bluuebunny/crossref_metadata_2025 huggingface dataset:
A Research of Pyogenic Granuloma Genesis Factor With Immunohistochemical Analysis
Authors: Park Si Hyun , Lee Jun Ho , Tak Min Sung , Lee Hyun Ju , Choi Hwan Jun
Published: October 2017

Pyogenic granuloma (PG) is a type of vascular tumor for which the growth mechanism is poorly understood. Estrogen and progesterone may influence vascular malformations by increasing neovascularization in the lesions. Pregnancy tumor is a term for PG that occurs on the gingival mucosa of pregnant women in response to local irritation or injury. The etiology and pathogenesis of this phenomenon are not fully understood. Hormonal imbalance has been hypothesized to be responsible for the development of gingival hyper-reactive inflammatory responses. Moreover, it has been shown in vitro that the female sex hormone is a potential regulator of the production of several growth factors, such as vascular endothelial growth factor (VEGF), basic fibroblast growth factor, and nerve growth factor, in various cell types. Epidermal growth factor receptor (EGFR) is also involved in a signaling cascade that influences proliferation and other tumor-promoting activities, as well as the responsiveness to chemotherapy. The aim of this study was to examine the relationship between PG pathogenesis and hormone imbalance in 21 patients. All specimens were analyzed by immunohistochemical staining with hematoxylin and eosin for the following hormones: estrogen receptor, progesterone receptor, VEGF, and EGFR. The analysis of the specimens showed that estrogen receptor and EGFR were not associated with PG, while VEGF was statistically related to PG. In addition, there was no significantly difference between sex, tumor location, or pregnancy. There are few studies about correlation between the pathogenesis of PG and sex hormones or growth factors demonstrated via immunohistochemical analysis. The results of this study indicate that estrogen and progesterone do not influence the pathogenesis of PG; however, VEGF may be associated with the pathogenesis of PG.
Salinity-induced phenotypic plasticity in threespine stickleback sperm activation
Authors: Taugbøl Annette , Mazzarella Anna B. , Cramer Emily R. A. , Laskemoen Terje
Published: October 2017

Phenotypic expression may be and often is influenced by an organism's developmental environment, referred to as phenotypic plasticity. The sperm cells of teleosts have been found to be inactive in the seminal plasma and are activated by osmotic shock for most fish species, through release in either hypertonic (for marine fish) or hypotonic (for freshwater fish) water. If this is the case, the regulatory system of sperm mobility should be reversed in salt- and freshwater fish. We tested this hypothesis by first activating sperm of salt- and freshwater populations of threespine stickleback in salt- and freshwater. The sperm from saltwater stickleback could be activated in either salinity, which matches the freshwater colonization history of the species, whereas the sperm from the freshwater population acted as predicted by the osmotic shock theory and was activated in freshwater only. As the freshwater population used here was calculated to be thousands of years old, we went on to test whether the trait(s) were plastic and sperm from freshwater males still could be activated in saltwater after individuals were exposed to saltwater. After raising freshwater stickleback in saltwater, we found the mature males to have active sperm in both saltwater and freshwater. Further, we also found the sperm of wild-caught freshwater stickleback to be active in saltwater after exposing those mature males to saltwater for only 2 days. This illustrates that the ability for stickleback sperm to be activated in a range of water qualities is an environmentally induced plastic trait.
Ribosome flow model with extended objects
Authors: Zarai Yoram , Margaliot Michael , Tuller Tamir
Published: October 2017

We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called theribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including non-homogeneous transition rates along mRNA, the fact that every ribosome covers several codons, and the fact that ribosomes cannot overtake one another. The RFMEO is a mean-field approximation of an important model from statistical mechanics called thetotally asymmetric simple exclusion process with extended objects(TASEPEO). We demonstrate that the RFMEO describes biophysical aspects of translation better than previous mean-field approximations, and that its predictions correlate well with those of TASEPEO. However, unlike TASEPEO, the RFMEO is amenable to rigorous analysis using tools from systems and control theory. We show that the ribosome density profile along the mRNA in the RFMEO converges to a unique steady-state density that depends on the length of the mRNA, the transition rates along it, and the number of codons covered by every ribosome, but not on the initial density of ribosomes along the mRNA. In particular, the protein production rate also converges to a unique steady state. Furthermore, if the transition rates along the mRNA are periodic with a common period Tthen the ribosome density along the mRNA and the protein production rate converge to a unique periodic pattern with period T, that is, the model entrains to periodic excitations in the transition rates. Analysis and simulations of the RFMEO demonstrate several counterintuitive results. For example, increasing the ribosome footprint may sometimes lead to an increase in the production rate. Also, for large values of the footprint the steady-state density along the mRNA may be quite complex (e.g. with quasi-periodic patterns) even for relatively simple (and non-periodic) transition rates along the mRNA. This implies that inferring the transition rates from the ribosome density may be non-trivial. We believe that the RFMEO could be useful for modelling, understanding and re-engineering translation as well as other important biological processes.
Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid
Authors: Prozorov Tanya , Almeida Trevor P. , Kovács András , Dunin-Borkowski Rafal E.
Published: October 2017

The mapping of electrostatic potentials and magnetic fields in liquids using electron holography has been considered to be unrealistic. Here, we show that hydrated cells ofMagnetospirillum magneticumstrain AMB-1 and assemblies of magnetic nanoparticles can be studied using off-axis electron holography in a fluid cell specimen holder within the transmission electron microscope. Considering that the holographic object and reference wave both pass through liquid, the recorded electron holograms show sufficient interference fringe contrast to permit reconstruction of the phase shift of the electron wave and mapping of the magnetic induction from bacterial magnetite nanocrystals. We assess the challenges of performingin situmagnetization reversal experiments using a fluid cell specimen holder, discuss approaches for improving spatial resolution and specimen stability, and outline future perspectives for studying scientific phenomena, ranging from interparticle interactions in liquids and electrical double layers at solid–liquid interfaces to biomineralization and the mapping of electrostatic potentials associated with protein aggregation and folding.
Antifungal activity of water-stable copper-containing metal-organic frameworks
Authors: Bouson Supaporn , Krittayavathananon Atiweena , Phattharasupakun Nutthaphon , Siwayaprahm Patcharaporn , Sawangphruk Montree
Published: October 2017

Although metal-organic frameworks (MOFs) or porous coordination polymers have been widely studied, their antimicrobial activities have not yet been fully investigated. In this work, antifungal activity of copper-based benzene-tricarboxylate MOF (Cu-BTC MOF), which is water stable and industrially interesting, is investigated against
Candida albicans
,
Aspergillus niger
,
Aspergillus oryzae
and
Fusarium oxysporum
. The Cu-BTC MOF can effectively inhibit the growth rate of
C. albicans
and remarkably inhibit the spore growth of
A. niger
,
A. oryzae
and
F. oxysporum
. This finding shows the potential of using Cu-BTC MOF as a strong biocidal material against representative yeasts and moulds that are commonly found in the food and agricultural industries.
Genital interactions during simulated copulation among marine mammals
Authors: Orbach Dara N. , Kelly Diane A. , Solano Mauricio , Brennan Patricia L. R.
Published: October 2017

Genitalia are morphologically variable across many taxa and in physical contact during intromission, but little is known about how variation in form correlates with function during copulation. Marine mammals offer important insights into the evolutionary forces that act on genital morphology because they have diverse genitalia and are adapted to aquatic living and mating. Cetaceans have a fibroelastic penis and muscular vaginal folds, while pinnipeds have a baculum and lack vaginal folds. We examined copulatory fit in naturally deceased marine mammals to identify anatomical landmarks in contact during copulation and the potential depth of penile penetration into the vagina. Excised penises were artificially inflated to erection with pressurized saline and compared with silicone vaginal endocasts and within excised vaginas in simulated copulation using high-resolution, diffusible iodine-based, contrast-enhanced computed tomography. We found evidence suggestive of both congruent and antagonistic genital coevolution, depending on the species. We suggest that sexual selection influences morphological shape. This study improves our understanding of how mechanical interactions during copulation influence the shape of genitalia and affect fertility, and has broad applications to other taxa and species conservation.
Species identity and depth predict bleaching severity in reef-building corals: shall the deep inherit the reef?
Authors: Muir Paul R. , Marshall Paul A. , Abdulla Ameer , Aguirre J. David
Published: October 2017

Mass bleaching associated with unusually high sea temperatures represents one of the greatest threats to corals and coral reef ecosystems. Deeper reef areas are hypothesized as potential refugia, but the susceptibility of Scleractinian species over depth has not been quantified. During the most severe bleaching event on record, we found up to 83% of coral cover severely affected on Maldivian reefs at a depth of 3–5 m, but significantly reduced effects at 24–30 m. Analysis of 153 species' responses showed depth, shading and species identity had strong, significant effects on susceptibility. Overall, 73.3% of the shallow-reef assemblage had individuals at a depth of 24–30 m with reduced effects, potentially mitigating local extinction and providing a source of recruits for population recovery. Although susceptibility was phylogenetically constrained, species-level effects caused most lineages to contain some partially resistant species. Many genera showed wide variation between species, including
Acropora,
previously considered highly susceptible. Extinction risk estimates showed species and lineages of concern and those likely to dominate following repeated events. Our results show that deeper reef areas provide refuge for a large proportion of Scleractinian species during severe bleaching events and that the deepest occurring individuals of each population have the greatest potential to survive and drive reef recovery.
Evolution in temperature-dependent phytoplankton traits revealed from a sediment archive: do reaction norms tell the whole story?
Authors: Hinners Jana , Kremp Anke , Hense Inga
Published: October 2017

The high evolutionary potential of phytoplankton species allows them to rapidly adapt to global warming. Adaptations may occur in temperature-dependent traits, such as growth rate, cell size and life cycle processes. Using resurrection experiments with resting stages from living sediment archives, it is possible to investigate whether adaptation occurred. For this study, we revived resting cysts of the spring bloom dinoflagellate
Apocalathium malmogiense
from recent and 100-year-old sediment layers from the Gulf of Finland, and compared temperature-dependent traits of recent and historic strains along a temperature gradient. We detected no changes in growth rates and cell sizes but a significant difference between recent and historic strains regarding resting cyst formation. The encystment rate of recent strains was significantly lower compared with historic strains which we interpret as an indication of adaptation to higher and more rapidly increasing spring temperatures. Low encystment rates may allow for bloom formation even if the threshold temperature inducing a loss of actively growing cells through resting cyst formation is exceeded. Our findings reveal that phenotypic responses of phytoplankton to changing temperature conditions may include hidden traits such as life cycle processes and their regulation mechanisms. This study emphasizes the potential of living sediment archives to investigate plankton responses and adaptation to global warming.
The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham Cycle
Authors: Ebenhöh Oliver , Spelberg Stephanie
Published: October 2017

The photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham Cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle’s structure was fuelled by the findings of Gibbs and Kandler in 1956 and 1957, when they observed that radioactive14CO2was dynamically incorporated in hexoses in a very atypical and asymmetrical way, a phenomenon later termed the ‘photosynthetic Gibbs effect’. Now, it is widely accepted that the photosynthetic Gibbs effect is not in contradiction to the reaction scheme proposed by Calvin, Benson and Bassham, but the arguments given have been largely qualitative and hand-waving. To fully appreciate the controversy and to understand the difficulties in interpreting the Gibbs effect, it is illustrative to illuminate the history of the discovery of the Calvin-Benson-Bassham Cycle. We here give an account of central scientific advances and discoveries, which were essential prerequisites for the elucidation of the cycle. Placing the historic discoveries in the context of the modern textbook pathway scheme illustrates the complexity of the cycle and demonstrates why especially dynamic labelling experiments are far from easy to interpret. We conclude by arguing that only mathematical models based on a sound theory are capable of resolving conflicting interpretations and providing a consistent quantitative explanation.
Adult Neurogenesis Conserves Hippocampal Learning Capacity
Authors: Alam Md Jahangir , Kitamura Takashi , Saitoh Yoshito , Ohkawa Noriaki , Kondo Takashi , Inokuchi Kaoru
Published: October 2017

Memory coding strengthens synaptic efficacy in the hippocampus via a long-term potentiation (LTP)-like mechanism. Given that animals are able to store memories of everyday experiences, hippocampal circuits should be able to avoid saturation of overall synaptic weight to preserve learning capacity. However, the underlying mechanism for this is still poorly understood. Here, we show that adult neurogenesis in rats plays a crucial role in the maintenance of the hippocampal learning capacity for learning. Artificial saturation with hippocampal LTP impaired learning capacity in contextual fear conditioning, which then completely recovered after 14 days, when LTP had decayed to the basal level. Ablation of neurogenesis by X-ray irradiation delayed the recovery of learning capacity, while enhancement of neurogenesis using running wheel sped up the recovery. Thus, one benefit of ongoing adult neurogenesis is the maintenance of hippocampal learning capacity through homeostatic renewing of hippocampal memory circuits. Decreased neurogenesis in aged animals may underlie declines in cognitive function with aging.
Aqueous ethanol permeation across Sterlitech flat sheet aquaporin membranes
Authors: Lewis Jeremy , Alshami Ali
Published: October 2017

Aquaporin (Aqp) embedded membranes have become a topic of recent research due to the superior selectivity of Aqp to water and its acceptable flux. Most researchers have utilized Aqp membranes for water purification purposes such as reverse and forward osmosis desalination of sea and brackish water and wastewater treatment. This paper investigated the permeation of aqueous ethanol across commercial aquaporin membranes for possible applications in ethanol dehydration in the process and biofuel refining industries. The study revealed that rather than being selectively rejected, ethanol was able to diffuse through the membrane with minimal changes in composition from feed to permeate, even at low feed concentrations of ethanol. The total flux across the membranes were shown to average 3.86 liters/m2h (LMH). The presence of ethanol increased the relative rate of water transport across the membrane. When comparing total flux of pure water to aqueous ethanol solutions, the flux was higher for solutions containing any ethanol.
Whole genome sequence and comparative analysis ofBorrelia burgdorferiMM1
Authors: Jabbari Neda , Glusman Gustavo , Joesch-Cohen Lena M. , Reddy Panga Jaipal , Moritz Robert L. , Hood Leroy , Lausted Christopher G.
Published: October 2017

Lyme disease is caused by spirochaetes of theBorrelia burgdorferisensu lato genospecies. Complete genome assemblies are available for fewer than ten strains ofBorrelia burgdorferisensu stricto, the primary cause of Lyme disease in North America. MM1 is a sensu stricto strain originally isolated in the midwestern United States. Aside from a small number of genes, the complete genome sequence of this strain has not been reported. Here we present the complete genome sequence of MM1 in relation to other sensu stricto strains and in terms of its Multi Locus Sequence Typing. Our results indicate that MM1 is a new sequence type which contains a conserved main chromosome and 15 plasmids. Our results include the first contiguous 28.5 kb assembly of lp28-8, a linear plasmid carrying thevlsantigenic variation system, from aBorrelia burgdorferisensu stricto strain.
Genomic divergence footprints in the bracovirus ofCotesia sesamiaeidentified by targeted re-sequencing approach
Authors: Gauthier Jérémy , Gayral Philippe , Le Ru Bruno Pierre , Jancek Séverine , Dupas Stéphane , Kaiser Laure , Gyapay Gabor , Herniou Elisabeth A.
Published: October 2017

The African parasitoid waspCotesia sesamiaeis structured in contrasted populations showing differences in host range and the recent discovery of a specialist related species,C. typhae, provide a good framework to study the mechanisms that link the parasitoid and their host range. To investigate the genomic bases of divergence between these populations, we used a targeted sequencing approach on 24 samples. We targeted a specific genomic region encoding the bracovirus, which is deeply involved in the interaction with the host. High sequencing coverage was obtained for all samples allowing the study of genetic variations between wasp populations and species. Combining population genetic estimations, the diversity (π), the relative differentiation (FST) and the absolute differentiation (dxy), and branch-site dN/dS measures, we identified six divergent genes impacted by positive selection belonging to different gene families. These genes are potentially involved in host adaptation and in the specialization process. Fine scale analyses of the genetic variations also revealed deleterious mutations and large deletions on certain genes inducing pseudogenization and loss of function. These results highlight the crucial role of the bracovirus in the molecular interactions between the wasp and its hosts and in the evolutionary processes of specialization.
Neural signatures of dynamic emotion constructs in the human brain
Authors: Grootswagers Tijl , Kennedy Briana L. , Most Steven B. , Carlson Thomas A.
Published: October 2017

How is emotion represented in the brain: is it categorical or along dimensions? In the present study, we applied multivariate pattern analysis (MVPA) to magnetoencephalography (MEG) to study the brain’s temporally unfolding representations of different emotion constructs. First, participants rated 525 images on the dimensions of valence and arousal and by intensity of discrete emotion categories (happiness, sadness, fear, disgust, and sadness). Thirteen new participants then viewed subsets of these images within an MEG scanner. We used Representational Similarity Analysis (RSA) to compare behavioral ratings to the unfolding neural representation of the stimuli in the brain. Ratings of valence and arousal explained significant proportions of the MEG data, even after corrections for low-level image properties. Additionally, behavioral ratings of the discrete emotions fear, disgust, and happiness significantly predicted early neural representations, whereas rating models of anger and sadness did not. Different emotion constructs also showed unique temporal signatures. Fear and disgust – both highly arousing and negative – were rapidly discriminated by the brain, but disgust was represented for an extended period of time relative to fear. Overall, our findings suggest that 1) dimensions of valence and arousal are quickly represented by the brain, as are some discrete emotions, and 2) different emotion constructs exhibit unique temporal dynamics. We discuss implications of these findings for theoretical understanding of emotion and for the interplay of discrete and dimensional aspects of emotional experience.
Tree-ensemble analysis tests for presence of multifurcations in single cell data
Authors: Macnair Will , Roditi Laura De Vargas , Ganscha Stefan , Claassen Manfred
Published: October 2017

We introduce TreeTop, an algorithm for single-cell data analysis to identify and assess statistical significance of branch points in biological processes with possibly multi-level branching hierarchies. We demonstrate branch point identification for processes with varying topologies, including T cell maturation, B cell differentiation and hematopoiesis. Our analyses are consistent with recent experimental studies suggesting a shallow hierarchy of differentiation events in hematopoiesis, rather than the classical multi-level hierarchy.
Neocortical microdissection at columnar and laminar resolution for molecular interrogation
Authors: Kole Koen , Celikel Tansu
Published: October 2017

The heterogeneous organization of the mammalian neocortex poses a challenge to elucidate the molecular mechanisms underlying its physiological processes. Although high-throughput molecular methods are increasingly deployed in neuroscience, their anatomical specificity is often lacking. Here we introduce a targeted microdissection technique that enables extraction of high-quality RNA and proteins at high anatomical resolution from acutely prepared brain slices. We exemplify its utility by isolating single cortical columns and laminae from the mouse primary somatosensory (barrel) cortex. Tissues can be isolated from living slices in minutes, and the extracted RNA and protein are of sufficient quantity and quality to be used for RNA-sequencing and mass spectrometry. This technique will help to increase the anatomical specificity of molecular studies of the neocortex, and the brain in general as it is applicable to any brain structure that can be identified using optical landmarks in living slices.
Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank
Authors: Tikkanen Emmi , Gustafsson Stefan , Amar David , Shcherbina Anna , Waggott Daryl , Ashley Euan A. , Ingelsson Erik
Published: October 2017

Background

Hand grip strength, a simple indicator of muscular strength, has been associated with a range of health conditions, including fractures, disability, cardiovascular disease and premature death risk. Twin studies have suggested a high (50-60%) heritability, but genetic determinants are largely unknown.

Aims

In this study, our aim was to study genetic variation associated with muscular strength in a large sample of 334,925 individuals of European descent from the UK Biobank, and to evaluate shared genetic aetiology with and causal effects of grip strength on physical and cognitive health.

Methods and Results

In our discovery analysis of 223,315 individuals, we identified 101 loci associated with grip strength at genome-wide significance (P<5×10−8). Of these, 64 were associated (P<0.01 and consistent direction) also in the replication dataset (N=111,610). Many of the lead SNPs were located in or near genes known to have a function in developmental disorders (FTO, SLC39A8, TFAP2B, TGFA, CELF1, TCF4, BDNF, FOXP1, KIF1B, ANTXR2), and one of the most significant genes based on a gene-based analysis (ATP2A1) encodes SERCA1, the critical enzyme in calcium uptake to the sarcoplasmic reticulum, which plays a major role in muscle contraction and relaxation. Further, we demonstrated a significant enrichment of gene expression in brain-related transcripts among grip strength associations. Finally, we observed inverse genetic correlations of grip strength with cardiometabolic traits, and positive correlation with parents’ age of death and education; and showed that grip strength was causally related to fitness, physical activity and other indicators of frailty, including cognitive performance scores.

Conclusions

In our study of over 330,000 individuals from the general population, the genetic findings for hand grip strength suggest an important role of the central nervous system in strength performance. Further, our results indicate that maintaining good muscular strength is important for physical and cognitive performance and healthy aging.
Simple nanofluidic devices for high-throughput, non-equilibrium studies at the single-molecule level
Authors: Fijen Carel , Fontana Mattia , Lemay Serge G. , Mathwig Klaus , Hohlbein Johannes
Published: October 2017

Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. Probing chemical and biological interactions and reactions with high throughput and time resolution, however, remains challenging and often requires surface-immobilized entities. Here, utilizing camera-based fluorescence microscopy, we present glass-made nanofluidic devices in which fluorescently labelled molecules flow through nanochannels that confine their diffusional movement. The first design features an array of parallel nanochannels for high-throughput analysis of molecular species under equilibrium conditions allowing us to record 200.000 individual localization events in just 10 minutes. Using these localizations for single particle tracking, we were able to obtain accurate flow profiles including flow speeds and diffusion coefficients inside the channels.

A second design featuring a T-shaped nanochannel enables precise mixing of two different species as well as the continuous observation of chemical reactions. We utilized the design to visualize enzymatically driven DNA synthesis in real time and at the single-molecule level. Based on our results, we are convinced that the versatility and performance of the nanofluidic devices will enable numerous applications in the life sciences.
Origins of fractional control in regulated cell death
Authors: Santos Luís C. , Vogel Robert , Chipuk Jerry E. , Birtwistle Marc R. , Stolovitzky Gustavo , Meyer Pablo
Published: October 2017

Individual cells in clonal populations often respond differently to environmental changes; for binary phenotypes, such as cell death, this can be measured as a fractional response. These types of responses have been attributed to cell-intrinsic stochastic processes and variable abundances of biochemical constituents, such as proteins, but the influence of organelles has yet to be determined. We use the response to TNF-related apoptosis inducing ligand (TRAIL) and a new statistical framework for determining parameter influence on cell-to-cell variability through the inference of variance explained, DEPICTIVE, to demonstrate that variable mitochondria abundance correlates with cell survival and determines the fractional cell death response. By quantitative data analysis and modeling we attribute this effect to variable effective concentrations at the mitochondria surface of the pro-apoptotic protein Bax. Further, we demonstrate that inhibitors of antiapoptotic Bcl-2 family proteins, used in cancer treatment, may increase the diversity of cellular responses, enhancing resistance to treatment.
Motility in multicellularChlamydomonas reinhardtii(Chlamydomonadales, Chlorophyceae)
Authors: Boyd Margrethe , Rosenzweig Fran , Herron Matthew
Published: October 2017

The advent of multicellularity was a watershed event in the history of life, yet the transition from unicellularity to multicellularity is not well understood. Multicellularity opens up opportunities for innovations in intercellular communication, cooperation, and specialization, which can provide selective advantages under certain ecological conditions. The unicellular algaChlamydomonas reinhardtiihas never had a multicellular ancestor yet it is closely related to the volvocine algae, a clade containing taxa that range from simple unicells to large, specialized multicellular colonies. Simple multicellular structures have been observed to evolve inC. reinhardtiiin response to predation or to settling rate-based selection. Structures formed in response to predation consist of individual cells grouped within a shared transparent extracellular matrix. Evolved isolates form such structures obligately under culture conditions in which their wild type ancestors do not, indicating that newly-evolved multicellularity is heritable.C. reinhardtiiis capable of photosynthesis, and possesses an eyespot and two flagella with which it moves towards or away from light in order to optimize input of radiant energy. Motility contributes toC. reinhardtiifitness because it allows cells or colonies to achieve this optimum. Utilizing phototaxis to assay motility, we determined that newly evolved multicellular strains do not exhibit significant directional movement, even though the flagellae of their constituent unicells are present and active. InC. reinhardtiithe first steps towards multicellularity in response to predation appear to result in a trade-off between motility and differential survivorship, a trade-off that must overcome by further genetic change to ensure the long-term success of the new multicellular organism.
Evolutionary variance analysis of the Glycoside Hydrolase Family 13: Structural evidence in classification and evolution
Authors: Hleap Jose Sergio , Blouin Christian
Published: October 2017

Glycoside Hydrolase Family 13 (GH13) structures are responsible for the hydrolysis of starch into smaller carbohydrates. They important in industrial applications and evolutionary studies. This family has been thoroughly documented in the the Carbohydrate-Active enZYmes Database (CAZY), and divided into subfamilies based mainly in sequence information. Here we give structural evidence into GH13 classification and evolution using structural information. Here we proposed a novel method that is sensitive enough to identify miss-classifications, or to provide evidence for further partition that can be of interests to bio-engineers and evolutionary biologists. We also introduced a method to explore the relative importance of residues with respect to the overall deformation that it causes to the overall structure in an evolutionary time scale. We found that the GH13 family can be classified into three main structural groups. There is a hierarchical structure within these clusters that can be use to inform other classification schemes. We also found that by using structural information, subtle structural shifts can be identified and that can be missed in sequence/phylogeny-only based classifications. When each structural group is explored, we found that identifying the most structurally variable sites can lead to identification of functionally (both catalytically and structurally) important residues.
A valence-selective X-ray fluorescence holography study of an yttrium oxide thin film
Authors: Stellhorn J. R. , Hosokawa S. , Happo N. , Tajiri H. , Matsushita T. , Kaminaga K. , Fukumura T. , Hasegawa T. , Hayashi K.
Published: October 2017

The first direct valence-selective structure determination by X-ray fluorescence holography is reported. The method is applied to investigate an epitaxial thin film of the rare earth monoxide YO, which has recently been synthesized by pulsed laser deposition. The surface of the sample is easily oxidized to Y2O3. In order to separate the structural information connected with the two different valence states of Y, the X-ray fluorescence holography measurements were performed close to the Y K absorption edge. Using the shift of the absorption edge for the different valence states, very different relative contributions of YO and Y2O3 are obtained. Thus, it is possible to distinguish the crystal structures of YO and Y2O3 in the thin-film sample.
Big data application framework and its feasibility analysis in library
Authors: Li Jun , Lu Ming , Dou Guowei , Wang Shanyong
Published: October 2017

Purpose

The purpose of this study is to introduce the concept of big data and provide a comprehensive overview to readers to understand big data application framework in libraries.

Design/methodology/approach

The authors first used the text analysis and inductive analysis method to understand the concept of big data, summarize the challenges and opportunities of applying big data in libraries and further propose the big data application framework in libraries. Then they used questionnaire survey method to collect data from librarians to assess the feasibility of applying big data application framework in libraries.

Findings

The challenges of applying big data in libraries mainly include data accuracy, data reduction and compression, data confidentiality and security and big data processing system and technology. The opportunities of applying big data in libraries mainly include enrich the library database, enhance the skills of librarians, promote interlibrary loan service and provide personalized knowledge service. Big data application framework in libraries can be considered from five dimensions: human resource, literature resource, technology support, service innovation and infrastructure construction. Most libraries think that the big data application framework is feasible and tend to apply big data application framework. The main obstacles to prevent them from applying big data application framework is the human resource and information technology level.

Originality/value

This research offers several implications and practical solutions for libraries to apply big data application framework.
Identifying domain relevant user generated content through noise reduction: a test in a Chinese stock discussion forum
Authors: Yan Xiangbin , Li Yumei , Fan Weiguo
Published: October 2017

Purpose

Getting high-quality data by removing the noisy data from the user-generated content (UGC) is the first step toward data mining and effective decision-making based on ubiquitous and unstructured social media data. This paper aims to design a framework for revoking noisy data from UGC.

Design/methodology/approach

In this paper, the authors consider a classification-based framework to remove the noise from the unstructured UGC in social media community. They treat the noise as the concerned topic non-relevant messages and apply a text classification-based approach to remove the noise. They introduce a domain lexicon to help identify the concerned topic from noise and compare the performance of several classification algorithms combined with different feature selection methods.

Findings

Experimental results based on a Chinese stock forum show that 84.9 per cent of all the noise data from the UGC could be removed with little valuable information loss. The support vector machines classifier combined with information gain feature extraction model is the best choice for this system. With longer messages getting better classification performance, it has been found that the length of messages affects the system performance.

Originality/value

The proposed method could be used for preprocessing in text mining and new knowledge discovery from the big data.
Instructional coaches’ perceptions of professional development
Authors: Chaaban Youmen , Abu-Tineh Abdullah
Published: October 2017

Purpose

The purpose of this paper is to examine the development of a professional development (PD) model for educator growth and learning that is embedded into the school context in Qatar. Because the success of a PD program in practice cannot be judged against its theoretical underpinnings, the paper goes on to examine the perceptions of instructional coaches on the effectiveness of the PD model.

Design/methodology/approach

Through the use of a qualitative, constant comparative approach, data were collected from 19 instructional coaches through open-ended surveys followed by focus group interviews. The instructional coaches provided information about the strengths of the PD program, the challenges they faced in their day-to-day implementation of the program, and their suggestions for the improvement of the program’s implementation and outcomes.

Findings

The instructional coaches reported several strengths, which were compatible with the literature on effective PD. However, the challenges they faced were deeply rooted within the inherent structure of the program, in addition to external challenges at both the school and Ministry of Education levels. Thus, a general consensus on the way that the program should be implemented was reached.

Originality/value

The study revealed the complexity inherent in transferring research-based principles and theory into practice. It indicated that the components of PD programs interact within complex social settings.
Inclusive education in Georgia: current trends and challenges
Authors: Tchintcharauli Tinatin , Javakhishvili Nino
Published: October 2017

This article presents the first comprehensive study of the Georgian inclusive education system launched nationwide in 2006. An internationally recognised tool, the ‘Pathway to Inclusion – Barometer of Inclusive Education’, was applied within the country to highlight the current position of inclusive education in Georgia. The collected data were analysed against results from other countries. The comparison shows that Georgia has made progress towards inclusion; however, considerable work is still required to address drawbacks in policy and its implementation. The development of a monitoring system is advised as an effective means of advancement towards increased inclusion in the education system.
The use of questions to scaffold narrative coherence and cohesion
Authors: Silva Macarena , Cain Kate
Published: October 2017

We examined the quality of 4‐ to 6‐year‐olds' production of narratives from picture sequences. Children (N = 81) first viewed a narrative picture sequence and then completed the narrative production task in each of two orders: either before or after answering a set of questions about the core elements of the story. Narratives elicited after questions were more coherent than those produced before the questions. In contrast, task order did not influence the cohesion of narratives nor the accuracy of responses to questions. An independent measure of memory was related to the gains in narrative coherence after answering questions. The results are discussed in relation to the role of questions as a guide to the structural elements of a narrative and a scaffold for understanding.
C‐reactive protein gene polymorphisms (rs1205) in Asian Indian patients with Takayasu arteritis: Associations and phenotype correlations
Authors: Nair Aswin M. , Goel Ruchika , Hindhumati Mohan , Shah Krati , Chandana Puneet , Jayaseelan Visalakshi , Jayakanthan Kabeerdoss , Joseph George , Danda Sumita , Danda Debashish
Published: October 2017

Background/Purpose

Normal C‐reactive protein (CRP) in active Takayasu arteritis (TA) is a dilemma. We attempted to validate our pilot study finding of rs1205 in CRP gene being protective against TA.

Methods

Genomic DNA of 104 patients and 185 sex‐matched healthy controls were genotyped for rs1205 by Taqman assay. Clinical details, demography, angiographic and activity scores (Indian Takayasu arteritis score 2010) were recorded prospectively at baseline and during follow‐up visits for 12 months. Minor allele frequency (MAF) and genotype distribution between patients and controls as well as patient subgroups were compared using χ2 test with Bonferroni correction (pc) and logistic regression was performed to determine independent associations.

Results

The majority of patients (n = 84) and controls (n = 166) were females. MAF of T allele of rs1205 was less frequent in patients (27%) as compared to controls (37.6%), P = 0.013, pc = 0.026 with an odds ratio of 0.632 irrespective of gender. Frequency of CC genotype was higher in cases (53.8%) than controls (37.3%), P = 0.006, pc = 0.018. A dominant model of genotype‐phenotype association revealed CC to be associated with more frequent coronary arterial and ascending aorta involvement than the other genotypes clubbed together (P = 0.01 and P = 0.014, respectively). Blunted CRP response seems to be less frequent in patients with CC genotype (P = 0.064).

Conclusion

T allele of rs1205 in CRP gene was less frequent in TA. CC genotype was associated with involvement of coronary arteries and ascending aorta. CC genotype was less commonly associated with blunted CRP response (CT + TT > CC).
Potential biomarkers in patients with systemic sclerosis
Authors: Delle Sedie Andrea , Riente Lucrezia , Maggiorini Lavinia , Pratesi Federico , Tavoni Antonio , Migliorini Paola , Puxeddu Ilaria
Published: October 2017

Aim

Reduced capillary density is considered the hallmark of systemic sclerosis (SSc) leads to tissue hypoxia, a condition that usually induces angiogenesis. The objective of our study is to investigate mediators regulating angiogenesis in SSc and to correlate their levels with serological and clinical parameters.

Methods

vascular endothelial growth factor, fibroblast growth factor‐2, endostatin, thrombospondin‐1 and soluble vascular cell and intracellular adhesion molecules (sICAM‐1 and sVCAM‐1) were measured in sera of SSc and normal subjects by enzyme‐linked immunosorbent assay.

Results

Among the pro‐ and anti‐angiogenic mediators, endostatin was significantly higher in SSc than in the control subjects. Out of the proteases involved in endostatin production, elastase but not cathepsin‐L, was significantly increased in SSc patients. The soluble adhesion molecules sICAM‐1 and sVCAM‐1 were significantly increased and they occur in parallel. sICAM‐1, but not sVCAM‐1 positively correlates with the inflammatory markers C‐reactive protein (CRP) and erythrocyte sedimentation rate (ESR).

Conclusions

Endostatin, elastase and the soluble adhesion molecules (sICAM‐1 and sVCAM‐1) are potentially involved in the pathogenesis of SSc. Moreover, the significant correlation observed between sICAM‐1 and CRP and ESR indicates that sICAM‐1 might be a useful biomarker of the inflammatory state of the disease.
In vivo properties of the disaggregase function of J‐proteins and Hsc70 in Caenorhabditis elegans stress and aging
Authors: Kirstein Janine , Arnsburg Kristin , Scior Annika , Szlachcic Anna , Guilbride D. Lys , Morimoto Richard I. , Bukau Bernd , Nillegoda Nadinath B.
Published: October 2017

Protein aggregation is enhanced upon exposure to various stress conditions and aging, which suggests that the quality control machinery regulating protein homeostasis could exhibit varied capacities in different stages of organismal lifespan. Recently, an efficient metazoan disaggregase activity was identified in vitro, which requires the Hsp70 chaperone and Hsp110 nucleotide exchange factor, together with single or cooperating J‐protein co‐chaperones of classes A and B. Here, we describe how the orthologous Hsp70s and J‐protein of Caenorhabditis elegans work together to resolve protein aggregates both in vivo and in vitro to benefit organismal health. Using an RNAi knockdown approach, we show that class A and B J‐proteins cooperate to form an interactive flexible network that relocalizes to protein aggregates upon heat shock and preferentially recruits constitutive Hsc70 to disaggregate heat‐induced protein aggregates and polyQ aggregates that form in an age‐dependent manner. Cooperation between class A and B J‐proteins is also required for organismal health and promotes thermotolerance, maintenance of fecundity, and extended viability after heat stress. This disaggregase function of J‐proteins and Hsc70 therefore constitutes a powerful regulatory network that is key to Hsc70‐based protein quality control mechanisms in metazoa with a central role in the clearance of aggregates, stress recovery, and organismal fitness in aging.
The CYCLOCALYX study: Ovulatory cycle affects circulating compartments of the endothelial glycocalyx in blood
Authors: Hulde Nikolai , Rogenhofer Nina , Brettner Florian , Eckert Nicole C. , Götzfried Isabella , Nguyen Thu , Pagel Judith‐I. , Kammerer Tobias , Hofmann‐Kiefer Klaus F. , Schelling Gustav , Dendorfer Andreas , Rehm Markus , Thaler Christian J.
Published: October 2017

Problem

The endothelial glycocalyx (EGX) plays an important role in vascular integrity. Recently, increased levels of EGX components were detected in the circulating blood of healthy pregnant women and were related to the increased tendency to edema formation during gestation. However, the EGX has not yet been systematically studied in non‐pregnant women during ovulatory cycles.

Method of study

Serum levels of EGX components syndecan‐1, heparan sulfate, and hyaluronan in healthy women (n = 16) at 3 phases of the ovulatory cycle (early follicular phase, at ovulation, and mid‐luteal phase) were compared with a control group of healthy men (n = 10). Using immunofluorescence microscopy in cultured human umbilical vein endothelial cells, the effects of progesterone and estrogen on the EGX were measured.

Results

Syndecan‐1 increased from 11.1 ± 2.4 ng/mL at ovulation to 12.6 ± 2.3 ng/mL in mid‐luteal phase (P = .031) and of heparan sulfate from 663 ± 35 ng/mL to 782 ± 55 ng/mL (P = .011). In contrast to estrogen, there was a detrimental effect of progesterone on the EGX in HUVECs.

Conclusion

The relationship between the natural menstrual cycle and the EGX as an indicator of vascular permeability may provide a new explanation for premenstrual edema in healthy women. This may be an attendant phenomenon of a regular physiological process, the hormonal downregulation of the vascular barrier during pregnancy.