correlated signaling behavior. These findings extend previous reports of social spacing, territoriality, and habitat preference among mormyrid species, suggesting that evolutionary divergence in electrosensory processing relates to differences in social behavior.
Sex- and melanic-specific variations in the oxidative status of adult tawny owls in response to manipulated reproductive effort
Authors: Emaresi Guillaume , Henry Isabelle , Gonzalez Esther , Roulin Alexandre , Bize Pierre
Published: November 2015

Oxidative stress, determined by the balance between the production of damaging reactive oxygen species (ROS) and antioxidant defences, is hypothesised to play an important role in shaping the cost of reproduction and life history trade-offs. To test this hypothesis, we manipulated reproductive effort in 94 breeding pairs of tawny owls (Strix aluco) to investigate the sex- and melanic-specific effects on markers of oxidative stress in red blood cells (RBCs). This colour polymorphic bird species shows sex-specific division of labour and melanic-specific history strategies. Brood sizes at hatching were experimentally enlarged or reduced to increase or decrease reproductive effort, respectively. We obtained an integrative measure of the oxidative balance by measuring ROS production by RBC, intracellular antioxidant gluthatione levels (tGSH) and membrane resistance to ROS. We found that light melanic males (the sex assuming offspring food provisioning) produced more ROS than darker conspecifics, but only when rearing an enlarged brood. In both sexes, light melanic individuals had also a larger pool of intracellular antioxidant glutathione than darker owls under relaxed reproductive conditions (i.e. reduced brood), but not when investing substantial effort in current reproduction (enlarged brood). Finally, resistance to oxidative stress was differently affected by the brood size manipulation experiment in males and females independently of their plumage coloration. Altogether, our results support the hypothesis that reproductive effort can alter the oxidative balance in a sex- and colour-specific way. This further emphasizes the close link between melanin-based coloration and life history strategies.
Fabrication of Self-Organized, Two-Dimensional Diluted Magnetic Semiconductors Based on Organic–Inorganic Layered Perovskite-Type Compounds
Authors: Kubota Kohei , Koshimizu Masanori , Saito Hirotoshi , Asai Keisuke
Published: November 2015

We have fabricated diluted magnetic semiconductors (DMSs) based on organic–inorganic layered perovskite-type compounds, in which multiple quantum well structures were formed. DMSs were synthesized by substituting a small fraction of the Pb2+ ions in the inorganic layers with Mn2+ or Cu2+. XRD, ESR, and magnetization results indicate that the samples form mixed crystals. The Mn-doped samples exhibited paramagnetism down to 10 K, whereas the Cu-doped samples exhibited ferromagnetism at temperatures lower than ca. 15 K. In addition, a clear exciton peak was observed in the absorption spectrum of each sample. These results indicate that self-organized DMS quantum wells were successfully fabricated.
Isolation and Structural Characterization of a Metallacyclic Compound by Selective Protection of a Single CO Ligand in a Ruthenium Complex
Authors: Oyama Dai , Hamada Takashi , Ukawa Narumi , Mochizuki Ryuta , Takase Tsugiko
Published: November 2015

The metallacyclic compound was isolated by chemical reduction after selective protection of a single CO ligand in a dicarbonylruthenium(II) complex bearing the redox-active bidentate pyridyl ligand, 2-(2-pyridyl)-1,8-naphthyridine. Spectroscopic and X-ray structural analyses of the metallacycle revealed hydrogenation of the naphthyridine unit.
Simple Preparation and Characterization of Viscoelastic Gels Induced by Multiple Intermolecular Interactions Using Low-Molecular-Weight Species
Authors: Kubo Takuya , Kuroda Kenta , Naito Toyohiro , Mukai Sada-atsu , Sano Tomoharu , Akiyoshi Kazunari , Otsuka Koji
Published: November 2015

We report simple preparation of viscoelastic gels induced by multiple intermolecular interactions using low-molecular-weight aromatic sulfonates and alkylammoniums in water. The flow properties of the gels could be controlled between viscoelastic gel to high-viscosity liquid by changing the number of sulfonates and the length of alkyl chain among the components. Rheology evaluations of these viscoelastic materials showed significant differences of G′ and G′′ depending on the components. Also, spin–lattice relaxation, T1 in swollen-resin magic angle spinning 13C NMR well supported the differences of the viscoelastic gels in “hardness” according to the strength of hydrophobic interactions and π–π interactions contributed to the hydrogelation by alkyl chains and aromatic rings, respectively. Furthermore, we demonstrated a possibility for self-healing of a viscoelastic gel prepared with sodium 1,3,6-naphthalene trisulfonate and hexadecyltrimethylammonium bromide.
Ductility and Damping Characteristics of PVA-FRC Beam Elements
Authors: Noushini A. , Samali B. , Vessalas K.
Published: November 2015

The structural behaviour of reinforced concrete beams incorporating polyvinyl alcohol (PVA) fibres is investigated in this study. A total of 10 reinforced concrete beams have been tested in order to investigate how the structural characteristics (i.e. ductility, energy dissipation capacity and damping ratio) of concrete beam elements are affected by addition of a certain amount of PVA fibres into the concrete. The structural properties and behaviour of PVA-FRC beams were assessed under the action of both monotonic and cyclic loads. Four-point static flexural, three-point cyclic and impact resonant frequency tests were conducted on PVA-FRC beams and results of which are compared with conventional reinforced concrete (RC) beams. Experimental results show that PVA fibre addition to the mix, generally, improves the ductility and damping ratio of the elements. Furthermore, PVA-FRC beams showed higher stiffness degradation rate and higher capacity to maintain their stiffness during the test.
Application of the Component Method to Aluminum Alloy Gusset Joints
Authors: Guo Xiaonong , Xiong Zhe , Luo Yongfeng , Qiu Liqiu , Huang Weijia
Published: November 2015

The stiffness of aluminium alloy gusset (AAG) joints plays a key role in the global buckling behaviour of single-layer reticulated shells. In this paper, the bending stiffness of AAG joints is mainly analysed by using the component method. Based on the M-φ curves obtained from a previous experimental program, a four-linear mathematical model which is used to evaluate the bending stiffness behaviour of AAG joints is proposed. To calculate the four-linear mathematical model, the deformation mechanism of AAG joints is discussed and the component model for the joint bending stiffness is developed. According to theoretical derivations and extensive finite element simulations, the formulae to estimate the whole range bending stiffness of AAG joints are presented. Finally, the applicability of the theoretical formulae is verified by comparing the theoretical results with the experimental results.
Shake Table Testing and Numerical Analysis of Transformer Substations Including Main Plant and Electrical Equipment Interaction
Authors: Wen Bo , Taciroglu Ertugrul , Niu Ditao
Published: November 2015

Transformer substations are among the most significant components of an electric power distribution system. These critical elements must remain operational during and after any extreme event, especially a severe earthquake. In past studies, the interaction between the main plant and the electrical equipment (EE) in a transformer substation was usually ignored. While a few considered this interaction through numerical simulations, there were no experimental studies to validate the findings. The aim of the present paper is to analyze the seismic reaction of a substation with explicit consideration of the dynamic interaction between the main plant and the EE mounted inside—achieved through a shaking table test and numerical simulations. A 1:8 scale model of a transformer substation plant with EE on its second floor is built and tested on a shaking table. Dynamic response data are gathered during seismic excitations of the substation, with and without the EE. These measurements and the corresponding validated numerical simulations clearly showed that there is obvious interaction between the plant and the EE. The stronger ground motions lead to a higher amplification of the seismic responses of the plant and the EE; and the observed acceleration amplification factors of the EE on the main plant are significantly greater than the factors recommended in the codes. In addition, the study shows that achieving the common performance objective of “ strong columns and weak beams,” may not be possible without explicitly considering the EE-main plant interaction effects, which cause the higher demands to migrate towards the column-ends. As such, those areas should be strengthened when designing substations against earthquakes.
Experimental Investigation of Non-Normality of Thermoacoustic Interaction in an Electrically Heated Rijke Tube
Authors: Mariappan Sathesh , Sujith R. I. , Schmid Peter J.
Published: November 2015

An experimental investigation of the non-normal nature of thermoacoustic interactions in an electrically heated horizontal Rijke tube is performed. Since non-normality and the associated transient growth are linear phenomena, the experiments have to be confined to the linear regime. The bifurcation diagram for the subcritical Hopf bifurcation into a limit cycle behavior has been determined, after which the amplitude levels, for which the system acts linearly, have been identified for different power inputs to the heater. There are two main objectives for this experimental investigation. The first one deals with the extraction of the linear eigenmodes associated with the acoustic pressure from experimental data. This is accomplished by the Dynamic Mode Decomposition (DMD) technique applied in the linear regime. The non-orthogonality between the eigenmodes is determined for various values of heater power. The second objective is to identify evidence of transient perturbation growth in the system. The total acoustic energy in the duct has been monitored as the thermoacoustic system evolves from its initial condition. Transient growth, on the order of previous theoretical studies, has been found, and its parameteric dependence on amplitude ratio and phase angle of the initial eigenmode components has been determined. This study represents the first experimental confirmation of non-normality in thermoacoustic systems.
Analysis the ECFM-3Z Combustion Model for Simulating the Combustion Process and Emission Characteristics in a HSDI Diesel Engine
Authors: Mobasheri Raouf
Published: November 2015

An advanced CFD simulation has been performed to analyze the ECFM-3Z (Extended Coherent Flame Model-3Z) combustion model for simulating the combustion process and emission characteristics in a high speed direct injection (HSDI) diesel engine. A four cylinders, HSDI diesel engine based on a Ford production engine with a 2nd generation Delphi common rail fuel injection system has been modeled in this research. 3D CFD simulation was carried out from intake valve closing (IVC) to exhaust valve opening (EVO). A good agreement of calculated and measured in-cylinder pressure trace as well as pollutant formation trends could be observed for all investigated operating points. Based on the confidence gained from validation, the study is extended to evaluate the effect of fuel injection timing on engine performance and emissions. For this purpose, a comprehensive study of the effect of injection timing with respect to performance and emissions has been considered. Three main injection timing, (1) 2.65 BTDC, (2) 0.65 BTDC and (3) 1.35 ATDC, all with 30 crank angle pilot separations has been used to investigate the effect of the injection timing. The results show that the current methodology can be applied as a beneficial tool for analyzing the parameters of the diesel combustion under HSDI operating condition.
An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions
Authors: Sengupta Raghuvir N. , Van Schie Sabine N.S. , Giambaşu George , Dai Qing , Yesselman Joseph D. , York Darrin , Piccirilli Joseph A. , Herschlag Daniel
Published: November 2015

Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such “off-pathway” species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2′- and 3′-deoxy (–H) and −amino (–NH2) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3′-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2′-OH making no interaction. Upon S binding, a rearrangement occurs that allows both –OH groups to contact a different active site metal ion, termed MC, to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function.
Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I
Authors: Lama Lodoe , Ryan Kevin
Published: November 2015

Many high-throughput small RNA next-generation sequencing protocols use 5′ preadenylylated DNA oligonucleotide adapters during cDNA library preparation. Preadenylylation of the DNA adapter's 5′ end frees from ATP-dependence the ligation of the adapter to RNA collections, thereby avoiding ATP-dependent side reactions. However, preadenylylation of the DNA adapters can be costly and difficult. The currently available method for chemical adenylylation of DNA adapters is inefficient and uses techniques not typically practiced in laboratories profiling cellular RNA expression. An alternative enzymatic method using a commercial RNA ligase was recently introduced, but this enzyme works best as a stoichiometric adenylylating reagent rather than a catalyst and can therefore prove costly when several variant adapters are needed or during scale-up or high-throughput adenylylation procedures. Here, we describe a simple, scalable, and highly efficient method for the 5′ adenylylation of DNA oligonucleotides using the thermostable RNA ligase 1 from bacteriophage TS2126. Adapters with 3′ blocking groups are adenylylated at >95% yield at catalytic enzyme-to-adapter ratios and need not be gel purified before ligation to RNA acceptors. Experimental conditions are also reported that enable DNA adapters with free 3′ ends to be 5′ adenylylated at >90% efficiency.
Περί των κοττιστών ήτοι των κυβιστών παρά Βυζαντινοίς
Authors: ΕΥΣΤΡΑΤΙΑΔΗΣ Μιχαήλ Π.
Published: November 2015

no abstract
Ευάγγελος Στράτης
Authors: ΦΙΛΑΔΕΛΦΕΥΣ Αλέξανδρος
Published: November 2015

no abstract
Μεσαιωνικά μνημεία Ωρωπού και Συκαμίνου
Authors: ΟΡΛΑΝΔΟΣ Αναστάσιος Κ.
Published: November 2015

no abstract
Εργασίαι αναστυλώσεως και συντηρήσεως βυζαντινών μνημείων
Authors: ΧΡΙΣΤΙΑΝΙΚΗ ΑΡΧΑΙΟΛΟΓΙΚΗ ΕΤΑΙΡΕΙΑ (ΧΑΕ)
Published: November 2015

no abstract