bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiautomated Spike Detection Software Persyst 13 Is Noninferior to Human Readers When Calculating the Spike-Wave Index in Electrical Status Epilepticus in Sleep
Authors: Joshi Charuta N. , Chapman Kevin E. , Bear Joshua J. , Wilson Scott B. , Walleigh Diana J. , Scheuer Mark L. 
Published: June 2018

Purpose:
Our objective was to use semiautomatic methods for calculating the spike-wave index (SWI) in electrical status epilepticus in slow-wave sleep (ESES) and to determine whether this calculation is noninferior to human experts (HEs).

Methods:
Each HE marked identical 300-second epochs for all spikes and calculated the SWI in sleep EEGs of patients diagnosed with ESES. Persyst 13 was used to mark spikes (high sensitivity setting) in the same 300-second epochs marked by HEs. The spike-wave index was calculated. Pairwise HE differences and pairwise Persyst 13 (P13)-HE differences for the SWI were calculated. Bootstrap resampling (BCa, N = 3,000) was performed to better estimate mean differences and their 95% confidence bounds between HE and P13-HE pairs. Potential noninferiority of P13 to HEs was tested by comparing the 95% confidence bounds of the mean differences between pairs for the SWI.

Results:
Twenty EEG records were analyzed. Each HE marked 100 minutes of EEG. HEs 1, 2, 3, and 4 marked 10,075, 8,635, 9,710, and 9,898 spikes, respectively. The highest and lowest 95% confidence bound of the mean difference in the SWI between HE pairs was: High: 10.3%; Low: −10.2%. Highest and lowest 95% confidence bound of the mean difference in the SWI between P13 and HE pairings was as follows: high, 9.5% and low, −6.7%. The lack of a difference between P13 and HEs supports that the algorithm is not inferior to HEs.

Conclusions:
Persyst 13 is noninferior to HEs in calculating the SWI in ESES, thus suggesting that an automated approach to SWI calculation may be a useful clinical tool.
GGA2 and RAB13 promote activity-dependent β1-integrin recycling
Authors: Sahgal Pranshu , Alanko Jonna , Icha Jaroslav , Paatero Ilkka , Hamidi Hellyeh , Arjonen Antti , Pietilä Mika , Rokka Anne , Ivaska Johanna 
Published: June 2018

Abstractβ1-integrins mediate cell-matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes like cancer cell invasion. Here we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin and its role in recycling of the active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion congruent with its ability to regulate the dynamics of active integrins. Using the proximity-dependent biotin identification (BioID) method, we identify two RAB family small GTPases, RAB13 and RAB10, associating with GGA2 and β1-integrin. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, reduces integrin activity, in focal adhesions, and cell migration, similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.
Mitochondrial genomes and phylogenetic analysis of Central American weakly-electric fishes:Apteronotus rostratus, Brachyhypopomus occidentalisandSternopygus dariensis
Authors: Aguilar Celestino , Miller Matthew J. , Loaiza Jose R. , Krahe Rüdiger , De León Luis F. 
Published: June 2018

AbstractElectric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. Over 200 species have originated in South America, but of these, only a few have managed to colonize the Central American Isthmus. Here, we assembled two complete and one nearly complete mitochondrial genomes (mitogenomes) for three Central American Gymnotiformes:Sternopygus dariensis, Brachyhypopomus occidentalisandApteronotus rostratus. We then explored the three species’ phylogenetic position in the context of South American electric fishes. Mitogenomes were organized in the standard fish mitogenome order, and presented sizes of 16,600, 16,540 and 15,940 base pairs (bp) (nearly complete) forS. dariensis, B. occidentalisandA. rostratus, respectively. We uncovered a novel 60 bp intergenic spacer (IGS) located between theCOIIand tRNALysgenes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genusApteronotuswas placed as the basal taxon of the order. Finally, we found high sequence divergence (13.3%) between ourB. occidentalisspecimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome ofB. occidentalisrepresents a different South American species that was misidentified. Indeed, phylogenetic analyses usingCytochrome bgene across the genus placed the previously reported individual withinB. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.
Using Fuzzy Sets to Deal with Uncertainty in Single-species, Single-season Occupancy Models
Authors: McCallum Malcolm L. 
Published: June 2018

AbstractOccupancy modeling is a valuable tool for managing wildlife populations. Current occupancy models provide estimates of occurrence based on a point estimate for the species detectability and presence-absence. However, detectability can vary based on many variables ranging from weather to personnel. Therefore, I propose the use of fuzzy sets rather than point estimates for detectability and binomial presence-absence data during calculations of occupancy. Fuzzy occupancy estimates are easier to determine, more robust, and generally more informative than traditional point-based occupancy models. Consequently, managers will have better information available for comparing occupancy values among sites. Fuzzy sets are especially useful when parameters of the study violate key data standards.
Mechanistic Insights into theCis-andTrans-acting Deoxyribonuclease Activities of Cas12a
Authors: Swarts Daan C. , Jinek Martin 
Published: June 2018

HIGHLIGHTSTarget ssDNA binding allosterically induces unblocking of the RuvC active sitePAM binding facilitates unwinding of dsDNA targetsNon-target DNA strand cleavage is prerequisite for target DNA strand cleavageAfter DNA cleavage, Cas12a releases the PAM-distal DNA productSUMMARYCRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA incisand non-target single stranded DNAs (ssDNA) intrans.To elucidate the molecular basis for both deoxyribonuclease cleavage modes, we performed structural and biochemical studies onFrancisella novicidaCas12a. We show how crRNA-target DNA strand hybridization conformationally activates Cas12a, triggering itstrans-acting, non-specific, single-stranded deoxyribonuclease activity. In turn,cis-cleavage of double-stranded DNA targets is a result of PAM-dependent DNA duplex unwinding and ordered sequential cleavage of the non-target and target DNA strands. Cas12a releases the PAM-distal DNA cleavage product and remains bound to the PAM-proximal DNA cleavage product in a catalytically competent,trans-active state. Together, these results provide a revised model for the molecular mechanism of Cas12a enzymes that explains theircis- andtrans-acting deoxyribonuclease activities, and additionally contribute to improving Cas12a-based genome editing.
The mirtron miR-1010 functions in concert with its host gene SKIP to maintain synaptic homeostasis
Authors: Amourda Christopher , Saunders Timothy E. 
Published: June 2018

SummaryMirtrons are non-canonical miRNAs arising by splicing and debranching from short introns. A plethora of introns have been inferred by computational analyses as potential mirtrons. Yet, few have been experimentally validated and their functions, particularly in relation to their host genes, remain poorly understood. Here, we found that larvae lacking the mirtron miR-1010 are unable to grow properly and pupariate. We show that miR-1010 downregulates nAcRβ2. Increase of cortical nAcRβ2 mediated by neural activity elevates the level of intracellular Ca2+, which in turn activates CaMKII and, further downstream, the transcription factor Adf-1. We reveal that Adf-1 initiates the expression of SKIP, the host gene of miR-1010. Preventing synaptic potentials from overshooting their optimal range requires both SKIP to temper synaptic potentials (incoherent feedforward loop) and miR-1010 to reduce nAcRβ2 mRNA levels (negative feedback loop). Our results demonstrate how a mirtron, in coordination with its host gene, contributes to maintaining homeostasis.
Conditioned increase of locomotor activity induced by haloperidol
Authors: De la Casa Luis G. , Carcel Lucía , Ruiz-Salas Juan C. , Vicente Lucía , Mena Auxiliadora 
Published: June 2018

AbstractDopamine antagonist drugs have profound effects on locomotor activity. In particular, the administration of the D2 antagonist haloperidol produces a state that is similar to catalepsy. In order to confirm whether the modulation of the dopaminergic activity produced by haloperidol can act as an unconditioned stimulus, we carried out two experiments in which the administration of haloperidol was repeatedly paired with the presence of distinctive contextual cues that served as a Conditioned Stimulus. Paradoxically, the results revealed a dose-dependent increase in locomotor activity following conditioning with dopamine antagonist (Experiments 1) that was susceptible of extinction when the conditioned stimulus was presented repeatedly by itself after conditioning (Experiment 2). These data are interpreted from an associative perspective, considering them as a result of a classical conditioning process.
Priming of leaf litter decomposition by algae seems of minor importance in natural streams during autumn
Authors: Elosegi Arturo , Nicolás Angie , Richardson John S. 
Published: June 2018

AbstractAllochthonous detritus from terrestrial origin is one of the main energy sources in forested headwater streams, but its poor nutritional quality makes it difficult to use by heterotrophs. It has been suggested that algae growing on this detritus can enhance its nutritional quality and promote decomposition. So far, most evidence of this “priming” effect is derived from laboratory or mesocosm experiments, and it is unclear what its importance is under natural conditions. We measured accrual of algae, phosphorus uptake capacity, and decomposition of poplar leaves in autumn in open- and closed-canopy reaches in 3 forest and 3 agricultural streams. Chlorophyll a abundance did not change significantly neither with stream type nor with canopy cover, although some between open and closed reaches, although in some agricultural streams it was higher in open than in closed canopy reaches. Canopy cover did not affect either phosphate uptake capacity or microbial decomposition. On the other hand, although there was no effect of canopy cover on invertebrate fragmentation rate, a significant interaction between canopy cover and stream suggests priming occurs at least in some streams. Overall, the results point to a weak effect of algae on litter decomposition in natural streams during autumn.
Root Colonization and Growth Promotion of Soybean, Wheat and Chinese Cabbage byBacillus cereusYL6
Authors: Ku Yongli , Xu Guoyi , Wang Fawei , Liu Haijin , Yang Xiangna , Tian Xiaohong , Cao Cuiling 
Published: June 2018

AbstractPhosphate-solubilizing bacteria (PSB) have been isolated and used in agricultural production. However, comprehensive research on PSB colonizing the rhizosphere of different plants and promoting plant growth is lacking. This study was conducted to study the growth-promoting effects and colonizing capacity of the PSB strain YL6. The YL6 strain not only increased the biomass of pot-planted soybean and wheat but also increased the yield and growth of Chinese cabbage under field conditions. The promotion of growth in these crops by strain YL6 was related to its capacities to dissolve inorganic and organic phosphorus and to produce a certain amount of indole-3-acetic (IAA) and gibberellin (GA). After YL6 was applied to soybean, wheat and Chinese cabbage, the rhizosphere soil available phosphorus (available P) content increased by 120.16%, 62.47% and 7.21%, respectively, and the plant total phosphorus increased by 198.60%, 6.20% and 78.89%, respectively, compared with those of plants without the addition of YL6. To determine whether the phosphate solubilizing bacteria colonized these plants, YL6 labeled with green fluorescent protein (YL6-GFP) was inoculated into plant rhizospheres. YL6-GFP first colonized the root surface and hairs and then penetrated into intercellular spaces and vessels. Collectively, these results demonstrate that YL6 promoted the growth of three different crops and colonized them in a similar way and therefore provide a solid foundation for probing into mechanisms by which phosphate-solubilizing bacteria affect plant growth.
Growth differentiation factor-15 regulates oxLDL-induced lipid homeostasis and autophagy in human macrophages
Authors: Ackermann Kathrin , Bonaterra Gabriel A. , Kinscherf Ralf , Schwarz Anja 
Published: June 2018

AbstractGrowth differentiation factor-15 (GDF-15), a divergent and distant member of the transforming growth factor-β superfamily, is suggested as a risk factor for cardiovascular diseases. Thus, we are interested to investigate the influence of GDF-15 in lipid homeostasis and autophagy in macrophages (MΦ) during foam cell formation. Our investigations represent the impairment of GDF-15 on modulators of autophagy and lipid homeostasis in PMA-differentiated human THP-1 MΦ. In this context,in vitroresulted GDF-15 silencing in a reduction of lipid accumulation, whereas the addition of recombinant (r)GDF-15 increased the lipid accumulation in human MΦ independent of oxidized (ox)LDL. Additionally, GDF-15 affected the expression of autophagy-relevant proteins (p62, Atg5 and Atg12/Atg5 protein complex) and the p62 accumulation in THP-1 MΦ. Hence, our data suggest that GDF-15 is involved in the regulation of the lipid homoeostasis of human MΦ by regulating autophagic processes.
A shared limiting resource leads to competitive exclusion in a cross-feeding system
Authors: Hammarlund Sarah P. , Chacón Jeremy M. , Harcombe William R. 
Published: June 2018

SummarySpecies interactions and coexistence are often highly dependent upon environmental conditions. This is especially true for cross-feeding bacteria that rely on one another for essential nutrients. The addition of a cross-fed nutrient to the environment can release one species from its dependence on another, thereby altering the species’ interaction and potentially affecting coexistence. Using invasion-from-rare experiments with cross-feeding bacteria, genome-scale metabolic modeling, and classical ecological models, we explored the potential for coexistence when one cross-feeding mutualist becomes independent. We show that whether nutrient addition shifts an interaction from mutualism to commensalism or parasitism depends on whether the limiting nutrient can be metabolized by only one species or by both species. Furthermore, we show that coexistence is only lost when the interaction becomes parasitism, and the obligate species has a slower maximum growth rate. Surprisingly, models suggest that rates of cross-fed nutrient production have a negligible effect. These results contribute to an understanding of how resource changes, whether intentional or not, will manipulate interactions and coexistence in microbial communities.
The Helix-Loop-Helix motif of human EIF3A regulates translation of proliferative cellular mRNAs
Authors: Volegova Marina P. , Hermosillo Cynthia , Cate Jamie H.D. 
Published: June 2018

ABSTRACTImproper regulation of translation initiation, a vital checkpoint of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) is associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiationin vitro.Here we show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, includingMYC. We demonstrate that the HLH motif of EIF3A acts specifically on the 5’-UTR ofMYCmRNA and modulates the function of EIF4A1 on select transcripts during translation initiation. In Ramos lymphoma cell lines, which are dependent on MYC overexpression, mutations in the HLH motif greatly reduce MYC expression, impede proliferation and sensitize cells to anti-cancer compounds. These results reveal the potential of the EIF3A HLH motif in eIF3 as a promising chemotherapeutic target.
Angular Substrate Preference and Molting Behavior of the Giant River Prawn, Macrobrachium rosenbergii and Its Implications for Cannibalism Management
Authors: McCallum Malcolm L. , Weston Samad D. , Tilahun Yonathan 
Published: June 2018

AbstractThe Giant River Prawn is an important commercial species from southeastern Asia and has a large global market. It has a complex life cycle in which it undergoes several molting sequences. Many arthropods require firm perches on which they can perform ecdysis. We investigated preference for substrate slope and its influence on ecdysis. We discovered that prawns occupy horizontal surfaces more frequently than others, but during pre-molt and molt stages, they shift their habitat use to non-horizontally sloped surfaces. Here, they will flex their shell and later molt. We recommend modification of cannibalism management in commercial facilities by providing sufficient vertical (strongly preferred) or high-sloped (greater than 30 degrees) surfaces to facilitate ecdysis, while providing much horizontal space for foraging and other activities. This should create habitat separation between foraging and highly susceptible freshly-molted prawns, thus leading to reduced cannibalism-related mortality.FundingThis work was supported by the USDA Evans Allen Program at Langston University, Project Number USDA-NIFA-OKLUMCCALLUM2017.Disclosure statementWe acknowledge that there is no financial interest or benefit that has arisen from the direct applications of our research.
Storage length and temperature influence infectivity and spore yield of two commonDaphniaparasites
Authors: Duffy Meghan A. , Hunsberger Katherine K. 
Published: June 2018

AbstractDaphniaand their parasites have emerged as a model system for understanding the ecology and evolution of infectious diseases. Two of the most commonly studiedDaphniaparasites are the bacteriumPasteuria ramosaand the fungusMetschnikowia bicuspidata. In addition to being the focus of numerous field studies, these two parasites have been used in many laboratory experiments. However, there is little information in the scientific literature about how the conditions under which these parasites are stored influence the infectivity and yield of transmission stages (“spores”). This is problematic because such information is critical for experiment design and data interpretation.We tested the influence of storage length (eight treatments ranging from 1 day to 1 year) and temperature (−20°C (freezer) vs. 4°C (refrigerator)) on spore infectivity and yield. We found thatPasteuriaspores survived well at both −20°C and 4°C, and remained infective even after storage for one year. However,Pasteuriaspore yields dropped over time, particularly at 4°C. In contrast,Metschnikowiaspores were killed within days at −20°C. At 4°C,Metschnikowiainfectivity declined steadily over a period of two months and, by four months, spores were no longer infective. Spore yield fromMetschnikowia-infected hosts was not significantly impacted by storage length, but trended downwards.Scientists working withPasteuriashould be aware that spore yield declines during storage, particularly in the refrigerator. Scientists working withMetschnikowiashould be aware that it is killed by freezer storage and that, even if it is stored in the refrigerator, infectivity declines within a few months. These results might have implications for parasite distributions in the field; for example, the high sensitivity ofMetschnikowiato freezing might help explain why it tends to be more common in deep lakes than in ponds or rock pools.
Contemporary Japanese art: between globalization and localization
Authors: Tagore-Erwin Eimi 
Published: June 2018

PurposeThe purpose of this paper is to identify and analyze the influence that globalization has had on the development of the contemporary Japanese art production. The study also aims to expand the global narrative of Japanese art by introducing concepts behind festivals for revitalization that have been occurring in Japan in recent years.Design/methodology/approachGuided by Culture Theorist Nira Yuval-Davies’ approach to the politics of belonging, the paper is situated within cultural studies and considers the development of contemporary art in Japan in relation to the power structures present within the global art market. This analysis draws heavily from the research of art historians Reiko Tomii, Adrian Favell, and Gennifer Weisenfeld, and is complemented by investigative research into the life of Art Director Kitagawa Fram, as well as observational analyses formed by on-site study of the Setouchi Triennale in 2015 and 2016.FindingsThe paper provides historical insight to the ways that the politics of belonging to the western world has created a limited benchmark for critical discussion about contemporary Japanese art. It suggests that festivals for revitalization in Japan not only are a good source of diversification, but also evidences criticism therein.Research limitations/implicationsDue to the brevity of this text, readers are encouraged to further investigate the source material for more in-depth understanding of the topics.Practical implicationsThe paper implies that art historiography should take a multilateral approach to avoid a western hegemony in the field.Originality/valueThis paper fulfills a need to reflect on the limited global reception to Japanese art, while also identifying one movement that art historians and theorists may take into account in the future when considering a Japanese art discourse.