bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent chromatin states, pervasive transcription, and sharedcis-regulatory sequences have shaped theC. elegansgenome
Authors: Bellush James M. , Whitehouse Iestyn 
Published: October 2019

AbstractDespite highly conserved chromatin states andcis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among animal species.C. elegansgene regulation is often assumed to be similar to that of other model organisms, yet evidence suggests the existence of distinct molecular mechanisms to pattern the developmental transcriptome, including extensive post-transcriptional RNA control pathways, widespread splice leader (SL) trans-splicing of pre-mRNAs, and the organization of genes into operons. Here, we performed ChIP-seq for histone modifications in highly synchronized embryos cohorts representing three major developmental stages, with the goal of better characterizing whether the dynamic changes in embryonic mRNA expression are accompanied by changes to the chromatin state. We were surprised to find that thousands of promoters are persistently marked by active histone modifications, despite a fundamental restructuring of the transcriptome. We employed global run-on sequencing using a long-read nanopore format to map nascent RNA transcription across embryogenesis, finding that the invariant open chromatin regions are persistently transcribed by Pol II at all stages of embryo development, even though the mature mRNA is not produced. By annotating our nascent RNA sequencing reads into directional transcription units, we find extensive evidence of polycistronic RNA transcription genome-wide, suggesting that nearby genes inC. elegansare linked by shared transcriptional regulatory mechanisms. We present data indicating that the sharing of cis-regulatory sequences has constrainedC. elegansgene positioning and likely explains the remarkable retention of syntenic gene pairs over long evolutionary timescales.
Step-wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor
Authors: Mugnai M.L. , Thirumalai D. 
Published: October 2019

AbstractMolecular motors, such as myosin, kinesin, and dynein, convert the energy released by the hydrolysis of ATP into mechanical work, which allows them to undergo directional motion on cytoskeletal tracks. This process is achieved through synchronization between the catalytic activity of the motor and the associated changes in its conformation. A pivotal step in the chemomechanical transduction in myosin motors occurs after they bind to the actin filament, which triggers the release of phosphate (Pi, product of ATP hydrolysis) and the rotation of the lever arm. Here, we investigate the mechanism of phosphate release in myosin VI, which has been debated for over two decades, using extensive molecular dynamics simulations involving multiple trajectories each severalμslong. Because the escape of phosphate is expected to occur on time-scales on the order of milliseconds in myosin VI, we observed Pirelease only if the trajectories were initiated with a rotated phosphate inside the nucleotide binding pocket. The rotation provided the needed perturbation that enabled successful expulsions of Piin several trajectories. Analyses of these trajectories lead to a robust mechanism of Pirelease in the class of motors belonging to the myosin super family. We discovered that although Pipopulates the traditional “back door” route, phosphate exits through various other gateways, thus establishing the heterogeneity in the escape routes. Remarkably, we observe that the release of phosphate is preceded by a step-wise hydration of the ADP-bound magnesium ion. In particular, the release of the anion occurredonly after four water moleculeshydrate the cation (Mg2+). By performing comparative structural analyses, we suggest that the hydration of magnesium is the key step in the phosphate release in a number of ATPases and GTPases that share a similar structure in the nucleotide binding pocket. Thus, nature may have evolved hydration of Mg2+by discrete water molecules as a general molecular switch for Pirelease, which is a universal step in the catalytic cycle of many machines which share little sequence or structural similarity.
Image-based Cell Phenotyping Using Deep Learning
Authors: Berryman Samuel , Matthews Kerryn , Lee Jeong Hyun , Duffy Simon P. , Ma Hongshen 
Published: October 2019

AbstractThe ability to phenotype cells is fundamentally important in biological research and medicine. Current methods rely primarily on fluorescence labeling of specific markers. However, there are many situations where this approach is unavailable or undesirable. Machine learning has been used for image cytometry but has been limited by cell agglomeration and it is unclear if this approach can reliably phenotype cells indistinguishable to the human eye. Here, we show disaggregated single cells can be phenotyped with a high degree of accuracy using low-resolution bright-field and non-specific fluorescence images of the nucleus, cytoplasm, and cytoskeleton. Specifically, we trained a convolutional neural network using automatically segmented images of cells from eight standard cancer cell-lines. These cells could be identified with an average classification accuracy of 94.6%, tested using separately acquired images. Our results demonstrate the potential to develop an “electronic eye” to phenotype cells directly from microscopy images indistinguishable to the human eye.
The natural environment as a disaster hazard
Authors: Finnigan Gerard A. 
Published: October 2019

PurposeThe rapid deterioration of the earth’s natural ecosystems are increasing the risk of human morbidity and mortality worldwide. Hydrometeorological hazards are concentrating contaminants from the damaged environment and exposing large vulnerable populations to life threating illnesses and death. This study performed a retrospective health risk assessment on two recent events where such impacts unfolded, namely, the 2015 south east Equatorial Asia smoke haze disaster and the 2016 Melbourne thunderstorm asthma epidemic. The purpose of this paper is to test if the characterisation of health risk warranted earlier and more effective risk reduction activities prior to the disasters occurring.Design/methodology/approachA retrospective health risk characterisation assessment was performed combing United Nations International Strategy for Disaster Risk Health Aspect in Disaster Risk Assessment (2017) framework with a thematic and targeted word literature review to identify the level of risk knowledge prior to each event. A risk characterisation matrix was then created to characterise the health risk of each hazard event.FindingsThe 2015 south east Equatorial Asia smoke haze disaster risk assessment was characterised as “extreme” health risk and the 2016 Melbourne thunderstorm asthma epidemic was characterised as “high” health risk.Practical implicationsReaching the goals of the Sendai Framework require strategies and plans which urgently address the catastrophic level of mortality risk posed by exposure to environmental contaminants.Originality/valueInnovative approaches and partnerships are necessary to mitigate the risk from the deteriorating health of the environment and natural ecosystems, along with disaster response initiatives that reduce exposure of vulnerable people on a large scale.
The ambiguities of money-making
Authors: Styhre Alexander , Remneland-Wikhamn Björn 
Published: October 2019

Purpose
Indie developers are part of the creative fringe of the video game industry, fashioning an identity for themselves as a community committed to the development of video games as a cultural expression and art form. In playing this role, money-making is ambiguous inasmuch as economic return is honorable if such interests remain unarticulated and execute minimal influence on the development work process, while the possibility of producing a successful commercial video game is simultaneously one of the primary motivations for new industry entrants. The paper aims to discuss this issue.

Design/methodology/approach
The paper reports on the empirical material drawn from a study of indie video game developers in Sweden, a leading country for video game development.

Findings
To reconcile tensions between video game development in terms of being both cultural/and artistic production and business activity, easily compromising the perceived authenticity of the subject in the eyes of audiences (e.g. hardcore gamers), indie developers distinguish between monetary motives ex ante and compensation ex post the release of the game. Indie developers thus emphasize the metonymic function of money as this not only indicates economic value and currency but also denotes a number of business practices that indie developers have otherwise avoided in their career planning as they believe these practices would restrain their creativity and skills.

Originality/value
The study contributes to the scholarship on video game development, the literature on creative industries, and the economic sociology literature examining the social meaning of money and how social norms and values are manifested in professional ideologies and practices.
Corridors or risk? Movement along, and use of, linear features varies predictably among large mammal predator and prey species
Authors: Dickie Melanie , McNay Scott R. , Sutherland Glenn D. , Cody Michael , Avgar Tal 
Published: October 2019

Abstract

Space‐use behaviour reflects trade‐offs in meeting ecological needs and can have consequences for individual survival and population demographics. The mechanisms underlying space use can be understood by simultaneously evaluating habitat selection and movement patterns, and fine‐resolution locational data are increasing our ability to do so.

We use high‐resolution location data and an integrated step‐selection analysis to evaluate caribou, moose, bear, and wolf habitat selection and movement behaviour in response to anthropogenic habitat modification, though caribou data were limited. Space‐use response to anthropogenic linear features (LFs) by predators and prey is hypothesized to increase predator hunting efficiency and is thus believed to be a leading factor in woodland caribou declines in western Canada.

We found that all species moved faster while on LFs. Wolves and bears were also attracted towards LFs, whereas prey species avoided them. Predators and prey responded less strongly and consistently to natural features such as streams, rivers and lakeshores. These findings are consistent with the hypothesis that LFs facilitate predator movement and increase hunting efficiency, while prey perceive such features as risky.

Understanding the behavioural mechanisms underlying space‐use patterns is important in understanding how future land‐use may impact predator–prey interactions. Explicitly linking behaviour to fitness and demography will be important to fully understand the implications of management strategies.
Responses of daphnids and other zooplankton populations to massive fish kill in Lake Suwa
Authors: Oh Hye‐Ji , Oda Yusuke , Ha Jin‐Yong , Nagata Takamaru , Hanazato Takayuki , Miyabara Yuichi , Sakamoto Masaki , Chang Kwang‐Hyeon 
Published: October 2019

AbstractIn 2016, a massive fish kill of the planktivorous pond smelt Hypomesus nipponensis occurred in Lake Suwa, Japan. Pond smelt, which is important fish species from commercial and cultural perspectives, influences the zooplankton community in the lake. Following the massive fish kill, Daphnia galeata appeared and their population density increased to previously unseen levels by summer 2017. To help recover the fish population, larval pond smelt were released into the lake. Consequently, D. galeata has rarely appeared in Lake Suwa since summer 2017, except for a low‐density population observed in May–June 2018. These phenomena indicated that fish predation is a possible primary factor for suppressing daphnid populations in shallow eutrophic lake. Zooplankton populations showed species‐specific responses to the alterations in predation pressure. When the D. galeata population peaked after the fish kill event, rotifers, which are small‐sized competitors of daphnids, and calanoids tended to decrease in density. Rotifers then increased with the decrease in the daphnid populations due to the recovery of fish. Alternatively, cyclopoids, which demonstrated a similar population density following the fish kill event, tended to decrease when the fish population recovered. The population densities of Leptodora cf. kindtii/richardi and Bosmina spp. did not significantly differ between before the massive kill event and after pond smelt recovery. It is believed that the changes in zooplankton population densities observed in the present study may provide insights for further monitoring of aquatic food webs in eutrophic water systems, including Lake Suwa, where re‐oligotrophication is occurring and biological interactions are changing.
Conversion of NaHCO3 to Na2CO3 with a growth of Arthrospira platensis cells in 660 m2 raceway ponds with a CO2 bicarbonation absorber
Authors: Guo Wangbiao , Cheng Jun , Ali Kubar Ameer , Kumar Santosh , Guo Caifeng 
Published: October 2019

SummaryThe weight ratio of Na2CO3/NaHCO3 was investigated in order to improve microalgal productivity in large‐scale industrial operations by converting NaHCO3 to Na2CO3 with a growth of Arthrospira platensis cells in 660 m2 raceway ponds. Two microalgal cultivation systems with a NaHCO3 by‐product (SPBP) and a CO2 bicarbonation absorber (CBAP) were firstly thoroughly introduced. There was a 13.3% decrease in the initial weight ratio of Na2CO3/NaHCO3 resulting in a 25.3% increase in the biomass growth rate with CBAP, compared to that of SPBP. Increased sunlight intensity, solution temperature and pH all resulted in both a higher absorbance and release, thereby increasing the weight ratio of Na2CO3/NaHCO3 during the growth of A. platensis. The biomass growth rate was peaked at 39.9 g m−2 day−1 when the weight ratio of Na2CO3/NaHCO3 was 3.7. Correspondingly, the cell pigments (chlorophyll a and carotenoid) and trichome size (helix pitch and trichome length) reached to a maximum state of 8.47 mg l−1, 762 μg l−1, 57 and 613 μm under the CBAP system.
Unveiling introgression in bumblebee (Bombus terrestris) populations through mitogenome‐based markers
Authors: Cejas D. , López‐López A. , Muñoz I. , Ornosa C. , De la Rúa P. 
Published: October 2019

SummaryThe bumblebee, Bombus terrestris, is an important pollinator commercially used on a global scale. The exported subspecies B. t. terrestris has colonised diverse environments, in some cases displacing wild pollinators to the verge of local extinction. In this sense, the native Iberian subspecies B. t. lusitanicus may be threatened by the subspecies B. t. terrestris, naturally distributed from the Pyrenees to Central Europe but also observed in southern Spain due to escapes from commercial nests. Mitochondrial genomes have a low recombination rate and a small effective population size owing to their maternal inheritance, thus providing an accurate approach to study hybridisation events between populations. Therefore, we present the sequences of the mitogenomes of both subspecies as a molecular framework to select suitable markers to detect possible introgression events between them. We used metagenomics to obtain approximately 17 kbp of the mitogenome from both subspecies. Their mitogenomes differed in 358 bp (excluding the AT‐rich region). Four mitogenomic fragments were selected to be tested as subspecific diagnostic markers. A RFLP detected in the gene nad2 (NADH dehydrogenase subunit 2) has proven to be an efficient, quick and cost‐effective tool to assess the dispersion of the non‐endemic subspecies into Iberian native populations. Subspecific haplotypes were observed in both morphological subspecies, suggesting introgression events in the northern natural contact area and in the new human‐mediated contact area in the south of the Iberian Peninsula.
Embryo collection from pigs post‐pseudopregnancy induced by estradiol dipropionate
Authors: Hirayama Yuri , Yoshioka Koji , Noguchi Michiko , Misumi Koji 
Published: October 2019

AbstractWe aimed to define whether embryo collection carried out after pseudopregnancy was of similar outcome and quality as after artificial abortion. To induce pseudopregnancy, 30 gilts or sows were given 20 mg intramuscular estradiol dipropionate (EDP) 10–11 days after the onset of estrus. Ten additional pigs were inseminated artificially at natural estrus as a control group. Prostaglandin F2α (PGF2α) was administered twice with a 24 hr interval beginning 15, 20, or 25 days after EDP‐treatment (n = 10 per group) or between 23 and 39 days after artificial insemination in control pigs. Following this, all pigs were given 1,000 IU equine chorionic gonadotropin and 500 IU human chorionic gonadotropin (hCG) and then inseminated. Embryos were recovered 6 or 7 days after hCG treatment and outcome was recorded. There was no significant difference in the number of normal embryos collected from the pigs with PGF2α initiated at different time points or from the control group. Embryonic developmental stages 7 days after hCG treatment also did not differ among groups. These results indicate that the use of EDP to induce pseudopregnancy, followed by PGF2α administration to synchronize estrus for subsequent embryo harvest, is a suitable alternative to the artificial abortion method.
Children’s Appraisals of Gender Nonconformity: Developmental Pattern and Intervention
Authors: Kwan Karen Man Wa , Shi Sylvia Yun , Nabbijohn A. Natisha , MacMullin Laura N. , VanderLaan Doug P. , Wong Wang Ivy 
Published: October 2019

Gender‐nonconforming (GN) children are often perceived less positively, which may harm their well‐being. We examined the development of such perceptions and an intervention to modify them. Chinese children’s appraisals were assessed using multiple measures (verbal responses, sharing, and rank order task) after viewing vignettes of gender‐conforming (GC) and GN hypothetical peers. In Study 1, children (N = 210; 4‐, 5‐, 8‐, and 9‐year‐olds) were less positive toward GN than GC peers, especially if they were older or if the peers were boys. In Study 2 (N = 211, 8‐ and 9‐year‐olds), showing children exemplars of GN peers who displayed positive and GC characteristics subsequently reduced bias against gender nonconformity. These findings inform strategies aimed at reducing bias against gender nonconformity.
Platelet‐rich fibrin to preserve alveolar bone sockets following tooth extraction: A randomized controlled trial
Authors: Areewong Kanokporn , Chantaramungkorn Montri , Khongkhunthian Pathawee 
Published: October 2019

AbstractBackgroundPlatelet‐rich fibrin (PRF) can be used in the alveolar socket preservation (ARP). However, the hard tissue‐regeneration property of PRF in alveolar socket preservation is still unclear.PurposeTo compare the new bone formation ratio between using PRF as a socket preservation material and normal wound healing, by means of histomorphometric analysis.Materials and MethodsThirty‐three healthy volunteers were recruited and randomized into PRF and control group. Minimally traumatic extractions were performed. Eighteen patients were treated with ARP using PRF, while the rest were left to heal naturally. Bone specimens were harvested using trephine bur 2 months after the extraction process. Histomorphometric analysis of new bone formation area compared with total socket area was performed using the software Fiji Is Just Image J (version 2, GNU General Public License).ResultsThirty‐three volunteers were participated. Twenty‐eight bone specimens were collected. The new bone formation ratio was higher in PRF group than in control group (31.33 ± 18% and 26.33 ± 19.63%, respectively). However, there was no statistically significant difference in the ratio between the PRF and control groups (P = .431).ConclusionsIt may be concluded that the use of PRF in ARP does not statistically significant enhance new bone formation after tooth extraction compared to normal wound healing (P > .05).
Stable isotopes infer the value of Australia’s coastal vegetated ecosystems from fisheries
Authors: Jänes Holger , Macreadie Peter I. , Nicholson Emily , Ierodiaconou Daniel , Reeves Simon , Taylor Matthew D. , Carnell Paul E. 
Published: October 2019

AbstractWild capture fisheries provide substantial input to the global economy through employment and revenue. The coastal zone is especially productive, accounting for just 7% of the total area of the ocean, but supporting an estimated 50% of the world's fisheries. Vegetated coastal ecosystems—seagrass meadows, tidal marshes and mangrove forests—are widely cited as providing nutritional input that underpin coastal fisheries production; however, quantitative evidence of this relationship is scarce. Using Australia as a case study, we synthesized fisheries stable isotope data to estimate nutritional input derived from coastal vegetated ecosystems and combined these “proportional contribution” estimates with total annual catch data from commercial fisheries to determine species‐specific dollar values for coastal vegetated ecosystems. Based on the data from 96 commercially important fish species across Australian states (total landings 14 × 106 tonnes pa), we provide a conservative estimate that Australia's coastal vegetated ecosystems contribute at least 78 million AUD per year to the fisheries economy. Two thirds of this contribution came from tidal marshes and seagrasses that were both equally valued at 31.5 million AUD per year (39.4%) followed by mangroves at 14.9 million AUD per year (18.6%). The highest dollar values of coastal ecosystems originated from eastern king prawn (Melicertus plebejus) and giant mud crab (Scylla serrata). This study demonstrates the substantial economic value supported by Australia's coastal vegetated ecosystems through commercial fisheries harvest. These estimates create further impetus to conserve and restore coastal wetlands and maintain their support of coastal fisheries into the future.
Irreversible versus repairable membrane poration: differences in permeabilization elicited by Bordetella Adenylate Cyclase Toxin and its hemolysin domain in macrophages
Authors: Etxaniz Asier , González‐Bullón David , Martín César , Alonso Maria Teresa , Ostolaza Helena 
Published: October 2019

Rapid plasma membrane repair in response to pore‐forming toxins is crucial for cell survival, but the molecular mechanisms employed by eukaryotic nucleated cells to maintain membrane integrity and the specificities of such pathways remain poorly understood. Here, we have explored the permeabilization elicited by the Bordetella pertussis adenylate cyclase toxin, a 200‐kDa protein toxin with α‐helical pore‐forming domain that forms pores of tunable size, and evaluated the response of target macrophages to such toxin poration. We show here that the response and the fate of target macrophages depend on toxin pore width. We find that the toxin′s hemolysin moiety induces a transient membrane permeabilization by forming wide enough pores allowing Ca2+ influx into the target cell cytosol. This activates a Ca2+‐dependent cellular response involving exocytosis and endocytosis steps eliminating toxin pores and restoring membrane integrity. In contrast, the full‐length native toxin, at low concentrations, forms very small pores that cause insidious perturbation of cell ion homeostasis that escapes control by the macrophage membrane repair response, eventually leading to cell death. Our data reveal that permeability to Ca2+ and ATP are key elements in the membrane repair pathway for eliminating α‐helical pores of bacterial origin.