bluuebunny/crossref_metadata_2025 huggingface dataset:
The Gap Rock Lighthouse: construction and typhoon damage
Authors: Deng K. Y. , Poon S. W.
Published: August 2019

This paper focuses on the Gap Rock lighthouse, a legendary maritime infrastructure built 130 years ago in the Chinese territory and an early example of joint venture among the Qing Dynasty, the British Empire and the Hong Kong Colonial Government over a course of two decades. Based on 4 years of cross-territorial archival and field research as well as in-depth interviews with descendants of two key stakeholders, the origin of this lasting legacy on the sea is traced, followed by a detailed account of its challenging processes of planning, design and construction, and of the considerable damage to the compound by a severe typhoon in 1893. A qualitative analysis of the key contributing factors of the damage was conducted by taking into consideration the Island's unique topography and the historical records of territorial weather reports. A re-construction of the typhoon impact on the Lighthouse is presented to explain the possible mistakes in its siting and design that eventually caused the severe damage. This serves as a reminder of the significance of a thorough geographical investigation for any infrastructure for all construction professionals in the face of climatic change.

This article is part of the theme issue ‘Environmental loading of heritage structures’.
High-resolution time-dependent probabilistic assessment of the hydraulic performance for historic coastal structures: application to Luarca Breakwater
Authors: Lara Javier L. , Lucio David , Tomas Antonio , Di Paolo Benedetto , Losada Inigo J.
Published: August 2019

Historic coastal structures have played a key role in small- to medium-size ports, being the driving force for the local development of coastal communities. Because coastal managers require reliable risk-based analysis of the whole life cycle of these coastal structures, previous lifetimes should be studied. This is a differentiating factor with respect to the newly built breakwaters. For this reason, in this work, a methodology for assessing how the hydraulic performance of an expired lifetime has evolved over the years is presented. It is performed following a probabilistic approach due to the uncertainty related to both the involved variables (wave climate, geometrical and structural breakwater variables) and the hydraulic response of the structure. The first ones are characterized by reliable probability distribution functions. The second ones are characterized by reliable formulae for the analysis of the hydraulic response. However, their non-conventional designs located in shallow-water locations require site-dependent formulae. To overcome this problem, a novel methodology to apply CFD numerical models is presented. Finally, it is integrated in a high-resolution time-dependent probabilistic methodology which takes into account the stochastic behaviour of all the involved variables, coastal and structural processes with a good uncertainty level.

This article is part of the theme issue ‘Environmental loading of heritage structures’.
Wolf Rock lighthouse: past developments and future survivability under wave loading
Authors: Raby A. C. , Antonini A. , Pappas A. , Dassanayake D. T. , Brownjohn J. M. W. , D'Ayala D.
Published: August 2019

Lighthouses situated on exposed rocky outcrops warn mariners of the dangers that lurk beneath the waves. They were first constructed when approaches to wave loading and structural response were relatively unsophisticated, essentially learning from previous failures. Here, we chart the evolution of lighthouses on the Wolf Rock, situated between Land's End and the Isles of Scilly in the UK. The first empirical approaches are described, followed by design aspects of the present tower, informed by innovations developed on other rocky outcrops. We focus on a particular development associated with the automation of lighthouses: the helideck platform. The design concept is described and the structure then scrutinized for future survivability, using the latest structural modelling techniques of the entire lighthouse and helideck. Model validation data were obtained through a complex logistical field operation and experimental modal analysis. Extreme wave loading for the model required the identification of the 250-year return period wave using a Bayesian method with informative prior distributions, for two different scenarios (2017 and 2067). The structural models predict responses of the helideck to wave loading which is characterized by differential displacements of 0.093 m (2017) and 0.115 m (2067) with associated high tension forces and plastic strain.

This article is part of the theme issue ‘Environmental loading of heritage structures’.
Historical review of lighthouse design under wind load: the Ile Vierge lighthouse
Authors: Domede Nathalie , Pena Luisa , Fady Nicolas
Published: August 2019

The purpose of the study presented here is to describe the design method used by engineers in the nineteenth and early twentieth centuries to size lighthouse structures and to compare them with current European standards. The historical information presented here is derived from two sources in particular: the archives of the Ile Vierge lighthouse, which was built at the northern tip of Brittany between 1897 and 1902, and the scientific journals, books and courses available at that time. Firstly, the article describes the structure of the Ile Vierge lighthouse, which is the tallest stone lighthouse in Europe. The wind load acting on lighthouses and chimneys was formulated in France by L. Fresnel in 1825. Fresnel's work is compared to W. J. M. Rankine's theory used in the UK. The safety coefficients applied with respect to the stability of the towers in France and the UK in the nineteenth-century are compared. On the occasion of the construction of the Ile Vierge lighthouse, the masonry strength under wind loads led to a discussion among engineers of the French lighthouse authorities. They also worried about the risk of excessive oscillations of the towers, which could cause a dysfunction of the lamp. Thirdly, the standard wind action defined in Eurocode 1 is applied to the Ile Vierge lighthouse. Calculation results are given. A comparative analysis of the ancient and modern methods is presented. Overall, this historical research shows that the designers of lighthouses in the nineteenth-century had the same objectives as today: to build strong, durable structures in which deformations under loads are compatible with serviceability.

This article is part of the theme issue ‘Environmental loading of heritage structures’.
Oral flora meningoencephalitis diagnosis by next-generation DNA sequencing
Authors: Heintz Eric , Pettengill Matthew A. , Gangat Mohamed Azhar , Hardy Dwight J. , Bonnez William , Sobhanie Mohammed Mahdee
Published: August 2019

Introduction. Standard culture methods may fail to detect the causative agents of bacterial infection for various reasons including specimen collection after antibiotic administration, or when standard techniques or environmental conditions are not appropriate for growth of the microorganisms. Conventional 16S rRNA gene sequencing is sometimes a useful alternative technique for identification of bacteria, but is confounded by polymicrobial infection. We present a case of a patient who developed a serious neurological infection for which causative oral flora organisms were observed by microscopy, failed to culture but were identified by next-generation DNA sequencing.

Case presentation. A male in his forties developed sinus pain and congestion, followed by facial and eye pain, and several weeks later acute-onset confusion and neck stiffness. Cerebrospinal fluid examination revealed pleocytosis and several bacterial morphologies, which were subsequently identified by next-generation sequencing as oral flora constituents

Porphyromonas endodontalis

,

Fusobacterium nucleatum

,

Streptococcus constellatus

,

Prevotella

species and

Parvimonas micra

.

Conclusion. Oral flora can cause meningoencephalitis and brain abscess formation if translocation occurs by injury or surgical procedures. Next-generation sequencing is often not available at healthcare facilities, or when available may not have been validated for a wide spectrum of specimen sources, but is available at reference laboratories and should be considered when routine methods fail to provide a diagnosis for serious infections.
RNA processing bodies are disassembled during Old World alphavirus infection
Authors: Liu Lifeng , Weiss Eva , Panas Marc D. , Götte Benjamin , Sellberg Stina , Thaa Bastian , McInerney Gerald M.
Published: August 2019

RNA processing bodies (P-bodies) are non-membranous cytoplasmic aggregates of mRNA and proteins involved in mRNA decay and translation repression. P-bodies actively respond to environmental stresses, associated with another type of RNA granules, known as stress granules (SGs). Alphaviruses were previously shown to block SG induction at late stages of infection, which is important for efficient viral growth. In this study, we found that P-bodies were disassembled or reduced in number very early in infection with Semliki Forest virus (SFV) or chikungunya virus (CHIKV) in a panel of cell lines. Similar to SGs, reinduction of P-bodies by a second stress (sodium arsenite) was also blocked in infected cells. The disassembly of P-bodies still occurred in non-phosphorylatable eIF2α mouse embryonal fibroblasts (MEFs) that are impaired in SG assembly. Studies of translation status by ribopuromycylation showed that P-body disassembly is independent of host translation shutoff, which requires the phosphorylation of eIF2α in the SFV- or CHIKV-infected cells. Labelling of newly synthesized RNA with bromo-UTP showed that host transcription shutoff correlated with P-body disassembly at the same early stage (3–4 h) after infection. However, inhibition of global transcription with actinomycin D (ActD) failed to disassemble P-bodies as effectively as the viruses did. Interestingly, blocking nuclear import with importazole led to an efficient P-bodies loss. Our data reveal that P-bodies are disassembled independently from SG formation at early stages of Old World alphavirus infection and that nuclear import is involved in the dynamic of P-bodies.
De novowhole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’
Authors: Shirasawa Kenta , Azuma Akifumi , Taniguchi Fumiya , Yamamoto Toshiya , Sato Akihiko , Hirakawa Hideki , Isobe Sachiko
Published: August 2019

This study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana×V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and aV. viniferaline. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.
The Secretomes of Painful Versus Nonpainful Human Schwannomatosis Tumor Cells Differentially Influence Sensory Neuron Gene Expression and Sensitivity
Authors: Ostrow Kimberly Laskie , Donaldson Katelyn J. , Caterina Michael J. , Belzberg Allan , Hoke Ahmet
Published: August 2019

Schwannomatosis is a multiple tumor syndrome in which patients develop benign tumors along peripheral nerves throughout the body. The first symptom with which schwannomatosis patients often present, prior to discovery of tumors, is pain. This pain can be debilitating and is often inadequately alleviated by pharmacological approaches. Schwannomatosis-associated pain can be localized to the area of a tumor, or widespread. Moreover, not all tumors are painful, and the occurrence of pain is often unrelated to tumor size or location. We speculate that some individual tumors, but not others, secrete factors that act on nearby nerves to augment nociception by producing neuronal sensitization or spontaneous neuronal firing. We created cell lines from human SWN tumors with varying degrees of pain. We have found that conditioned medium (CM) collected from painful SWN tumors, but not that from nonpainful SWN tumors, sensitized DRG neurons, causing increased sensitivity to depolarization by KCl, increased response to noxious TRPV1 and TRPA1 agonists and also upregulated the expression of pain-associated genes in DRG cultures. Multiple cytokines were also detected at higher levels in CM from painful tumors. Taken together our data demonstrate a differential ability of painful versus non-painful human schwannomatosis tumor cells to secrete factors that augment sensory neuron responsiveness, and thus identify a potential determinant of pain heterogeneity in schwannomatosis.
Wax ester production in nitrogen-rich conditions by metabolically engineeredAcinetobacter baylyiADP1
Authors: Luo Jin , Efimova Elena , Losoi Pauli , Santala Ville , Santala Suvi
Published: August 2019

Metabolic engineering can be used as a powerful tool to redirect cell resources towards product synthesis, also in conditions that are not optimal. An example of a synthesis pathway strongly dependent on external conditions is the production of storage lipids, which typically requires high carbon/nitrogen ratio.Acinetobacter baylyiADP1 is known for its ability to produce industrially interesting storage lipids, namely wax esters (WEs). Here, we engineered the central carbon metabolism ofA. baylyiADP1 by deletion of the geneaceAencoding for isocitrate lyase in order to allow redirection of carbon towards WEs. The production was further enhanced by overexpression of fatty acyl-CoA reductase Acr1 in the wax ester production pathway. This strategy led to 3-fold improvement in yield (0.075 g/g glucose) and 3.15-fold improvement in titer (1.82 g/L) and productivity (0.038 g/L/h) by a simple one-stage batch cultivation with glucose as carbon source. The engineered strain accumulated up to 27% WEs of cell dry weight. The titer and cellular WE content are the highest reported to date among microbes. We further showed that the engineering strategy alleviated the inherent requirement for high carbon/nitrogen ratio and demonstrated the production of wax esters using nitrogen-rich substrates including casamino acids, yeast extract and baker’s yeast hydrolysate, which support biomass production but not WE production in wild-type cells. The study demonstrates the power of metabolic engineering in overcoming natural limitations in the production of storage lipids.
Indication of a reduction in the cover of thin-leaved plants in Danish grasslands over an eight-year period
Authors: Damgaard Christian
Published: August 2019

Across four grassland habitat types, the cover of thin-leaved plants was found to decrease significantly, but generally only limited trait selection was observed on leaf traits (SLA and LDMC) in a study of an extensive Danish grassland vegetation dataset from an eight-year period. The mostly negative result of this study may partly be due to the relatively conservative analysis, where the continuous plant trait variables are used for grouping plant species into functional types, which are then treated as dependent variables. This procedure is in contrast to most other analyses of trait selection, where it is the community weighted mean of the traits that is used as the dependent variable. However, it is not the traits, but rather individual plants that are sampled and, consequently, it is important to consider the sampling of species abundance in the statistical modelling of plant traits. This misapprehension has not received sufficient proper attention in the plant trait literature.
Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid
Authors: Zander Mark , Lewsey Mathew G. , Clark Natalie M. , Yin Lingling , Bartlett Anna , Saldierna Guzmán J. Paola , Hann Elizabeth , Langford Amber E. , Jow Bruce , Wise Aaron , Nery Joseph R. , Chen Huaming , Bar-Joseph Ziv , Walley Justin W. , Solano Roberto , Ecker Joseph R.
Published: August 2019

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA that spans from the activity of master and secondary-regulatory transcription factors, through gene expression outputs and alternative splicing to protein abundance changes, protein phosphorylation and chromatin remodeling. We integrated time series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enable us to predict previously unknown points of crosstalk from JA to other signaling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behavior, the general principles of which provide a framework for analysis of cross-regulation between other hormone and stress signaling pathways.
Syndecan-4 is required for VE-Cadherin trafficking during pathological angiogenesis
Authors: Rossi Giulia De , Vähätupa Maria , Cristante Enrico , Liyanage Sidath E. , May Ulrike , Pellinen Laura , Aittomäki Saara , Cordova Zuzet Martinez , Pesu Marko , Uusitalo-Järvinen Hannele , Bainbridge James W. , Järvinen Tero A.H. , Whiteford James R.
Published: August 2019

New blood vessel formation, or angiogenesis, is characteristic of chronic diseases such as cancer, rheumatoid arthritis and vision-threatening conditions. Vascular Endothelial growth factor (VEGFA) and its receptor VEGFR2 drive neovascularization and hyperpermeability in these pathologies. One consequence of VEGFR2 activation is decreased stability of endothelial cell (EC) junctions through internalization of VE-Cadherin, allowing re-arrangement of sprouting ECs. Evidence suggests roles for heparan sulfate proteoglycans in angiogenesis and we show that Syndecan-4 (SDC4) expression is upregulated during pathological angiogenesis and is required for efficient VE-Cadherin internalization. Angiogenic responses in both tumor and neovascular eye disease models are impaired in Syndecan-4 null mice (Sdc4-/-), as is dermal hyper-permeability response to VEGFA. We show SDC4 resides at EC junctions and interacts with VE-Cadherin, an association lost upon VEGFA-stimulation, and this is SDC4 phosphorylation-dependent. Finally, we show that pathological angiogenic responses can be inhibited in a model of age-related macular degeneration by targeting SDC4. This study identifies SDC4 as a key component of VE-Cadherin trafficking and, as such, a critical regulator of pathological angiogenesis and vascular permeability.
MarkedNeurospora crassastrains for competition experiments and Bayesian methods for fitness estimates
Authors: Kronholm Ilkka , Ormsby Tereza , McNaught Kevin J. , Selker Eric U. , Ketola Tarmo
Published: August 2019

The filamentous fungusNeurospora crassa, a model microbial eukaryote, has a life cycle with many features that make it suitable for studying experimental evolution. However, it has lacked a general tool for estimating relative fitness of different strains in competition experiments. To remedy this need, we constructedN. crassastrains that contain a modifiedcsr-1locus and developed an assay for detecting the proportion of the marked strain using a post PCR high resolution melting assay. DNA extraction from spore samples can be performed on 96-well plates, followed by a PCR step, which allows many samples to be processed with ease. Furthermore, we suggest a Bayesian approach for estimating relative fitness from competition experiments that takes into account the uncertainty in measured strain proportions. We show that there is a fitness effect of the mating type locus, as mating typemat ahas a higher competitive fitness thanmat A. Thecsr-1* marker also has a small fitness effect, but is still a suitable marker for competition experiments. As a proof of concept, we estimate the fitness effect of theqde-2mutation, a gene in the RNA interference pathway, and show that its competitive fitness is lower than what would be expected from its mycelial growth rate alone.
Transcriptome-based Analysis of Tomato Genotypes Resistant to Bacterial spot (Xanthomonas perforans)Race T4
Authors: Shi Rui , Panthee Dilip R.
Published: August 2019

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato caused by multiple species ofXanthomonas. We performed the RNA-Seq analysis of three tomato lines with different level of resistance toXanthomonas perforansrace T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations.

Analysis between inoculated and control samples revealed that resistant line PI 270443 had more DEGs (834), followed by susceptible line NC 714 (373), and intermediate line NC 1CELBR (154). Gene functional analysis based onGene Ontology(GO) terms revealed that more GO terms (51) were enriched for up-regulated DEGs in the resistant line PI 270443, and more down-regulated DEGs (67) were enriched in the susceptible line NC 714. The specific analysis for DEGs in biotic stress pathway using MapMan software showed more up-regulated biotic stress pathway DEGs (67) for PI 270443 compared to more down-regulated DEGs (125) for susceptible NC 714 line. One interesting feature was that resistant PI 270443 has three up-regulated DEGs for PR-protein, and susceptible line NC 714 has one down-regulated R gene, which is disease-related.

Analysis of sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11 which has multiple reported resistance QTLs to BS race T4 is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR-resistance proteins with sequence variation between the resistant and susceptible tomato lines were identified near the knownRx4resistance gene on chr11. These findings may be useful for further molecular breeding of tomato.
Heterogeneous transcriptome response to DNA damage at single cell resolution
Authors: Park Sung Rye , Namkoong Sim , Zhang Zac Zezhi , Friesen Leon , Chen Yu-Chih , Yoon Euisik , Kim Chang H. , Kwak Hojoong , Kang Hyun Min , Lee Jun Hee
Published: August 2019

Cancer cells often heterogeneously respond to genotoxic chemotherapy, leading to fractional killing and chemoresistance1, 2, which remain as the major obstacles in cancer treatment. It is widely believed that DNA damage induces a uniform response in regulating transcription and that cell fate is passively determined by a threshold mechanism evaluating the level of transcriptional responses3. On the contrary to this assumption, here we show that a surprisingly high level of heterogeneity exists in individual cell transcriptome responses to DNA damage, and that these transcriptome variations dictate the cell fate after DNA damage. Many DNA damage response genes, including tumor suppressor p53 targets, were exclusively expressed in only a subset of cells having specific cell fate, producing unique stress responses tailored for the fate that the cells are committed to. For instance, CDKN1A, the best known p53 target inhibiting cell cycle, was specifically expressed in a subset of cells undergoing cell cycle checkpoint, while other pro-apoptotic p53 targets were expressed only in cells undergoing apoptosis. A small group of cells exhibited neither checkpoint nor apoptotic responses, but produced a unique transcriptional program that conferred strong chemoresistance to the cells. The heterogeneous transcriptome response to DNA damage was also observed at the protein level in flow cytometry. Our results demonstrate that cell fate heterogeneity after DNA damage is mediated by distinct transcriptional programs generating fate-specific gene expression landscapes. This finding provides an important insight into understanding heterogeneous chemotherapy responses of cancer cells.
Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution
Authors: Ostevik Kate L. , Samuk Kieran , Rieseberg Loren H.
Published: August 2019

Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous ad-hoc methods while being systematic, repeatable, and is applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolarisssp.petiolarisandH. petiolarisssp.fallax.

Using syntR, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years – a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm thatHelianthushas an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.
Diversification of CORVET tethers facilitates transport complexity inTetrahymena thermophila
Authors: Sparvoli Daniela , Zoltner Martin , Field Mark C. , Turkewitz Aaron
Published: August 2019

In endolysosomal networks, two hetero-hexameric tethers called HOPS and CORVET are found widely throughout eukaryotes. The unicellular ciliateTetrahymena thermophilapossesses elaborate endolysosomal structures, but curiously both it and related protozoa lack the HOPS tether and several other trafficking genes while retaining the related CORVET complex.Tetrahymenaencodes multiple paralogs of most CORVET subunits, which assemble into six distinct complexes. Each complex has a unique subunit composition and, significantly, shows unique localization, indicating participation in distinct pathways. One pair of complexes differ by a single subunit (Vps8), but have late endosomal vs. recycling endosome locations. While Vps8 subunits are thus prime determinants for targeting and functional specificity, determinants exist on all subunits except Vps11. This unprecedented expansion and diversification of CORVET provides a potent example of tether flexibility, and illustrates how ‘backfilling’ following secondary losses of trafficking genes can provide a mechanism for evolution of new pathways.
Geometric purity, kinematic scaling and dynamic optimality in drawing movements beyond ellipses
Authors: Matic Adam , Gomez-Marin Alex
Published: August 2019

Drawing movements have been shown to comply with a power law constraining local curvature and instantaneous speed. In particular, ellipses have been extensively studied, enjoying a 2/3 exponent. While the origin of such non-trivial relationship remains debated, it has been proposed to be an outcome of the least action principle whereby mechanical work is minimized along 2/3 power law trajectories. Here we demonstrate that such claim is flawed. We then study a wider range of curves beyond ellipses that can have 2/3 power law scaling. We show that all such geometries are quasi-pure with the same spectral frequency. We then numerically estimate that their dynamics produce minimum jerk. Finally, using variational calculus and simulations, we discover that equi-affine displacement is invariant across different kinematics, power law or otherwise. In sum, we deepen and clarify the relationship between geometric purity, kinematic scaling and dynamic optimality for trajectories beyond ellipses. It is enticing to realize that we still do not fully understand why we move our pen on a piece of paper the way we do.

Highlights

Several curves beyond ellipses have power-law kinematics with 2/3 exponent.

The curvature spectrum of each of such geometries is quasi-pure at frequency 2.

Their dynamics are shown to comply with minimum of jerk.

But the 2/3 power law is not an outcome of minimizing mechanical work.

Yet, equi-affine displacement is invariant upon different kinematics.

Graphical abstract

“We must represent any change, any movement, as absolutely indivisible.” — Henri Bergson
A Nanoemulsion as an Effective Treatment Against Human Pathogenic Fungi
Authors: Garcia Alexis , Fan Yong Yi , Vellanki Sandeep , Huh Eun Young , Vanegas DiFernando , Wang Su He , Lee Soo Chan
Published: August 2019

The emergence of immunocompromising diseases such as HIV/AIDS or other immunosuppressive medical conditions have opened an opportunity for fungal infections to afflict patients globally. An increase antifungal drug resistant fungi have posed a serious threat to patients. Combining these circumstances with a limited variety of antifungal drugs available to treat patients has left us in a situation where we need to develop new therapeutic approaches that are less prone to development of resistance by pathogenic fungi. In this study we present the utilization of the nanoemulsion NB-201 to control human pathogenic fungi. We found that the NB-201 exhibited in vitro activity against C. albicans, including both planktonic growth and biofilms. Furthermore, treatments with NB-201 significantly reduced the fungal burden at the infection site and presented enhanced healing process after subcutaneous infections by multidrug resistant C. albicans in a murine host system. NB-201 also exhibited in vitro growth inhibition activity against other fungal pathogens, including Cryptococcus spp, Aspergillus fumigatus, and Mucorales. Due to the nature of the activity of this nanoemulsion, there is a minimized chance of drug resistance to develop, thus presents a novel treatment to control fungal wound or skin infections.
Streaming of repeated noise in primary and secondary fields of auditory cortex
Authors: Saderi Daniela , Buran Bradley N , David Stephen V
Published: August 2019

Statistical regularities in natural sounds facilitate the perceptual segregation of auditory sources, or streams. Repetition is one cue that drives stream segregation in humans, but the neural basis of this perceptual phenomenon remains unknown. We demonstrated a similar perceptual ability in animals by training ferrets to detect a stream of repeating noise samples (foreground) embedded in a stream of random samples (background). During passive listening, we recorded neural activity in primary (A1) and secondary (PEG) fields of auditory cortex. We used two context-dependent encoding models to test for evidence of streaming of the repeating stimulus. The first was based on average evoked activity per noise sample and the second on the spectro-temporal receptive field (STRF). Both approaches tested whether changes in the neural response to repeating versus random stimuli were better modeled by scaling the response to both streams equally (global gain) or by separately scaling the response to the foreground versus background stream (stream-specific gain). Consistent with previous observations of adaptation, we found an overall reduction in global gain when the stimulus began to repeat. However, when we measured stream-specific changes in gain, responses to the foreground were enhanced relative to the background. This enhancement was stronger in PEG than A1. In A1, enhancement was strongest in units with low sparseness (i.e., broad sensory tuning) and with tuning selective for the repeated sample. Enhancement of responses to the foreground relative to the background provides evidence for stream segregation that emerges in A1 and is refined in PEG.
Saving large fish through harvest slots outperforms the classical minimum-length limit when the aim is to achieve multiple harvest and catch-related fisheries objectives
Authors: Ahrens Robert N. M. , Allen Micheal S. , Walters Carl , Arlinghaus Robert
Published: August 2019

We address the problem of optimal size-selective exploitation in an age-structured fish population model by systematically examining how density- and size-dependency in growth, mortality and fecundity affect optimal harvesting patterns when judged against a set of common fisheries objectives. Five key insights are derived. First, while minimum-length limits often maximize the biomass yield, exploitation using harvest slots (i.e., regulations that protect both immature and very large individuals) can generate within 95% of maximum yield, and harvest slots generally maximize the number of fish that are harvested. Second, density-dependence in growth and size-dependent mortality predict more liberal optimal size-limits than those derived under assumptions of no density and size-dependence. Third, strong density-dependence in growth maximizes the production of trophy fish in the catch only when some modest harvest is introduced; the same holds for numbers harvested, when the stock-recruitment function follows the Ricker-type. Fourth, the inclusion of size-dependent maternal effects on fecundity or egg viability has only limited effects on optimal size limits, unless the increase in fecundity with mass (“hyperallometry”) is very large. Extreme hyperallometry in fecundity also shifts the optimal size-limit for biomass yield from the traditional minimum-length limit to a harvest slot. Fifth, harvest slots generally provide the best compromises among multiple objectives. We conclude that harvest slots, or more generally dome-shaped selectivity to harvest, can outperform the standard minimum-length selectivity. The exact configuration of optimal size limits crucially depends on objectives, local fishing pressure, the stock-recruitment function and the density and size-dependency of growth, mortality and fecundity.
Lossless and Contamination-Free Digital PCR
Authors: Liao Peiyu , Jiang Mengcheng , Chen Zitian , Zhang Fangli , Sun Yue , Nie Jun , Du Meijie , Wang Jianbin , Fei Peng , Huang Yanyi
Published: August 2019

The realization of the vast potential of digital PCR (dPCR), to provide extremely accurate and sensitive measurements in the clinical setting, has thus far been hindered by challenges such as assay robustness and high costs. Existing popular dPCR platforms that target the clinic have not reached wide-spread adoption, due to problems with sample loss and risk of contamination during sample preparation, compartmentalization, and transfers; limitations of dynamic range and signal-to-noise in the result readout also restricts broad applications. Here we introduce a lossless and contamination-free dPCR technology termed CLEAR-dPCR, which addresses these challenges by completing the dPCR sample preparation, PCR reaction, and readout all in one tube. We achieve this by adjusting the refractive index of the aqueous PCR mix to make the emulsion optically transparent, and devised a light-sheet microscope to capture 3D images of the cleared emulsion for results readout. This approach demonstrates improved accuracy over existing dPCR platforms, and enables a greatly increased dynamic range to be comparable to that of real-time quantitative PCR (qPCR). CLEAR-dPCR is an easy to operate, sensitive and accurate dPCR platform that we envision will fulfill the potential of dPCR for routine use clinical diagnosis.
Flexible regions in the molecular architecture of Human fibrin clots structurally resolved by XL-MS and integrative structural modeling
Authors: Klykov Oleg , van der Zwaan Carmen , Heck Albert J.R. , Meijer Alexander B. , Scheltema Richard A.
Published: August 2019

Upon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots that assist in wound healing. Limited insights into their molecular architecture, due to the sheer size and insoluble character of fibrin clots, have however restricted our ability to develop novel treatments for clotting diseases. The so far resolved disparate structural details did provide insights into linear elongation; however, molecular details like the C-terminal domain of theα-chain, the heparin-binding domain on theβ-chain, and others involved in lateral aggregation are lacking. To illuminate these dark areas, we applied crosslinking mass spectrometry (XL-MS) to obtain biochemical evidence in the form of over 300 distance constraints and combined this with structural modeling. These restraints additionally define the interaction network of the clots and e.g. provide molecular details for the interaction with Human Serum Albumin (HSA). We were able to construct the models of fibrinogenα(excluding two highly flexible regions) andβ, confirm these models with known structural arrangements and map how the structure laterally aggregates to form intricate lattices together with fibrinogenγ. We validate the final model by mapping mutations leading to impaired clot formation. From a list of 22 mutations, we uncovered structural features for all, including a crucial role forβArg’196 in lateral aggregation. The resulting model will be invaluable for research on dysfibrinogenemia and amyloidosis, as it provides insights into the molecular mechanisms of thrombosis and bleeding disorders related to fibrinogen variants. The structure is provided in the PDB-DEV repository.
Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
Authors: Jacobsen Thomas , Yi Gloria , Asafen Hadel Al , Jermusyk Ashley A. , Beisel Chase L. , Reeves Gregory T.
Published: August 2019

Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5’ untranslated region (UTR) vs. 3’UTR) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.
1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector
Authors: Tolstikova A. , Levantino M. , Yefanov O. , Hennicke V. , Fischer P. , Meyer J. , Mozzanica A. , Redford S. , Crosas E. , Opara N. L. , Barthelmess M. , Lieske J. , Oberthuer D. , Wator E. , Mohacsi I. , Wulff M. , Schmitt B. , Chapman H. N. , Meents A.
Published: August 2019

Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.
A new lanthanum coordination polymer built from a semi-rigid tripodal carboxylic acid ligand: synthesis, crystal structure and properties
Authors: Zhou Lian , Shi Pei-Dong , Guo Xiao-Kun , Feng Xiu-Cun , Wang Lin-Lin , Zhang Jun
Published: August 2019

By employing the semi-rigid multidentate carboxylic acid ligand 4,4′,4′′-{[(2,4,6-trimethylbenzene-1,3,5-triyl)tris(methylene)]tris(oxy)}tribenzoic acid (denoted H3
L), a new lanthanum coordination polymer, namely poly[[bis(dimethylformamide)(μ6-4,4′,4′′-{[(2,4,6-trimethylbenzene-1,3,5-triyl)tris(methylene)]tris(oxy)}tribenzoato)lanthanum(III)] dimethylformamide tetrasolvate 0.25-hydrate], {[La(C33H27O9)(C3H7NO)2]·4C3H7NO·0.25H2O}
n
or {[La(L)(DMF)2]·4(DMF)·0.25(H2O)}
n
(DMF is dimethylformamide) (1), was prepared and characterized by single-crystal X-ray diffraction, elemental analysis, thermogravimetric analysis, IR spectroscopy and photoluminescence studies. The asymmetric unit contains one LaIII cation, one anionic L
3− ligand, two coordinated DMF molecules, four free DMF molecules and one-quarter of a free water molecule. Compound 1 possesses (3,6)-connected two-dimensional kgd topology sheets consisting of secondary building units of La2 clusters and L
3− ligands, which further stack into three-dimensional supramolecular networks through π–π interactions. Compound 1 exhibits a photoluminescence emission at room temperature, with a peak at 410 nm, owing to a ligand-centred excited state.
Corrosion inhibition of aluminum by oxalate self-assembling monolayer
Authors: Satyabama P. , Rajendran Susai , Nguyen Tuan Anh
Published: August 2019

Purpose

This paper aims to evaluate the inhibition efficiency (IE) of oxalate ions in controlling corrosion of aluminum at pH 10.

Design/methodology/approach

The IE has been determined by the classical weight loss method. The corrosion behavior of aluminum was investigated by using potentiodynamic polarization and electrochemical impedance measurements. Ultra violet (UV)-visible and Fluorescence spectra have been used to analyze the film formed on the aluminum surface after immersion.

Findings

The maximum IE was 88 per cent, which was offered by a mixture of 250 ppm oxalate ions and 50 ppm [Zn2+]. Potentiodynamic polarization data revealed that the protective film was formed on the metal surface. UV-visible and Fluorescence spectra indicated the presence of Al3+−oxalate complex in the protective film formed on aluminum substrate after immersion in [OX]/[Zn2+] solution.

Originality/value

The findings of this work shed more light on the corrosion inhibition of aluminum by oxalate self-assembling monolayers.
Directions for future research on the integration of SOA, BPM, and BRM
Authors: Fischer Marcus , Imgrund Florian , Janiesch Christian , Winkelmann Axel
Published: August 2019

Purpose

Digital transformation has been changing the economic environment of enterprises in recent years. To remain competitive, they rely on an extensible software architecture, flexible workflow execution, and automated decision management. The concepts of service-oriented architectures (SOA), business process management (BPM), and business rules management (BRM) provide an adequate, yet isolated means of addressing many of these requirements. The paper aims to discuss these issues.

Design/methodology/approach

This study adapts from established research frameworks to structure the current state of research on the integration of SOA, BPM and BRM. The authors highlight the current research scope, point to disregarded topics and sketch out multidisciplinary research approaches.

Findings

While the three concepts are often discussed only in isolation or pairwise, approaches that integrate them are scarce. Against this backdrop, this study defines three types of research opportunities and identifies several directions for future research that should be explored from a technological as well as organizational perspective. Given the breadth of open questions, the authors present sources for each area of our research framework, which can serve as starting points for future investigations.

Practical implications

Except for well-established support for separate tasks and technologies, there is a lack of integrated standards, methods and platforms, which for example enable integrated decision-making across BPM and SOA.

Originality/value

Our contribution builds on established frameworks and clearly shows that the discussion on the integration of SOA, BPM and BRM cannot yet be regarded as sufficient. The research agenda highlights which areas explicitly benefit from a more precise consideration.
Structural analysis of how place attachment and risk perceptions affect the willingness to live in an earthquake-prone area
Authors: Chen Tzu-Ling
Published: August 2019

Purpose

The purpose of this paper is to explore the effects of place attachment and risk perception with bounded rationality on the willingness to live in a high-earthquake-risk area.

Design/methodology/approach

The study establishes a hypothetical model on the basis of the theory of planned behavior, place attachment and risk perception. A structural equation model (SEM) measures the relationships between the variables.

Findings

Place attachment affects individuals and their preferences; it makes them willing to continue living in high-earthquake-risk areas. Additionally, risk perception with bounded rationality (fatalism and optimism bias) might make people believe there is only a slight risk of physical injury or property damage. The overall findings moderately suggest that land-use regulations along fault zone areas are not necessarily driving households away, and such allowance of residential use in the current zoning regulation might mislead people that it is a safe area.

Research limitations/implications

This study uses questionnaires in fault zone-regulated areas where only the fault line has zoning regulations. In addition, the application of SEM has to build upon theory and further examine both direct and indirect effects. The assessment criteria of the model might be limited by the sample amount, causing certain model-fitting results, which are not that significant. The overall findings might be limited by the geographical location and cannot be generalized to other areas in Taiwan.

Practical implications

A more thorough assessment of land-use planning in earthquake-risk areas should consider households’ risk perceptions and adaptation behaviors.

Originality/value

Land-use regulations along fault zone areas might reveal earthquake risk in such areas or mislead people that it is a safe area. Place attachment and risk perceptions might affect individuals’ judgments of whether such risk exists or not. The results could be referred to disaster management in high-earthquake-risk areas.