bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive comparison of four species of Onchidiidae provides insights on morphological and molecular adaptations of invertebrates from shallow seas to wetlands
Authors: Xu Guolv , Yang Tiezhu , Wang Dongfeng , Li Jie , Liu Xin , Wu Xin , Shen Heding
Published: January 2018

Background.The Onchidiidae family provides ideal species of marine invertebrates for the study of the evolution from seas to wetlands. However, different species of Onchidiidae have rarely been considered in comparative studies.

Methods.A total of 40 samples were collected from four species (10 specimens per onchidiid). In addition, we systematically investigated the histological and molecular differences to elucidate the morphological foundations underlying these adaptations.

Results.Histological analysis enabled the structural comparison of respiratory organs (gill, lung-sac, dorsal skin) among onchidiids. Transcriptome sequencing of four representative onchidiids was performed to further expound the molecular mechanisms with their respective habitats. Twenty-six Single nucleotide polymorphism (SNP) markers of Onchidium struma presented the DNA polymorphism determining some visible genetic traits. Non-muscle myosin heavy chain II (NMHC II) and myosin heavy chain (MyHC) played an essential role in amphibian developmental processes and are expressed differentially invarious onchidiids and tissues. The species with higher terrestrial ability and higher integrated expression of Os-MHC (NMHC II gene) and MyHC gene illustrated the expression level associated with the evolutionary degree.

Conclusions.The present study indicates that different adaptions occurred in four species in various environments.We hope to provide a valuable reference point and a source of inspiration for amphibian investigatorsstudying the morphological characteristics and molecular mechanisms underlying the transition of invertebrates from shallow seas to wetlands.
De novo assembly and identification of antennal transcriptome reveals an olfactory system in Heortia vitessoides (Lepidoptera: Crambidae)
Authors: Cheng Jie , Wang Chun-Yan , Lyu Zi-Hao , Chen Jing-Xiang , Lin Tong
Published: January 2018

Olfactory systems in insects are used to detect volatile chemical odors, and play crucial roles in survival, reproduction, and mediating key behaviors. Here, RNA sequencing technology was used to sequence and assemble the antennal transcriptome of Heortia vitessoides, a defoliating pest in Aquilaria sinensis (Loureiro) Sprenger forests and a non-model species with no genomic resources. Analysis of the transcriptome of female and male antennae generated 22.16 gigabases of genomic data, from which 52,383 unigenes were assembled. We identified 80 candidate olfactory genes: eight for odorant binding proteins (OBPs), 14 for chemosensory proteins (CSPs), 35 odorant receptors (ORs), 18 ionotropic receptors (IRs), three gustatory receptors (GRs), and two for sensory neuron membrane proteins (SNMPs). Furthermore, phylogenetic trees and fragments per kilobase of transcript per million fragments mapped (FPKM) were used to analyze these olfactory genes. This study is the first comprehensive antennal transcriptome analysis for H. vitessoides, and these novel olfactory genes will increase understanding of the molecular mechanism of chemoreception and further contribute to exploring strategies to manage this insect.
The response of photosynthetic functions of F1 cutting seedlings from Physocarpus amurensis Maxim × Physocarpus opulifolius “Diabolo” and the parental leaves to saline stress
Authors: Xu Nan , Zhong Haixiu , Li Xin , Yin Zepeng , Zhu Wenxu , Zhang Huihui
Published: January 2018

This paper selected clonal cutting seedlings from the F1 hybrid varieties of Physocarpus amurensis Maxim (♀) × Physocarpus opulifolius “Diabolo” (♂) as research material to study the response of the photosynthetic gas exchange parameters and chlorophyll fluorescence parameters of Physocarpus amurensis hybrids and their parental leaves to NaCl stress (with concentrations of 0, 50, 100 and 200 mmol·L-1). The results showed that under saline stress, the stomatal conductance (Gs), transpiration rate (Tr), and net photosynthetic rate (Pn) of the three kinds of P. amurensis all significantly decreased. When the NaCl concentration was below 100 mmol·L-1, the intercellular CO2 concentration (Ci) of leaves of the three samples declined with the increase of salt concentration; however, when the concentration increased to 200 mmol·L-1, Ci did not decrease significantly, especially when the Ci of P. opulifolius “Diabolo” presented a slight increase. This indicated that the decline of photosynthetic carbon assimilation capacity induced by saline stress was the consequence of interaction between stomatal factors and non-stomatal factors, and the non-stomatal factors played an important role when the saline concentration was below 200 mmol·L-1. Compared with P. amurensis, the photosynthetic gas exchange capability of P. opulifolius “Diabolo” leaves was more sensitive to saline stress, and the limitation of non-stomatal factors was relatively evident, but the photosynthetic capacity of hybrid Physocarpus amurensis Maxim leaves with the desired purple color was improved compared with Physocarpus amurensis. Under saline stress, the PSII activity of the three kinds of P. amurensis leaves declined, the electron transfer was inhibited, and obvious signs of photoinhibition were present. With the increase of saline concentration, the Vk of P. amurensis and hybrid P. amurensis leaves presented a decreasing trend, but the Vk of P. opulifolius “Diabolo” leaves increased slightly. This suggested that the effects of saline stress on the oxygen-evolving complex (OEC) of the three P. amurensis sample types were relatively limited and only the OEC of P.s opulifolius “Diabolo” leaves were slightly sensitive to saline stress. The VJ of all the leaves of the three Physocarpus amurensis types increased under saline stress, and increased significantly when the saline concentration increased to 200 mmol·L-1, indicating that saline stress obviously impeded the electron transfer chain from QA to QB on the PSII receptor side of the leaves. Moreover, high saline concentrations would cause thylakoid membrane dissociation.The salt tolerance of photosynthetic functions of hybrid Physocarpus amurensis (♀) × Physocarpus opulifolius “Diabolo” (♂) leaves was improved compared with that of parental Physocarpus opulifolius “Diabolo,” and the hybrid shows obvious hybrid vigor in the aspect of photosynthesis.
Sexual attractiveness: a comparative approach of morphological, behavioral neurophysiological signaling in women and nonhuman primate females
Authors: Wallner Bernard , Windhager Sonja , Schaschl Helmut , Nemeth Matthias , Pflueger Lena S , Fieder Martin , Domjanic Jacqueline , Millesi Eva , Seidler Horst
Published: January 2018

This comprehensive review focuses on comparative data in nonhuman primates and humans in relation to signaling secondary sex characteristics (SSC), sexual behavior, and neurophysiology of sexuality during the female cycle. Obviously, sexual activities of primates are not limited to specific cycle phases. In higher evolved primate species no distinction can be drawn between sexual interactions as a prerequisite for reproduction or as a pleasurable tool. However, cyclic depended changes of body morphology and behavior, such as feeding, risk taking, mood changes, are documented for both groups. Neurophysiologically, homologous brain areas, sex steroids and receptor compartments are involved in mediating sexual and pleasure during all cycle stages. The interaction between the subcortical reward system and the social brain network and its projection to the prefrontal cortex are of importance. The advertising of SSC indicate analogous strategies between human one male social units and multifemale-multimale groups in nonhuman primates. Women do advertise SSC permanently after the onset of puberty. In contrast, some nonhuman primate species express attractive signals during specific cycle stages and prolong them beyond fertile periods. The physiological and morphological nature of primate SSC and their flexibility of expression in relation to their information content for males will be discussed during different cycle periods for both groups. Because of permanent sexual attractiveness in humans the use of clothes as a specific eye catcher to advertise SSC in relation to biological function will be illustrated. The latter is suggested to be an example of culture-biology adaptation in human sexual behavior.
The impact of floating dust on net photosynthetic rate of Populus euphratica in early spring, at Zepu, northwestern China
Authors: XUE Zhiguo , SHEN Zhenxing , HAN Wei , XU Shanyang , MA Xiaohua , FEI Bingqiang , ZHANG Tian , CHANG Tian
Published: January 2018

Floating dust weather is an annual natural phenomenon in early spring in south of Xinjiang UygurAutonomous Region, northwestern China. Floating dust in air can influence human health and plant growth. Populus euphratica is a rare tree species which can grow in hot and dry conditions. Some investigations have evaluated the effect of floating dust on plants by means of artificial dust to which simulates the natural sand and dust, but the mechanism by which plants respond to sand is poorly understood. The investigation presented in this paper focused on a comparison of the variation in net photosynthetic rate (Pn) before and during floating dust weather, to elucidate the mechanisms involved. Stomatal conductance (gs) and Pn appeared to increase during floating dust weather;in contrast, stomatal limitation (Ls) and non-stomatal limitation (Lns) decreased with photosynthetic active radiation in the range 500 to 2000 μmol m−2s−1,which is optimum for plant growth. Aerosol ions, including potassium, dissolved in water collected by foliar structures or tender stems, may come into contact with intercellular stroma and improve chloroplast activity or ribulose-1,5-bisphosphate carboxylase/ oxygenase (Rubisco) levels, such as potassium, thereby influencing Ls and Lns. Moreover, potassium, phosphorus, nitrogen and sodium in aerosols appeared to increase Pn, and this may be due to nutrient compounds in aerosols, which may have a similar effect to spraying fertilizer on leaves. In addition, the high relative humidity and carbon dioxide concentration in air during floating dust weather may facilitate an increase in Pn.
Histological and histochemical investigation of the compound eye of the whiteleg shrimp (Litopenaeus vannamei)
Authors: Chang Hao-Kai , Lin Cheng-Chung , Hsuan Shih-Ling
Published: January 2018

The compound eye is the primary visual system in crustaceans. Although the histological structure and histochemical characteristics of compound eyes of some insect and crab species are now well understood, no such studies have been undertaken in the whiteleg shrimp (Litopenaeus vannamei). In this study, eye samples from L. vannamei were fixed and paraffin sections were stained using several histochemical methods. The histological structure of each layer of the compound eye was examined and compared using different histochemical staining methods. It was found that the compound eye of L. vannamei consisted of cuticle, cornea, ommatidia, optic nerve layer, lamina ganglionaris, and medulla in an outside-in order. The cuticle of L. vannamei eyes was very thin, composed of a single epicuticle layer, as confirmed by Masson’s trichrome stain. The screening pigments produced by screening pigment cells were arranged at the junction of the ommatidia and optic nerve layer; these pigments stained differentially after different histochemical staining methods suggesting the screening pigment cells can be classified into different types. Notably, clusters of foamy glandular cells (FGCs) were observed in the optic nerve layer; these stained positively with periodic acid-Schiff and toluidine blue, and appeared blue after Masson’s trichrome stain. Immunohistochemical (IHC) staining was used to further define the origin and characteristics of FGCs. The IHC analysis showed that FGCs were positive for vimentin and synaptophysin (SYN), suggesting their neuroendocrine nature. In the medulla internalis and medulla terminalis, the neural clusters that surround the neurophil could be divided into three types by differences in morphology: the largest and the smallest cell clusters were neuron clusters and neurosecretory cells, respectively; the middle-sized cell clusters appeared SYN-positive and have not previously been described. Overall, this study is the first to provide a detailed description of the normal features of the compound eye of L. vannamei. The identification of different types of screening pigments in the ommatidia, the endocrine nature of FGcs in the optic nerve layer, and the novel neural clusters between the medulla internalis and medulla terminalis, will be important information for further study into the compound eye of L. vannamei.
Murine miR-483-3p promotes proliferation and suppresses differentiation of C2C12 cells by targeting SRF
Authors: Huang Jing , Liu Ying , Fu Liangliang , Li Hegang , Xie Bingkun , Ma Guojian
Published: January 2018

Myogenesis is a complicated process, which is regulated by numerous regulators. MicroRNAs (miRNAs) are conserved non-coding RNAs of ~22 nucleotides, which regulate post-transcriptional gene expression in many physiological and pathophysiological processes. Recent studies have indicated that microRNAs are critical regulators of muscle development. Here, we report miR-483-3p as a new essential regulator of muscle development, mediating myoblast proliferation and myogenic differentiation. miR-483-3p is strongly and almost exclusively expressed in muscle-related tissues such as leg muscle, back muscle, and heart. Its expression is downregulated during mouse development. Overexpression of miR-483-3p in C2C12 cells promotes proliferation and suppresses myogenic differentiation. A dual-luciferase reporter assay demonstrated miR-483-3p direct targets to the 3′-UTR of the SRF gene. Overexpression of miR-483-3p reduced SRF protein levels in C2C12 myoblasts. These results reveal a novel function of miR-483-3p as a positive regulator of C2C12 proliferation and inhibitor of myogenic differentiation via SRF downregulation.
Resolving differences in observed impacts of invasive lionfish and clarifying advice to managers
Authors: Ingeman Kurt E. , Albins Mark A. , Benkwitt Cassandra E. , Green Stephanie J. , Kindinger Tye L. , Tuttle Lillian J. , Hixon Mark A.
Published: January 2018

Hackerott et al. (2017) report that Indo-Pacific lionfish “had no apparent effect on native prey communities” (p. 9) on continuous reef-sites of the Belizean Barrier Reef (BBR). Based on a lack of observational evidence, they challenge existing evidence for the effects of predation by lionfish on native prey community structure and assert that previous experimentally measured effects are inflated by “unnaturally high lionfish densities” (p. 10). Managers may mistakenly interpret these conclusions as evidence that invasive lionfish are of little concern and that active management of lionfish should not be a conservation priority. We find the arguments presented in Hackerott et al. (2017) unconvincing and potentially misleading. Here, we seek to evaluate their conclusions in the context of the body of work on the lionfish invasion, and to clarify advice to marine resource managers in the invaded range. Specifically, we argue that (1) the low lionfish densities observed in Hackerott et al. (2017) are not predicted to cause observable lionfish effects—so the results offer no countervailing evidence; (2) the study design is ill-suited to identify lionfish-induced changes in prey abundance, were they to occur; (3) the analytical methods employed (correlation between lionfish and prey densities) do not represent a BACI design nor offer a reliable test of predatory effects; and (4) the authors minimize potentially important regional management activities that could affect lionfish population densities and mischaracterize the body of lionfish research that has come before. Scientists should rigorously challenge popular scientific narratives.However, the foundation of such challenges must be carefully designed experiments, sound methodology, and conservative interpretation of one’s findings.
A new technology for predicting the fiber content in hemp bast
Authors: Gang Deng , liang Ding Ming , Xia Cheng , Hu Liu Fei
Published: January 2018

Hemp (Cannabis sativa L.) is a traditional fiber crop, which is becoming one of the most important industrial fibers, with a promising future in many fields. To accelerate the breeding of hemp cultivars with increased fiber content, it is important to establish a pre-flowering method that can be used to predict the potential fiber content in hemp bast. This study investigated the correlation between fiber content in the stem bast portion and in the entire stem. In addition, the variation in the bast fiber content during the sampling period was studied in three hemp cultivars. It was clear that the bast fiber content in hemp stems was determined up to 40 d before emergence of the staminate buds. The fiber content of the bast (in a sample piece 30cm long and covering one-quarter of the stem girth, sampled at two-fifths of the plant height from the soil, 20 d before the staminate buds emerged) was shown to be representative of the fiber content of the entire stem. In conclusion, this new method would allow breeders to select the hemp plants for high bast fiber content during the early to middle growth periods, before the male buds emerged, potentially accelerating the genetic improvement of fiber content in industrial hemp.
Bacteria as “ink” for writing the initials of names on agar
Authors: Ng Wenfa
Published: January 2018

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created to help them remember the strong friendships they fostered with their fellow course mates during their final year research projects. Besides the fun activity of “Bacterial calligraphy”, the surface patterning technique can also serve as a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates for investigating possible interactions between different microbe species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, at http://jmbe.asm.org/index.php/jmbe/article/view/414 as an open access article.
Bacteria as “ink” for writing the initials of names on agar
Authors: Ng Wenfa
Published: January 2018

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created to help them remember the strong friendships fostered during their final year research projects. Besides the fun activity of “Bacterial calligraphy”, the surface patterning technique can also serve as a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates for investigating possible interactions between different microorganism species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414
Bacteria as “ink” for writing the initials of names on agar
Authors: Ng Wenfa
Published: January 2018

Mementos encapsulate memories and serve as triggers for their recollections. By using a purple pigment producing bacterium as “ink” for writing on agar, a picture memento depicting the initials of students’ names was created to help them recollect, in future, the strong friendships that they fostered during their final year research projects. Besides the fun activity of “Bacterial calligraphy”, the surface patterning technique can also serve as a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates may find use in understanding possible interactions between different microorganism species. A synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Bacterial Calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174 as an open access article, URL http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414 .
Identifying microbes from environmental water samples in a discovery-based learning module
Authors: Ng Wenfa
Published: January 2018

What is the microbe we are dealing with? Irrespective of cholera or anthrax, we want to know the disease causative microorganism as quickly as possible since prompt identification of the etiological organism would help control disease spread - and potentially save lives through provision of appropriate care and medicine. But despite the promulgation of rapid microbe identification tools (such as those based on mass spectrometry), most undergraduate curricula continue to focus on culture and nucleic acid-based identification techniques since they are widely used for detecting and identifying microbes in clinical and environmental samples. Mass spectrometry-based methods, however, have increasingly complemented traditional approaches in clinical and research laboratories - but they rarely feature in undergraduate curricula. Motivated by the desire to bridge the curriculum gap, I developed an inquiry-based laboratory exercise for introducing students to the operating principles and methodology of mass spectrometry enabled microbe identification. By requiring students to identify microbes in environmental water samples (a real life problem with unknown answers), the exercise piqued the students’ interest in learning, while helping stir their curiosity in science through an interesting field activity where they put on a scientist’s hat in solving a mystery. This synopsis article summarizes a piece of published education research and expands on the discussion of concepts underlying matrix-assisted laser desorption/ionization time of flight mass spectrometry MALDI-TOF MS microbe identification. Specifically, the article discusses the relative advantages and disadvantages of the pattern recognition and proteome database search approaches for analyzing mass spectra data. In addition, the effect of different sample preparation protocols on identification accuracy is also discussed in detail. Finally, the pedagogy utility of field and inquiry-based education tools is also discussed in greater detail from a post-publication perspective. A full length synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools”, and supplementary material is published in the Journal of Microbiology and Biology Education, Vol. 14, No. 1,
Towards extracellular secretion of poly-β-hydroxybutyric acid (PHB) biodegradable polymer
Authors: Ng Wenfa
Published: January 2018

Challenging disposal problems are associated with plastics use due to its poor biodegrability and emissions of hazardous chemicals during incineration. Poly-β-hydroxybutyric acids (PHB), a lipid based storage polymer in bacteria, is biodegradable, biorenewable and biocompatible, and thus, presents a tantalizing possibility for reducing the environmental impacts associated with plastics use. Progressive elucidation of PHB biosynthesis routes provides the understanding necessary for its production through recombinant microorganisms. Originally nature’s solution for helping bacteria moderate fluctuations in nutrient availability, PHB biosynthetic pathway has multiple nodes at which contemporary genetic engineering efforts for overproducing the polymer can be focused. Other means for increasing cellular PHB concentration include optimizing fermentation conditions and growth medium composition. But, intracellular accumulation of PHB (principally as inclusion bodies) and difficulty of extracting it is the main reason for its high cost and lack of competitiveness. Hence, improving cost efficiency of extraction and purification are important for increasing PHB’s market competitiveness vis-à-vis petroleum derived plastics. Additionally, use of toxic solvents and surfactants during PHB extraction also expands its environmental footprint while also contaminating the end-product. Thus, compared with increasing production titer, eliminating the extraction step would go further in reducing PHB’s relative price (cost), and improves its environmental sustainability. However, high hydrophobicity induces PHB to aggregate into inclusion bodies, which points to the need for engineering microbes able to export PHB. Multiple pathways exist for protein export, but none exists for lipids. Hence, a variety of recognition proteins, carrier proteins and transporters, and crucially, their recognition motifs for energy mediated (i.e., hydrolysis of ATP or GTP) transport of PHB through the likely lipid based transport channel must be constituted for extracellular secretion of PHB. Such a goal would require rational engineering of recognition, carrier, transport and channel proteins or their derivation from existing ones through directed evolution. The above possibility set sights on the future, but what is in store at the moment or the foreseeable future? Creating “leaky” bacteria strains for facile “export” of PHB may be a feasible path forward. “Leakiness” can be realized by using current recombinant DNA technology for overexpressing PHB in cells: (i) without a cell envelope, (ii) one with a significantly weakened one, or alternatively, (iii) a cell envelope or peptidoglycan layer with a random/engineered pore structure. Casting glances further out into the future, research into extracellular PHB secretion would likely open up avenues into production and export of lipid biopolymer or macromolecular complexes from recombinant organisms.
Walking down computational chemistry memory lane one acronym at a time
Authors: Ng Wenfa
Published: January 2018

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future; particularly in delineating the context surrounding specific events that, in turn, help provide a deeper understanding of their underlying causes and implications. To the uninitiated, the computational chemistry literature appears intimating given the pervasive use of acronyms and eponymous method names. While jargons expedite communication of complex ideas between specialists, and add clarity to a discussion (e.g., explaining complicated concepts in plain language may not capture subtle - but important - nuances in meaning), they nevertheless presents a significant barrier to understanding for researchers in other fields. Specifically, an inability to comprehend the meaning of the various terms and jargons used would significantly impede understanding and navigating the literature – and may translate into difficulty in selecting appropriate tools for the task at hand. Scientific progress (incremental and breakthroughs) is built upon prior work. By placing various computational methods and techniques along a chronological thread, a commentary article aims to demystify the tangled web of acronyms and terms that populate the electronic structure calculations literature and highlights the interrelationships between methods – particularly, how one method evolved from another. Additionally, the chronological framework also allows readers to appreciate developments in computational chemistry through the lens of major “epochs” (e.g., transition from semi-empirical methods to first-principles calculations), and the centrality of key ideas (e.g., Schrodinger equation and Born-Oppenheimer approximation) in charting progress in the field. Finally, the chronological time-line delineated also provides an opportune backdrop for examining the longstanding question of whether computational power (both capacity and speed) or theoretical insights play a more important role in advancing computational chemistry research. Particularly, availability of large amount of computing power at declining cost, and advent of graphics processing unit (GPU) powered parallel computing are enabling tools for solving hitherto intractable problems. Nevertheless, the article argues, using Born-Oppenheimer approximation as an example, that theoretical insights’ role in unlocking problems through simple – but insightful – assumptions is often overlooked. Collectively, the article should be useful as a primer for researchers to gain a more holistic understanding of computational chemistry, and students wishing to learn more about the conceptual basis and purpose of various electronic structure calculations methods prior to venturing into the field’s expansive literature.
What drives computational chemistry forward: theory or computational power?
Authors: Ng Wenfa
Published: January 2018

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future; particularly in delineating the context surrounding specific events that, in turn, help provide a deeper understanding of their underlying causes and implications. Scientific progress (whether incremental or breakthroughs) is built upon prior work. Chronological examination of the field’s evolution reveals the existence of major “epochs” (e.g., transition from semi-empirical methods to first-principles calculations), and the centrality of key ideas (e.g., Schrodinger equation and Born-Oppenheimer approximation) in potentiating progress in the field. The longstanding question of whether computing power (both capacity and speed) or theoretical insights play a more important role in advancing computational chemistry was examined by taking into account the field’s development holistically. Particularly, availability of large amount of computing power at declining cost, and advent of graphics processing unit (GPU) powered parallel computing are enabling tools for solving hitherto intractable problems. Nevertheless, the article argues, using Born-Oppenheimer approximation as an example, that theoretical insights’ role in unlocking problems through simple (but insightful) assumptions is often overlooked. Collectively, the essay should be useful as a primer for appreciating major development periods in computational chemistry, from which, counterfactual questions illuminate the relative importance of intuition and advances in computing in moving the field forward.
What drives computation chemistry forward: theory or computing power?
Authors: Ng Wenfa
Published: January 2018

History is often thought to be dull and boring – where large numbers of facts are memorized for passing exams. But the past informs the present and future, especially in delineating the context surrounding specific events that, in turn, help provide a deeper understanding of their causes and implications. Scientific progress (whether incremental or breakthroughs) is built upon prior work. Chronological examination of the field’s evolution reveals the existence of major “epochs” (e.g., transition from semi-empirical methods to first principles calculations), and the centrality of key ideas (e.g., Schrodinger equation and Born Oppenheimer approximation) in potentiating progress in the field. The longstanding question of whether computing power (both capacity and speed) or theoretical insights play a more important role in advancing computation chemistry was examined by taking into account the field’s development holistically. Specifically, availability of large amount of computing power at declining cost, and advent of graphics processing unit (GPU) powered parallel computing are enabling tools for solving up to now intractable problems. On the other hand, this essay argues (using Born Oppenheimer approximation as an example) that theoretical insights’ role in unlocking problems through simple (but insightful) assumptions is often overlooked. Collectively, the essay should be useful as a primer for appreciating major development periods in computation chemistry, from which counterfactual questions illuminate the relative importance of intuition and advances in computer science in moving the field forward.
Why not do phylogeography on every chthamalid barnacle? The case of Jehlius cirratus
Authors: Wares John P
Published: January 2018

Here I evaluate the population genetic structure of the barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from close to 2500km of the linear range of this barnacle, there is little evidence for population structure. Hudson's Snn value across all sites is not significantly different from null expectation, and no other phylogeographic structure is evident. Unbalanced sample sizes and their effect on such population genetic and phylogeographic analyses are discussed, but the general conclusion of this study is that J. cirratus can be considered panmictic along the Chilean coast.
Evidence of Ostrea lurida (Carpenter 1864) population structure in Puget Sound, WA
Authors: Heare J. Emerson , Blake Brady , Davis Jonathan P. , Vadopalas Brent , Roberts Steven B.
Published: January 2018

For long term persistence of species, it is important to consider population structure. 28 Traits that hold adaptive advantage such as reproductive timing and stress resilience may differ 29 among locales. Knowledge and consideration of these traits should be integrated into 30 conservation efforts. A reciprocal transplant experiment was carried out monitoring survival, 31 growth, and reproduction using three established populations of Ostrea lurida within Puget 32 Sound, Washington. Performance differed for each population. Ostrea lurida from Dabob Bay 33 had higher survival at all sites but lower reproductive activity and growth. Oysters from Oyster 34 Bay demonstrated greater reproductive activity at all sites with moderate growth and survival. 35 Together these data suggest the existence of O. lurida population structure within Puget Sound 36 and provide information on how broodstock should be selected for restoration purposes.
Evidence of Ostrea lurida (Carpenter 1864) population structure in Puget Sound, WA
Authors: Heare J. Emerson , Blake Brady , Davis Jonathan P. , Vadopalas Brent , Roberts Steven B.
Published: January 2018

For long-term persistence of species, population structure is important. Traits that hold adaptive advantage such as reproductive timing and stress resilience may differ among locales. Knowledge and consideration of these traits should be integrated into conservation efforts. To test for adaptive differences between Olympia oyster populations a reciprocal transplant experiment was carried out monitoring survival, growth, and reproduction using three established populations of Ostrea lurida within Puget Sound, Washington. Performance differed for each population. Ostrea lurida from Dabob Bay had higher survival at all sites but lower reproductive activity and growth. Oysters from Oyster Bay demonstrated greater proportion of brooding females at a majority of sites with moderate growth and survival. Together these data suggest the existence of O. lurida population structure within Puget Sound and provide information on how broodstock should be selected for restoration purposes.
The seasonal reproduction number of dengue fever impacts of climate on transmission
Authors: Polwiang Sittisede
Published: January 2018

Background: The dengue fever is a mosquito-borne viral disease and a regular epidemic in Thailand. The peak of the dengue epidemic period is around June to August during the rainy season. It is believed that the climate is an important factor for dengue transmission.Method: A mathematical model for vector-host infectious disease was used to calculate the impacts of climate to the transmission of dengue virus. In this study, the data of climate and dengue fever cases were derived from Chiang Mai during 2008-2015, Thailand. The value of seasonal reproduction number was calculated to evaluate the potential, severity and persistence of dengue infection.Results: The mosquito population was increasing exponentially from the start of the rainy season in early May and reached its the peak in late June. The simulations suggest that the greatest potential for the dengue transmission occurs when the temperature is 28.9ºC. The seasonal reproduction numbers were larger than one from late March to end of August and reaching the peak in June. The highest incidences occurred in August due to the delay of transmission humans-mosquito-humans. Increasing mean temperature by 1.2ºC, the number of incidences increases 43.7%. However, a very high or very low temperature reduces the number of infection.Discussion and Conclusion: The results show that the dengue infection depends on the seasonal variation of the climate. The rainfall provides places for the mosquitoes to lay eggs and develop to adult stage. The temperature plays an important role in the life cycle and behavior of the mosquitoes. A very high or very low temperature reduces the risk of the dengue infection.
Alteration in microRNA‐17‐92 dynamics accounts for differential nature of cellular proliferation
Authors: Sengupta Dola , Govindaraj Vinodhini , Kar Sandip
Published: January 2018

MicroRNAs associated with the mir‐17‐92 cluster are crucial regulators of the mammalian cell cycle, as they inhibit transcription factors related to the E2F family that tightly control decision‐making events for a cell to commit for active cellular proliferation. Intriguingly, in many solid cancers, these mir‐17‐92 cluster members are overexpressed, whereas in some hematopoietic cancers they are down‐regulated. Our proposed model of the Myc/E2F/mir‐17‐92 network demonstrates that the differential expression pattern of mir‐17‐92 in different cell types can be conceived due to having a contrasting E2F dynamics induced by mir‐17‐92. The model predicts that by explicitly altering the mir‐17‐92‐related part of the network, experimentally it is possible to control cellular proliferation in a cell type‐dependent manner for therapeutic intervention.
Diffuse Extension of the Southern Mariana Margin
Authors: Martinez Fernando , Stern Robert J. , Kelley Katherine A. , Ohara Yashuhiko , Sleeper Jonathan D. , Ribeiro Julia M. , Brounce Maryjo
Published: January 2018

Extension within the southern Mariana margin occurs both normal to and parallel to the trench. Trench‐normal extension takes place along focused and broad backarc spreading axes forming crust that is passively accreted to the rigid Philippine Sea plate flank to the northwest. To the southeast, trench‐parallel extension has split apart the Eocene‐Miocene forearc terrain accreting new crust diffusely over a 150–200 km wide zone forming a pervasive volcano‐tectonic fabric oriented at high angles to the trench and the backarc spreading center. Earthquake seismicity indicates active extension over this forearc region and basement samples date young although waning volcanic activity. Such diffuse formation of new oceanic crust and lithosphere is unusual; in most oceanic settings extension rapidly focuses to narrow plate boundary zones—a defining feature of plate tectonics. Diffuse crustal accretion has been inferred to occur during subduction zone infancy, however. We hypothesize that in a near‐trench extensional setting, the continual addition of water from the subducting slab creates a weak overriding hydrous lithosphere that deforms broadly. This process counteracts mantle dehydration and strengthening proposed to occur at mid‐ocean ridges that may help to focus deformation and melt delivery to narrow plate boundary zones. The observations from the southern Mariana margin suggest that where lithosphere is weakened by high water content narrow seafloor spreading centers cannot form. These conditions likely prevail during subduction zone infancy, explaining the diffuse contemporaneous volcanism inferred in this setting.
Cascadia Onshore‐Offshore Site Response, Submarine Sediment Mobilization, and Earthquake Recurrence
Authors: Gomberg J.
Published: January 2018

Local geologic structure and topography may modify arriving seismic waves. This inherent variation in shaking, or “site response,” may affect the distribution of slope failures and redistribution of submarine sediments. I used seafloor seismic data from the 2011 to 2015 Cascadia Initiative and permanent onshore seismic networks to derive estimates of site response, denoted Sn, in low‐ and high‐frequency (0.02–1 and 1–10 Hz) passbands. For three shaking metrics (peak velocity and acceleration and energy density) Sn varies similarly throughout Cascadia and changes primarily in the direction of convergence, roughly east‐west. In the two passbands, Sn patterns offshore are nearly opposite and range over an order of magnitude or more across Cascadia. Sn patterns broadly may be attributed to sediment resonance and attenuation. This and an abrupt step in the east‐west trend of Sn suggest that changes in topography and structure at the edge of the continental margin significantly impact shaking. These patterns also correlate with gravity lows diagnostic of marginal basins and methane plumes channeled within shelf‐bounding faults. Offshore Sn exceeds that onshore in both passbands, and the steepest slopes and shelf coincide with the relatively greatest and smallest Sn estimates at low and high frequencies, respectively; these results should be considered in submarine shaking‐triggered slope stability failure studies. Significant north‐south Sn variations are not apparent, but sparse sampling does not permit rejection of the hypothesis that the southerly decrease in intervals between shaking‐triggered turbidites and great earthquakes inferred by Goldfinger et al. (2012, 2013, 2016) and Priest et al. (2017) is due to inherently stronger shaking southward.
Measuring Mountain River Discharge Using Seismographs Emplaced Within the Hyporheic Zone
Authors: Anthony R. E. , Aster R. C. , Ryan S. , Rathburn S. , Baker M. G.
Published: January 2018

Flow and sediment transport dynamics in fluvial systems play critical roles in shaping river morphology, in the design and use of riverine infrastructure, and in the broader management of watersheds. However, these properties are often difficult to measure comprehensively. Previous work has suggested the use of proximal seismic signals resulting from flow and bed load transport to construct more complete records of these fluvial processes. We investigate a small (184 km2; < 20 m3/s), snowmelt‐fed mountain river in the Northern Colorado Rocky Mountains during May–August 2015 to capture peak runoff with colocated measurements of discharge and seismic noise. Three‐component seismometers were placed in close proximity to the channel bank (~1 m) within the hyporheic zone (at times submerged beneath the water table). We recorded a broad spectrum of seismic signals excited by discharge, including novel, low‐frequency (0.1–2 Hz) signals observed predominantly on the horizontal components. The characteristics of these low‐frequency signals are not consistent with an elastically propagating seismic wave. We instead infer that they likely arise from the sensor tilting in response to viscoelastic deformation occurring near the channel and propose large‐scale turbulent eddies as a forcing mechanism. Calibrating horizontal seismic power with hydrograph flow rates over the course of a rainstorm for individual sensors, we demonstrate that these unique signals can be used to accurately estimate river discharge with simple regressions. This technique shows promise for augmenting seismic monitoring of rivers by enabling discharge rates to be estimated from outside the channel using easily deployed and noninvasive seismic instrumentation.
Motion analysis of furniture under seismic excitation using the finite element method
Authors: Isobe Daigoro , Yamashita Takuzo , Tagawa Hiroyuki , Kaneko Mika , Takahashi Toru , Motoyui Shojiro
Published: January 2018

Improperly secured furniture, especially on the upper floors of high‐rise buildings under long‐period ground motion, can prove dangerous to human life. Fallen items of furniture such as chairs and desks could become fatal obstacles that prevent efficient evacuation. In this research, an effective numerical code for analyzing the motion of furniture subjected to seismic excitations was developed. The numerical code is based on the adaptively shifted integration — Gauss technique, which is a finite element scheme that provides higher computational efficiency than the conventional code. The frictional contact between objects was fully considered by employing a sophisticated penalty method. Various excitation tests of furniture were conducted on a shake‐table. In the experiments, steel cabinets were excited by seismic waves and displacement data were recorded by a motion capture system. The numerical results were validated through a comparison with the shake‐table test results.
Skin Conformal Polymer Electrodes for Clinical ECG and EEG Recordings
Authors: Stauffer Flurin , Thielen Moritz , Sauter Christina , Chardonnens Séverine , Bachmann Simon , Tybrandt Klas , Peters Christian , Hierold Christofer , Vörös Janos
Published: January 2018

Preparation‐free and skin compliant biopotential electrodes with high recording quality enable wearables for future healthcare and the Internet of Humans. Here, super‐soft and self‐adhesive electrodes are presented for use on dry and hairy skin without skin preparation or attachment pressure. The electrodes show a skin‐contact impedance of 50 kΩ cm2 at 10 Hz that is comparable to clinical standard gel electrodes and lower than existing dry electrodes. Microstructured electrodes inspired by grasshopper feet adhere repeatedly to the skin with a force of up to 0.1 N cm−2 without further attachment even during strong movement or deformation of the skin. Skin compliance and adhesive properties of the electrodes result in reduction of noise and motion artifacts superior to other dry electrodes reaching the performance of commercial gel electrodes. The signal quality is demonstrated by recording a high‐fidelity electrocardiograms of a swimmer in water. Furthermore, an electrode with soft macropillars is used to detect alpha activity in the electroencephalograms from the back of the head through dense hair. Compared to gel electrodes, the soft biopotential electrodes are nearly imperceptible to the wearer and cause no skin irritations even after hours of application. The electrodes presented here could combine unobtrusive and long‐term biopotential recordings with clinical‐grade signal performance.
Inexpensive Ruthenium NNS‐Complexes as Efficient Ester Hydrogenation Catalysts with High C=O vs. C=C Selectivities
Authors: Stadler Bernhard M. , Puylaert Pim , Diekamp Justus , van Heck Richard , Fan Yuting , Spannenberg Anke , Hinze Sandra , de Vries Johannes G.
Published: January 2018

Ru(NNS)(PPh3)Cl2 (NNS=2‐(methylthio)‐N‐(pyridin‐2‐yl‐methyl)ethan‐1‐amine) was employed in the hydrogenation of α,β‐unsaturated esters, reaching selectivities for the allylic alcohol up to 95% in the hydrogenation of iso‐butylcinnamate. In addition, several ester substrates were hydrogenated with catalyst loadings as low as 0.05 mol%. Surprisingly, selectivity of the hydrogenation of the C=O vs the C=C bonds strongly depends on the solvent.

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