bluuebunny/crossref_metadata_2025_split huggingface dataset:
ŌvSim: a Simulation of the Population Dynamics of Mammalian Ovarian Follicles
Authors: Johnson Joshua , Chen Xin , Xu Xiao , Emerson John W. 
Published: December 2015

AbstractNo two ovaries are alike, and indeed, the same ovary can change its architecture from day to day. This is because ovarian follicles are present in different numbers, positions, and states of maturation throughout reproductive life. All possible developmental states of follicles can be represented at any time, along with follicles that have committed to death (termed follicle atresia). Static histological and whole-mount imaging approaches allow snapshots of what is occurring within ovaries, but our views of dynamic follicle growth and death have been limited to these tools. We present a simple Markov chain model of the complex mouse ovary, called “ŌvSim”. In the model, follicles can exist in one of three Markov states with stationary probabilities, Hold (growth arrest), Grow, and Die. The probability that individual primordial follicles can growth activate daily, the fraction of granulosa cells that survive as follicles grow, and the probability that individual follicles can commit to atresia daily are user definable parameters. When the probability of daily growth activation is stationary at 0.005, the probability of atresia for all follicles is near 0.1, and the probability of granulosa cell survival is modeled around 0.88, ŌvSim simulates the growth and fate of each of the approximately 3000 postpubertal mouse ovarian follicles in a fashion that approximates actual biological measurements (e.g., follicle counts). ŌvSim thus offers a starting platform to simulate mammalian ovaries and to explore factors that might impact follicle development and global organ function.Author SummaryŌvSim is a computer simulation of the dynamic growth of mouse ovarian follicles. The program is offered as the beginning of a research and teaching platform to model asynchronous follicle growth and survival or death.
Biological screens from linear codes: theory and tools
Authors: Erlich Yaniv , Gilbert Anna , Ngo Hung , Rudra Atri , Thierry-Mieg Nicolas , Wootters Mary , Zielinski Dina , Zuk Or 
Published: December 2015

AbstractMolecular biology increasingly relies on large screens where enormous numbers of specimens are systematically assayed in the search for a particular, rare outcome. These screens include the systematic testing of small molecules for potential drugs and testing the association between genetic variation and a phenotype of interest. While these screens are “hypothesis-free,” they can be wasteful; pooling the specimens and then testing the pools is more efficient. We articulate in precise mathematical ways the type of structures useful in combinatorial pooling designs so as to eliminate waste, to provide light weight, flexible, and modular designs. We show that Reed-Solomon codes, and more generally linear codes, satisfy all of these mathematical properties. We further demonstrate the power of this technique with Reed-Solomonbased biological experiments. We provide general purpose tools for experimentalists to construct and carry out practical pooling designs with rigorous guarantees for large screens.
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits
Authors: Czech Lucas , Huerta-Cepas Jaime , Stamatakis Alexandros 
Published: December 2015

AbstractPhylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Virtually all empirical evolutionary data studies contain a visualization of the inferred tree with branch support values. Ambiguous semantics in tree file formats can lead to erroneous tree visualizations and therefore to incorrect interpretations of phylogenetic analyses.Here, we discuss problems that can and do arise when displaying branch values on trees after re-rooting. Branch values are typically stored as node labels in the widely-used Newick tree format. However, such values are attributes of branches. Storing them as node labels can therefore yield errors when re-rooting trees. This depends on the mostly implicit semantics that tools deploy to interpret node labels.We reviewed 10 tree viewers and 10 bioinformatics toolkits that can display and re-root trees. We found that 14 out of 20 of these tools do not permit users to select the semantics of node labels. Thus, unaware users might obtain incorrect results when rooting trees inferred by common phylogenetic inference programs. We illustrate such incorrect mappings for several test cases and real examples taken from the literature. This review has already led to improvements and workarounds in 8 of the tested tools. We suggest tools should provide an option that explicitly forces users to define the semantics of node labels.
Post-embryonic hourglass patterns mark ontogenetic transitions in plant development
Authors: Drost Hajk-Georg , Bellstäedt Julia , Ó’Maoiléidigh Diarmuid S. , Silva Anderson T. , Gabel Alexander , Weinholdt Claus , Ryan Patrick T. , Dekkers Bas J.W. , Bentsink Leónie , Hilhorst Henk , Ligterink Wilco , Wellmer Frank , Grosse Ivo , Quint Marcel 
Published: December 2015

AbstractThe historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plantArabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found post-embryonically. We found that the two main phase changes during the life cycle ofArabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.
Electrochemical behavior and corrosion resistance of electrodeposited nano-particles Zn-Co-Fe alloy
Authors: Abou-Krisha Mortaga , Assaf Fawzi , Alduaij Omar , Alshammari Abdulrahman G , El-Sheref Fatma 
Published: December 2015

Purpose
– The purpose of this study was to compare the electrodeposition behavior and corrosion resistance of ternary and binary alloys.

Design/methodology/approach
– Potentiodynamic polarization resistance measurement and anodic linear sweep voltammetry techniques were used for the corrosion study. The surface morphology and chemical composition of the deposits were examined using scanning electron microscopy and atomic absorption spectroscopy, respectively. The phase structure was characterized by X-ray diffraction analysis. Electrodeposition behavior was carried out using cyclic voltammetry and galvanostatic techniques.

Findings
– It was found that the obtained ternary alloy exhibited better corrosion resistance and a more-preferred surface appearance compared to the binary alloys that were electrodeposited under similar conditions.

Research limitations/implications
– The ternary alloy showed better anticorrosion properties compared to binary deposits that were electroplated successfully from the plating baths. The Zn-Co-Fe alloy could be used advantageously in industry because the ternary alloy exhibits the collective properties of the binary alloys in one alloy via the electrodeposition of Zn-Ni-Co alloy.

Social implications
– Increasing the corrosion resistance implies to social economic increases.

Originality/value
– To date, the electrodeposition of Zn-Co-Fe alloy was studied in only a small number of articles. It was found that the presence of Co or Fe could provide a useful coating on the steel that would reduce its susceptibility to corrosion attack.
Corrosion process of D32 steel used for offshore oil platform in splash zone
Authors: Liu JianGuo , Li Zili , Li Yantao , Hou BaoRong 
Published: December 2015

Purpose
– This paper aims to study the corrosion behavior of D32 steel suffered to marine splash zone. Type D32 structural steel has good mechanical properties and is commonly used for offshore oil platform construction in China. To ensure the safety of marine steel structure, it is important to study the corrosion process of D32 steel in the splash zone.

Design/methodology/approach
– The corrosion behavior of D32 steel in splash zone environments was studied using polarization curves and electrochemical impedance spectroscopy. The electrochemical results were obtained from the corroded steel samples exposed in the splash zone of a bespoke simulate device, while corrosion morphologies and corrosion products of the steel samples were characterized using scanning electron microscopy and X-ray diffraction.

Findings
– In wet–dry cyclic exposure, the reaction was a self-perpetuating process of chemical oxidation and electrochemical reduction. The rust itself took part in the reduction processes and, hence, increased the corrosion rate of the steel samples.

Originality/value
– Finally, the corrosion process of D32 steel in splash zone is considered.
Effects of water on the SCC of low carbon steel in ethanolic media
Authors: Moyo Fortunate , Van der Merwe Josias Willem 
Published: December 2015

Purpose
– This paper aims to determine the effect of water on the SCC of low carbon steel in ethanol in the absence of supporting salts.

Design/methodology/approach
– Slow strain rate test was done to determine SCC susceptibility. Fractured samples were examined using optical microscopy and scanning electron microscopy.

Findings
– While the results demonstrated that water alone had no effect on the SCC susceptibility of low carbon steel in ethanol, 2.5 volume per cent moisture gave indications of cracking tendencies.

Originality/value
– With South Africa and the world over turning to bioethanol and ethanol blended fuels as a means of reducing its carbon foot print, there are concerns over the corrosive nature of ethanol on common engineering metals like low carbon steels.
EM3B2 – a semantic integration engine for materials science
Authors: Zhao Chongchong , Dong Chao , Zhang Xiaoming 
Published: December 2015

Purpose
– The integration and retrieval of the vast data have attracted sufficient attention, thus the W3C workgroup releases R2RML to standardize the transformation from relational data to semantic-aware data. However, it only provides a data transform mechanism to resource description framework (RDF). The generation of mapping alignments still needs manual work or other algorithms. Therefore, the purpose of this paper is to propose a domain-oriented automatic mapping method and an application of the R2RML standard.

Design/methodology/approach
– In this paper, materials science is focussed to show an example of domain-oriented mapping. source field concept and M3B2 (Metal Materials Mapping Background Base) knowledge bases are established to support the auto-recommending algorithm. As for the generation of RDF files, the idea is to generate the triples and the links, respectively. The links of the triples follow the object-subject relationship, and the links of the object properties can be achieved by the range individuals and the trail path.

Findings
– Consequently based on the previous work, the authors proposed Engine for Metal Materials Mapping Background Base (EM3B2), a semantic integration engine for materials science. EM3B2 not only offers friendly graphical interfaces, but also provides auto-recommending mapping based on materials knowledge to enable users to avoid vast manually work. The experimental result indicates that EM3B2 supplies accurate mapping. Moreover, the running time of E3MB2 is also competitive as classical methods.

Originality/value
– This paper proposed EM3B2 semantic integration engine, which contributes to the relational database-to-RDF mapping by the application of W3C R2RML standard and the domain-oriented mapping.
MAPK cascade‐mediated regulation of pathogenicity, conidiation and tolerance to abiotic stresses in the entomopathogenic fungus Metarhizium robertsii
Authors: Chen Xiaoxuan , Xu Chuan , Qian Ying , Liu Ran , Zhang Qiangqiang , Zeng Guohong , Zhang Xin , Zhao Hong , Fang Weiguo 
Published: December 2015

SummaryMetarhizium robertsii has been used as a model to study fungal pathogenesis in insects, and its pathogenicity has many parallels with plant and mammal pathogenic fungi. MAPK (Mitogen‐activated protein kinase) cascades play pivotal roles in cellular regulation in fungi, but their functions have not been characterized in M. robertsii. In this study, we identified the full complement of MAPK cascade components in M. robertsii and dissected their regulatory roles in pathogenesis, conidiation and stress tolerance. The nine components of the Fus3, Hog1 and Slt2‐MAPK cascades are all involved in conidiation. The Fus3‐ and Hog1‐MAPK cascades are necessary for tolerance to hyperosmotic stress, and the Slt2‐ and Fus3‐MAPK cascades both mediate cell wall integrity. The Hog1 and Slt2‐MAPK cascades contribute to pathogenicity; the Fus3‐MAPK cascade is indispensable for fungal pathogenesis. During its life cycle, M. robertsii experiences multiple microenvironments as it transverses the cuticle into the haemocoel. RNA‐seq analysis revealed that MAPK cascades collectively play a major role in regulating the adaptation of M. robertsii to the microenvironmental change from the cuticle to the haemolymph. The three MAPKs each regulate their own distinctive subset of genes during penetration of the cuticle and haemocoel colonization, but they function redundantly to regulate adaptation to microenvironmental change.
Prostate stem cell antigen gene TT genotype and development of intestinal metaplasia in Helicobacter pylori infection
Authors: Uotani Takahiro , Sugimoto Mitsushige , Ichikawa Hitomi , Tanaka Shingo , Nagashima Hiroyuki , Uchida Tomohisa , Graham David Y. , Yamaoka Yoshio 
Published: December 2015

ObjectivesGastric cancer is etiologically related to interactions between Helicobacter pylori (H. pylori) infection, environmental and host factors. Gastric carcinoma is associated with a cascade of increasing atrophic gastric mucosal damage. Prostate stem cell antigen (PSCA) polymorphisms have been associated with an increased risk of gastric cancer. We aimed to examine the interaction between PSCA polymorphisms and H. pylori in the progression of H. pylori‐related gastritis.MethodsThe genotypes (TT, TC and CC) of PSCA single nucleotide polymorphism rs2294008 among H. pylori infected and uninfected Bhutanese were compared with the severity of H. pylori‐related gastritis [neutrophils, monocytes, atrophy scores, H. pylori density, and the presence and extent of intestinal metaplasia (IM)] using the updated Sydney system.ResultsBiopsies from 339 participants were included. The proportion of biopsies with IM was significantly (P < 0.05) greater in those with the TT genotype than in either those with the CT or CC genotype. Although no significant differences were found in inflammation or H. pylori density scores, the scores for IM at both gastric corpus and antrum among participants infected by H. pylori with the TT genotype was significantly (P < 0.05) greater than in the C allele carriers.ConclusionPSCA TT genotype is associated with a more than a threefold increase in the prevalence and the extent of gastric mucosal IM compared to C allele carriers among H. pylori‐infected Bhutanese.
Ritonavir‐Induced Suicidal Death of Human Erythrocytes
Authors: Waibel Sabrina , Bissinger Rosi , Bouguerra Ghada , Abbès Salem , Lang Florian 
Published: December 2015

AbstractThe antiviral drug ritonavir has been shown to trigger suicidal death or apoptosis of tumour cells and has thus been considered for the treatment of malignancy. In analogy to apoptosis of nucleated cells, erythrocytes may enter eryptosis, the suicidal erythrocyte death characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Triggers of eryptosis include Ca2+ entry with increase in cytosolic Ca2+ activity ([Ca2+]i), oxidative stress and ceramide. The present study explored whether and how ritonavir induces eryptosis. To this end, flow cytometry was employed to estimate cell volume from forward scatter, phosphatidylserine exposure at the cell surface from Annexin‐V binding, [Ca2+]i from Fluo3 fluorescence, abundance of reactive oxygen species (ROS) from 2',7'‐dichlorodihydrofluorescein diacetate (DCFDA) fluorescence and ceramide abundance utilizing specific antibodies. As a result, a 48‐hr exposure of human erythrocytes to ritonavir significantly increased the percentage of Annexin‐V‐binding cells (≥5 μg/ml), significantly decreased forward scatter (≥5 μg/ml), significantly increased Fluo3 fluorescence (20 μg/ml), slightly, but significantly increased DCFDA fluorescence (20 μg/ml) and slightly, but significantly increased ceramide abundance (20 μg/ml). The effect of ritonavir on Annexin‐V binding was significantly blunted, but not fully abolished by the removal of extracellular Ca2+. In conclusion, ritonavir triggers erythrocyte shrinkage and phosphatidylserine translocation at the erythrocyte cell membrane, an effect in part due to the stimulation of Ca2+ entry, oxidative stress and ceramide.
Varenicline and Nicotine Patch Therapies in Young Adults Motivated to Quit Smoking: A Randomized, Placebo‐controlled, Prospective Study
Authors: Tuisku Anna , Salmela Merita , Nieminen Pentti , Toljamo Tuula 
Published: December 2015

AbstractThis study compares the nicotine patch to placebo in young adult light smokers, and the nicotine patch to varenicline in heavy smokers. Volunteer daily smokers were recruited into a randomized, placebo‐controlled study via community media, colleges and the army (aged 18–26 years). Those subjects with light tobacco dependence were randomized to (i) placebo patch (n = 86) and (ii) nicotine patch 10 mg/16 hr for 8 weeks (n = 94), and those with stronger dependence to (iii) nicotine patch 15 mg/16 hr for 8 weeks (n = 51) and (iv) varenicline for 12 weeks (n = 60). The primary outcome variable was self‐reported smoking abstinence at week 12. Secondary outcome variables were self‐reported smoking abstinence at weeks 4 and 26, and self‐reported abstinence verified by saliva cotinine level at week 12. The prevalence of self‐reported smoking abstinence did not differ statistically significantly in light smokers during the follow‐up (week 4: 19.8% for placebo patch and 26.6% for nicotine patch 10 mg/16 hr; week 12: 17.4% versus 23.4%; week 26: 15.1% versus 20.2%), but the groups of heavy smokers differed significantly for 12 weeks (week 4: 19.6% for nicotine patch 15 mg/16 hr and 73.3% for varenicline, p < 0.001; week 12: 15.7% versus 36.7%, p = 0.018). This statistically significant difference did not endure for the entire follow‐up (week 26: 9.8% versus 18.3%, p = 0.280). However, saliva cotinine verified abstinence at week 12 did not support self‐reported abstinence. Varenicline may be more effective than the nicotine patch as a smoking cessation pharmacotherapy among young adult heavy smokers in the short‐term.
Modelling of the Effect of End‐Tidal Carbon Dioxide on Cerebral Oxygen Saturation in Beach Chair Position under General Anaesthesia
Authors: Kim So Yeon , Chae Dong Woo , Chun Yong‐Min , Jeong Kyu Hee , Park Kyungsoo , Han Dong Woo 
Published: December 2015

AbstractPatients undergoing shoulder surgery in the beach chair position (BCP) under general anaesthesia may be at risk of cerebral desaturation. Increasing end‐tidal carbon dioxide (EtCO2) is the most convenient and powerful method for the management of cerebral desaturation. The purpose of this study was to investigate the quantitative relationship between EtCO2and cerebral oxygen saturation (rSO2) and to identify the associated influencing factors. Fifty‐one patients undergoing arthroscopic shoulder surgery in theBCPunder general anaesthesia completed this study. Desflurane and remifentanil were used, and EtCO2was steadily increased and then decreased by adjusting the ventilator settings every 3 min. so that time lag ofrSO2response to EtCO2changes could be delineated. Near‐infrared spectroscopy was used to monitorrSO2response. An indirect response model was used to examine the relationship between EtCO2andrSO2. To determine the relevant covariates, a stepwise approach was used. There was a linear relationship betweenrSO2and EtCO2with a slight delay in the peak ofrSO2relative to EtCO2. Increase in end‐tidal desflurane concentration led to a slower response ofrSO2to the changes of EtCO2(p = 0.0002). The presence of diabetes mellitus reduced the reactivity ofrSO2to EtCO2changes (p < 0.0001). This model‐based approach revealed that diabetes mellitus attenuates the response ofrSO2to changes in EtCO2. The management of cerebral desaturation by hypercapnia in patients with diabetes may be less effective than in non‐diabetic patients under general anaesthesia with BCP.
Geomorphology, sedimentology and minimum exposure ages of streamlined subglacial landforms in the NW Himalaya, India
Authors: Saha Sourav , Sharma Milap C. , Murari Madhav K. , Owen Lewis A. , Caffee Marc W. 
Published: December 2015

Streamlined subglacial landforms that include drumlins in three study areas, the upper Chandra valley around Chandra Tal, the upper Spiti Valley and the middle Yunam Valley of the NW Himalaya of India were mapped and studied using geomorphic, sedimentological and geochronological methods. These streamlined subglacial landforms include a variety of morphological types, including: (i) half egg‐shaped forms; (ii) complex superimposed forms; (iii) dome‐shaped forms; (iv) inverse forms; and (v) flat‐topped symmetrical forms. Sedimentological data indicate that subglacial deformational processes are responsible for the formation of the streamlined subglacial landforms in the Chandra Tal and upper Spiti Valley study areas. In contrast, streamlined landforms in the middle Yunam Valley are the result of melt‐out and subglacial erosional processes. In the Yunam Valley study area, 11 new cosmogenic 10Be surface exposure ages were obtained for boulders inset into the crests of streamlined subglacial landforms and moraines, and also for a bedrock surface. The streamlined landforms date to 8–7 ka, providing evidence of an early Holocene valley glaciation, and older moraines date to ∼17–15 and 79–52 ka, representing other significant valley glacial advances in the middle Yunam Valley. The subglacial landforms in the Chandra Valley provide evidence for a ≥300‐m‐thick Lateglacial glacier that advanced southeast, overtopping the Kunzum Range, and advancing into the upper Spiti Valley. The streamlined subglacial landforms in these study areas of the NW Himalaya highlight the usefulness of such landforms in developing glacial chronostratigraphy and for understanding the dynamics of Himalayan glaciation.