bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a visual approach in the exploration of shape grammars
Authors: Strobbe Tiemen , Pauwels Pieter , Verstraeten Ruben , De Meyer Ronald , Van Campenhout Jan 
Published: October 2015

AbstractThe concept of shape grammars has often been proposed to improve or support creative design processes. Shape grammar implementations have the potential to both automate parts of the design process and allow exploration of design alternatives. In many of the existing implementations, the main focus is either on capturing the rationale of a particular existing grammar or on allowing designers to develop a new grammar. However, little attention is typically given to the actual representation of the design space that can be explored in the interface of the implementation. With such representation, a shape grammar implementation could properly support designers who are still in the process of designing and may not yet have a clear shape grammar in mind. In this article, an approach and a proof-of-concept software system is proposed for a shape grammar implementation that provides a visual and interactive way to support design space exploration in a creative design process. We describe the method by which this software system can be used and focus on how designers can interact with the exploration process. In particular, we point out how the proposed approach realizes several important amplification strategies to support design space exploration.
Representativeness of the German National Register for Congenital Heart Defects: a clinically oriented analysis
Authors: Helm Paul C. , Koerten Marc-André , Abdul-Khaliq Hashim , Baumgartner Helmut , Kececioglu Deniz , Bauer Ulrike M. M. 
Published: October 2015

AbstractBackgroundApproximately 6000 children are born with CHD in Germany each year. It is increasingly rare that these children die from their chronic illness. In the present study, data recorded in the National Register for Congenital Heart Defects with respect to the prevalence of specific lesions and sex distribution are compared with that recorded in a published German prevalence study (Prevalence Study) and with the meta-analysis by van der Linde et al.MethodsA descriptive data analysis was performed using a minimal data set. The demographic data included sex and birth year; the medical data comprised the cardiovascular diagnosis according to the short list of the International Paediatric and Congenital Cardiac Code.ResultsAs the data analysis shows, the National Register is a clinical register including primarily clinical cases/cases relevant to healthcare. The prevalence values and sex ratios recorded in the register are closer to the values given in the literature than those determined by the Prevalence Study. Severe CHD was slightly over-represented in the National Register compared with the van der Linde et al meta-analysis. The deviations with respect to prevalence values are within an acceptable range.ConclusionWith its 48,000 patients, the National Register plays a unique and important role for research in the field of CHD. Samples from the National Register can be used as a gold standard for future studies, as the patient population registered in it can be considered representative of CHD in Germany and Europe.
Anxiety and depression in patients after surgery for head and neck cancer in Japan
Authors: Suzuki Miho , Deno Minako , Myers Mie , Asakage Takahiro , Takahashi Koji , Saito Kenichi , Mori Yoshiyuki , Saito Hiroto , Ichikawa Yuji , Yamamoto-Mitani Noriko , Miyashita Mitsunori 
Published: October 2015

AbstractObjective:The present study sought to examine the impact of physical symptoms, facial disfigurement, adequacy of preoperative information, and social support on anxiety and depression in Japanese patients with head and neck cancer (HNC) who had undergone surgery.Method:A cross-sectional study with 194 patients was conducted using a self-administered questionnaire. This instruments included the Hospital Anxiety and Depression Scale (HADS), the European Organization for Research and Treatment of Cancer (EORTC) Head and Neck cancer module (QLQ–H&N35), and a Social Support Scale developed by Okabayashi et al. (1997).Results:The majority (56.7%) had surgery two or more years before completing the questionnaire. More than 25% of respondents showed anxiety or depression. Higher levels of perceived social support were associated with lower rates of anxiety and depression (p < 0.01). Sensory problems were associated with anxiety, and reduced sexuality was associated with depression (p < 0.01). Perceived disfigurement and adequacy of preoperative information were not associated with anxiety or depression.Significance of Results:Survivors of HNC experience anxiety and depression for an extended period of time. Social support may alleviate the severity of these disorders. More research is needed to confirm the impact of facial disfigurement and that of the preoperative information provided by surgeons on psychological distress in HNC patients.
Metal-to-insulator switching in quantum anomalous Hall states
Authors: Kou Xufeng , Pan Lei , Wang Jing , Fan Yabin , Choi Eun Sang , Lee Wei-Li , Nie Tianxiao , Murata Koichi , Shao Qiming , Zhang Shou-Cheng , Wang Kang L. 
Published: October 2015

AbstractAfter decades of searching for the dissipationless transport in the absence of any external magnetic field, quantum anomalous Hall effect (QAHE) was recently achieved in magnetic topological insulator films. However, the universal phase diagram of QAHE and its relation with quantum Hall effect (QHE) remain to be investigated. Here, we report the experimental observation of the giant longitudinal resistance peak and zero Hall conductance plateau at the coercive field in the six quintuple-layer (Cr0.12Bi0.26Sb0.62)2Te3 film, and demonstrate the metal-to-insulator switching between two opposite QAHE plateau states up to 0.3 K. Moreover, the universal QAHE phase diagram is confirmed through the angle-dependent measurements. Our results address that the quantum phase transitions in both QAHE and QHE regimes are in the same universality class, yet the microscopic details are different. In addition, the realization of the QAHE insulating state unveils new ways to explore quantum phase-related physics and applications.
Large cooperativity and microkelvin cooling with a three-dimensional optomechanical cavity
Authors: Yuan Mingyun , Singh Vibhor , Blanter Yaroslav M. , Steele Gary A. 
Published: October 2015

AbstractIn cavity optomechanics, light is used to control mechanical motion. A central goal of the field is achieving single-photon strong coupling, which would enable the creation of quantum superposition states of motion. Reaching this limit requires significant improvements in optomechanical coupling and cavity coherence. Here we introduce an optomechanical architecture consisting of a silicon nitride membrane coupled to a three-dimensional superconducting microwave cavity. Exploiting their large quality factors, we achieve an optomechanical cooperativity of 146,000 and perform sideband cooling of the kilohertz-frequency membrane motion to 34±5 μK, the lowest mechanical mode temperature reported to date. The achieved cooling is limited only by classical noise of the signal generator, and should extend deep into the ground state with superconducting filters. Our results suggest that this realization of optomechanics has the potential to reach the regimes of ultra-large cooperativity and single-photon strong coupling, opening up a new generation of experiments.
Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association
Authors: Strachan Norval J. C. , Rotariu Ovidiu , Lopes Bruno , MacRae Marion , Fairley Susan , Laing Chad , Gannon Victor , Allison Lesley J. , Hanson Mary F. , Dallman Tim , Ashton Philip , Franz Eelco , van Hoek Angela H. A. M. , French Nigel P. , George Tessy , Biggs Patrick J. , Forbes Ken J. 
Published: October 2015

AbstractGenetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei’s genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei’s genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.
Structural basis of Ornithine Decarboxylase inactivation and accelerated degradation by polyamine sensor Antizyme1
Authors: Wu Donghui , Kaan Hung Yi Kristal , Zheng Xiaoxia , Tang Xuhua , He Yang , Vanessa Tan Qianmin , Zhang Neng , Song Haiwei 
Published: October 2015

AbstractOrnithine decarboxylase (ODC) catalyzes the first and rate-limiting step of polyamine biosynthesis in humans. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. Excessive accumulation of polyamines has a cytotoxic effect on cells and elevated level of ODC activity is associated with cancer development. To maintain normal cellular proliferation, regulation of polyamine synthesis is imposed by Antizyme1 (AZ1). The expression of AZ1 is induced by a ribosomal frameshifting mechanism in response to increased intracellular polyamines. AZ1 regulates polyamine homeostasis by inactivating ODC activity and enhancing its degradation. Here, we report the structure of human ODC in complex with N-terminally truncated AZ1 (cAZ1). The structure shows cAZ1 binding to ODC, which occludes the binding of a second molecule of ODC to form the active homodimer. Consequently, the substrate binding site is disrupted and ODC is inactivated. Structural comparison shows that the binding of cAZ1 to ODC causes a global conformational change of ODC and renders its C-terminal region flexible, therefore exposing this region for degradation by the 26S proteasome. Our structure provides the molecular basis for the inactivation of ODC by AZ1 and sheds light on how AZ1 promotes its degradation.
Shifts in leaf N:P stoichiometry during rehabilitation in highly alkaline bauxite processing residue sand
Authors: Goloran Johnvie B. , Chen Chengrong , Phillips Ian R. , Elser James J. 
Published: October 2015

AbstractLarge quantities of sodic and alkaline bauxite residue are produced globally as a by-product from alumina refineries. Ecological stoichiometry of key elements [nitrogen (N) and phosphorus (P)] plays a critical role in establishing vegetation cover in bauxite residue sand (BRS). Here we examined how changes in soil chemical properties over time in rehabilitated sodic and alkaline BRS affected leaf N to P stoichiometry of native species used for rehabilitation. Both Ca and soil pH influenced the shifts in leaf N:P ratios of the study species as supported by consistently significant positive relationships (P < 0.001) between these soil indices and leaf N:P ratios. Shifts from N to P limitation were evident for N-fixing species, while N limitation was consistently experienced by non-N-fixing plant species. In older rehabilitated BRS embankments, soil and plant indices (Ca, Na, pH, EC, ESP and leaf N:P ratios) tended to align with those of the natural ecosystem, suggesting improved rehabilitation performance. These findings highlight that leaf N:P stoichiometry can effectively provide a meaningful assessment on understanding nutrient limitation and productivity of native species used for vegetating highly sodic and alkaline BRS and is a crucial indicator for assessing ecological rehabilitation performance.
High-fat diet prevents adaptive peripartum-associated adrenal gland plasticity and anxiolysis
Authors: Perani Clara V. , Neumann Inga D. , Reber Stefan O. , Slattery David A. 
Published: October 2015

AbstractMaternal obesity is associated with lower basal plasma cortisol levels and increased risk of postpartum psychiatric disorders. Given that both obesity and the peripartum period are characterized by an imbalance between adrenocorticotropic hormone (ACTH) and cortisol, we hypothesized that the adrenal glands undergo peripartum-associated plasticity and that such changes would be prevented by a high-fat diet (HFD). Here, we demonstrate substantial peripartum adrenal gland plasticity in the pathways involved in cholesterol supply for steroidogenesis in female rats. In detail, the receptors involved in plasma lipid uptake, low density lipoprotein (LDL) receptor (LDLR) and scavenger receptor class B type 1 (SRB1), are elevated, intra-adrenal cholesterol stores are depleted and a key enzyme in de novo cholesterol synthesis, hydroxymethylglutaryl coenzyme A reductase (HMGCR), is downregulated; particularly at mid-lactation. HFD prevented the lactation-associated anxiolysis, basal hypercorticism and exaggerated the corticosterone response to ACTH. Moreover, we show that HFD prevented the downregulation of adrenal cholesterol stores and HMGCR expression and LDLR upregulation at mid-lactation. These findings show that the adrenal gland is an important regulator of peripartum-associated HPA axis plasticity and that HFD has maladaptive consequences for the mother, partly by preventing these neuroendocrine and also behavioural changes.
Diurnal rhythms in the human urine metabolome during sleep and total sleep deprivation
Authors: Giskeødegård Guro F. , Davies Sarah K. , Revell Victoria L. , Keun Hector , Skene Debra J. 
Published: October 2015

AbstractUnderstanding how metabolite levels change over the 24 hour day is of crucial importance for clinical and epidemiological studies. Additionally, the association between sleep deprivation and metabolic disorders such as diabetes and obesity requires investigation into the links between sleep and metabolism. Here, we characterise time-of-day variation and the effects of sleep deprivation on urinary metabolite profiles. Healthy male participants (n = 15) completed an in-laboratory study comprising one 24 h sleep/wake cycle prior to 24 h of continual wakefulness under highly controlled environmental conditions. Urine samples were collected over set 2–8 h intervals and analysed by 1H NMR spectroscopy. Significant changes were observed with respect to both time of day and sleep deprivation. Of 32 identified metabolites, 7 (22%) exhibited cosine rhythmicity over at least one 24 h period; 5 exhibiting a cosine rhythm on both days. Eight metabolites significantly increased during sleep deprivation compared with sleep (taurine, formate, citrate, 3-indoxyl sulfate, carnitine, 3-hydroxyisobutyrate, TMAO and acetate) and 8 significantly decreased (dimethylamine, 4-DTA, creatinine, ascorbate, 2-hydroxyisobutyrate, allantoin, 4-DEA, 4-hydroxyphenylacetate). These data indicate that sampling time, the presence or absence of sleep and the response to sleep deprivation are highly relevant when identifying biomarkers in urinary metabolic profiling studies.
The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models
Authors: Pires Mathias M. , Cantor Maurício , Guimarães Paulo R. , de Aguiar Marcus A. M. , dos Reis Sérgio F. , Coltri Patricia P. 
Published: October 2015

AbstractThe network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation.
Proteasome Activation is Mediated via a Functional Switch of the Rpt6 C-terminal Tail Following Chaperone-dependent Assembly
Authors: Sokolova Vladyslava , Li Frances , Polovin George , Park Soyeon 
Published: October 2015

AbstractIn the proteasome, the proteolytic 20S core particle (CP) associates with the 19S regulatory particle (RP) to degrade polyubiquitinated proteins. Six ATPases (Rpt1-Rpt6) of the RP form a hexameric Rpt ring and interact with the heptameric α ring (α1–α7) of the CP via the Rpt C-terminal tails individually binding to the α subunits. Importantly, the Rpt6 tail has been suggested to be crucial for RP assembly. Here, we show that the interaction of the CP and Rpt6 tail promotes a CP-Rpt3 tail interaction and that they jointly mediate proteasome activation via opening the CP gate for substrate entry. The Rpt6 tail forms a novel relationship with the Nas6 chaperone, which binds to Rpt3 and regulates the CP-Rpt3 tail interaction, critically influencing cell growth and turnover of polyubiquitinated proteins. CP-Rpt6 tail binding promotes the release of Nas6 from the proteasome. Based on disulfide crosslinking that detects cognate α3-Rpt6 tail and α2-Rpt3 tail interactions in the proteasome, decreased α3-Rpt6 tail interaction facilitates robust α2-Rpt3 tail interaction that is also strongly ATP-dependent. Together, our data support the reported role of Rpt6 during proteasome assembly and suggest that its function switches from anchoring for RP assembly into promoting Rpt3-dependent activation of the mature proteasome.
Methylation-mediated BMPER expression in fibroblast activation in vitro and lung fibrosis in mice in vivo
Authors: Huan Caijuan , Yang Ting , Liang Jiurong , Xie Ting , Cheng Luis , Liu Ningshan , Kurkciyan Adrianne , Monterrosa Mena Jessica , Wang Chen , Dai Huaping , Noble Paul W. , Jiang Dianhua 
Published: October 2015

AbstractIdiopathic pulmonary fibrosis (IPF) is a progressive lung disease. Although the pathogenesis is poorly understood, evidence suggests that genetic and epigenetic alterations, such as DNA methylation, may play a key role. Bone morphogenetic proteins (BMPs) are members of the transforming growth factor-β (TGF-β) superfamily and are important regulators in IPF. Here we identified BMP endothelial cell precursor-derived regulator (BMPER) as a key regulator of fibroblast activation. BMPER is a secreted glycoprotein that binds directly to BMPs and may regulate TGF-β/BMP signaling, but its role in lung fibrosis is not clear. BMPER is highly expressed in human IPF lung fibroblasts compared to normal lung fibroblasts. Demethylation agent 5′-azacytidine decreased BMPER expression in fibroblasts and attenuated the invasion and migration of IPF lung fibroblasts. Furthermore, siRNA-mediated reduction of BMPER in the human lung fibroblasts impaired cell migration and invasion. 5′-azacytidine treatment additionally regulated BMPER expression and reduced lung fibrosis in mice in vivo. These findings demonstrate that methylation of specific genes in fibroblasts may offer a new therapeutic strategy for IPF by modulating fibroblast activation.
Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response
Authors: Garg Rohini , Narayana Chevala VVS , Shankar Rama , Jain Mukesh 
Published: October 2015

AbstractDNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance and suggest a role in abiotic stress adaptation in rice.
Impact of Soil Composition and Electrochemistry on Corrosion of Rock-cut Slope Nets along Railway Lines in China
Authors: Chen Jiao , Chen Zhaoqiong , Ai Yingwei , Xiao Jingyao , Pan Dandan , Li Wei , Huang Zhiyu , Wang Yumei 
Published: October 2015

AbstractTaking the slope of Suiyu Railway to study, the research separately studied soil resistivity, soil electrochemistry (corrosion potential, oxidization reduction potential, electric potential gradient and pH), soil anions (total soluble salt, Cl−, SO42− and "Equation missing") and soil nutrition (moisture content, organic matter, total nitrogen, alkali-hydrolysable nitrogen, available phosphorus and available potassium) at different slope levels and conducted corrosion grade evaluation on artificial soil according to its single index and comprehensive indexes. Compared with other factors, water has the biggest impact on the corrosion of slope protection net, followed by anion content. Total soluble salt has the moderate impact on the corrosion of slope protection net and stray current has the moderate impact on the corrosion of mid-slope protection net. Comprehensive evaluation on the corrosive degree of soil samples indicates that the corrosion of upper slope is moderate and the corrosion of mid-slope and lower slope is strong. Organic matter in soil is remarkably relevant to electric potential gradient. Available nitrogen, available potassium and available phosphorus are remarkably relevant to anions. The distribution of soil nutrient is indirectly relevant to slope type.