bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing
Authors: Helmkampf Martin , Bellinger M Renee , Geib Scott M , Sim Sheina B , Takabayashi Misaki 
Published: June 2019

AbstractThe rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700 Mb, although the high fraction of repetitive sequence introduced considerable uncertainty. Repeat analysis indicated that 42% of the assembly consisted of interspersed, mostly unclassified repeats, and almost 3% tandem repeats. We also identified 36,691 protein-coding genes with a median coding sequence length of 807 bp, together spanning 7% of the assembly. The high repeat content and heterozygosity of the genome proved a challenging scenario for assembly, requiring additional steps to merge haplotypes and resulting in a higher than expected fragmentation at the scaffold level. Despite these challenges, the assembly turned out to be comparable in most quality measures to that of other available coral genomes while being considerably more cost-effective, especially with respect to long-read sequencing methods. Provided high-molecular-weight DNA is available, linked-read technology may thus serve as a valuable alternative capable of providing quality genome assemblies of nonmodel organisms.
Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase
Authors: Nelson Jessica M , Hauser Duncan A , Gudiño José A , Guadalupe Yessenia A , Meeks John C , Salazar Allen Noris , Villarreal Juan Carlos , Li Fay-Wei 
Published: June 2019

Abstract
Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant–microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.
Physical activity and the built environment: perceptions of policy-makers in Oman
Authors: Mabry Ruth M , Al Siyabi Huda , Kannan Muhssen , Al Siyabi Amal 
Published: June 2019

Abstract
The prevalence of physical activity is low in the Sultanate of Oman. The built environment is a key barrier to physical activity in the region. Our aim is to examine urban planners’ perceptions of the relevance and feasibility of the proposed urban planning and design interventions in the draft WHO technical package on physical activity. Semi-structured interviews were conducted with 11 professionals using a pre-tested interview guide. Interviews were audio-recorded and transcribed. Content analysis based on the socio-ecological framework (policy, physical, socio-cultural and information environment) was used to identify the perceived urban design challenges and solutions. Urban sprawl due to haphazard urban and transport design, limited accessibility to parks and sports facilities, negative perceptions about active travel and limited understanding of physical activity were key challenges identified by interviewees. Participants suggested strengthening governance through policy and intersectoral collaboration, improving community design and accessibility to parks, considering the needs of diverse populations and improving knowledge and attitudes of physical activity as priority when adapting the WHO technical package to Oman. Mid-level managers prioritized three interventions from the package: the need for political commitment and capacity building on how the built environment can promote physical activity, a national political on physical activity that promotes a safe infrastructure for active transport, and accessibility to sports and recreational facilities. Negative perceptions of active travel and cultural expectations that constrain mobility requires a society-wide paradigm shift, the first objective of the WHO global action plan.
Robotic resection of a thymoma behind the left innominate vein
Authors: Zhang Hanlu , Zheng Yu , Chen Long-Qi , Wang Yun 
Published: June 2019

Abstract
Anatomical variations of one or both thymic upper poles located behind the left innominate vein (LIV) are found in some patients; however, minimally invasive dissection of ectopic thymic tissues behind the LIV is technically complex. We describe a case of a dumbbell-shaped thymoma behind the LIV. The patient was successfully treated with trans-subxiphoid robot-assisted thoracoscopic extended thymectomy. Both the LIV and tumour capsule were preserved intact. In our opinion, robotic surgery might expand the indications for minimally invasive thymectomy. It can be applied in selected difficult cases and sternotomy can be avoided in some situations.
Associations of individual social capital with subjective well-being and mental health among migrants: a survey from five cities in China
Authors: Zhu Yongkai , Gao Junling , Nie Xin , Dai Junming , Fu Hua 
Published: June 2019

Abstract

Background
We aimed to examine the associations of cognitive and structural social capital with subjective well-being (SWB) and mental health among internal migrants in five cities in China.

Methods
We conducted healthy cities surveys from June 2017 to April 2018. In total, 3038 migrants submitted surveys. Generalized linear regressions for SWB and logistic regressions for mental health were used to examine the associations of social capital, SWB and mental health after controlling for covariates.

Results
The median level of SWB was 75.7 (interquartile range 62.9–85.7). Self-rated health and physical activity were positively associated with SWB. The SWB level among migrants who perceived high individual social cohesion was much higher than that of their counterparts (unstandardized coefficients, β=7.01 [95% confidence interval {CI} 5.82 to 8.21]). The prevalence of poor mental health was 10.0%. High social cohesion (odds ratio [OR] 0.32 [95% CI 0.24 to 0.44]) and high social participation (OR 0.77 [95% CI 0.57 to 0.97]) were significantly associated with a low ratio of poor mental health when compared with their counterparts.

Conclusions
Cognitive social capital is positively associated with SWB, while both cognitive and structural social capitals were negatively associated with poor mental health. It is beneficial to migrants’ mental health and SWB to promote social participation and social cohesion.
‘I treat it but I don’t know what this disease is’: a qualitative study on noma (cancrum oris) and traditional healing in northwest Nigeria
Authors: Farley Elise , Bala Hussaina Muhammad , Lenglet Annick , Mehta Ushma , Abubakar Nura , Samuel Joseph , de Jong Annette , Bil Karla , Oluyide Bukola , Fotso Adolphe , Stringer Beverley , Cuesta Julita Gil , Venables Emilie 
Published: June 2019

AbstractBackgroundNoma, a neglected disease mostly affecting children, with a 90% mortality rate if untreated, is an orofacial gangrene that disintegrates the tissues of the face in &lt;1 wk. Noma can become inactive with early stage antibiotic treatment. Traditional healers, known as mai maganin gargajiya in Hausa, play an important role in the health system and provide care to noma patients.MethodsWe conducted 12 in-depth interviews with caretakers who were looking after noma patients admitted at the Noma Children's Hospital and 15 traditional healers in their home villages in Sokoto state, northwest Nigeria. We explored perceptions of noma, relationship dynamics, healthcare practices and intervention opportunities. Interviews were audiorecorded, transcribed and translated. Manual coding and thematic analysis were utilised.ResultsTraditional healers offered specialised forms of care for specific conditions and referral guidance. They viewed the stages of noma as different conditions with individualised remedies and were willing to refer noma patients. Caretakers trusted traditional healers.ConclusionsTraditional healers could play a crucial role in the early detection of noma and the health-seeking decision-making process of patients. Intervention programmes should include traditional healers through training and referral partnerships. This collaboration could save lives and reduce the severity of noma complications.
Determination of New Psychoactive Substances in Whole Blood Using Microwave Fast Derivatization and Gas Chromatography/Mass Spectrometry
Authors: Cláudia Margalho , Pedro Almeida , Tiago Rosado , Francisco Corte Real , Eugenia Gallardo 
Published: June 2019

Abstract
The production and consumption of new psychoactive substances (NPSs) has been raising a major concern worldwide. Due to easy access and available information, many NPSs continue to be synthesized with an alarming increase of those available to purchase, despite all the control efforts created. A new analytical method was developed and validated to determine a group of phenethylamines and synthetic cathinones: cathinone, flephedrone, buphedrone, 4-MTA, α-PVP, methylone, 2C-P, ethylone, pentylone, MDPV and bromo-dragonFLY in whole blood. A mixed-mode solid phase extraction was applied to 250 μL of sample, and the extracts were derivatized with fast microwave technique before being analyzed by gas chromatography–mass spectrometry (GC–MS). The validation procedure followed the Scientific Working Group for Forensic Toxicology (SWGTOX) guidelines with parameters that included selectivity, linearity, limits of detection and quantification, intra- and inter-day precision and accuracy, recoveries and stability.
The method presented linearity between 5 and 500 ng/mL for cathinone, buphedrone, 4-MTA, methylone, 2C-P and bromo-dragonFLY, 10–500 ng/mL for flephedrone, ethylone, pentylone and MDPV, and 40–500 ng/mL for α-PVP, with determination coefficients above 0.99 for all analytes. Recoveries ranged between 70.3% and 116.6%, and regarding intra- and inter-day precision, the relative mean errors were typically lower than 8.6%. The method was successfully applied to over 100 authentic samples from the Laboratory of Chemistry and Forensic Toxicology, Centre Branch, of the National Institute of Legal Medicine and Forensic Sciences, Portugal.
Wildflower Seed Sales as Incentive for Adopting Flower Strips for Native Bee Conservation: A Cost-Benefit Analysis
Authors: Delphia Casey M , O’Neill Kevin M , Burkle Laura A 
Published: June 2019

AbstractImproving pollinator habitat on farmlands is needed to further wild bee conservation and to sustain crop pollination in light of relationships between global declines in pollinators and reductions in floral resources. One management strategy gaining much attention is the use of wildflower strips planted alongside crops to provide supplemental floral resources for pollinators. However, farmer adoption of pollinator-friendly strategies has been minimal, likely due to uncertainty about costs and benefits of providing non-crop flowering plants for bees. Over 3 yr, on four diversified farms in Montana, United States, we estimated the potential economic profit of harvesting and selling wildflower seeds collected from flower strips implemented for wild bee conservation, as an incentive for farmers to adopt this management practice. We compared the potential profitability of selling small retail seed packets versus bulk wholesale seed. Our economic analyses indicated that potential revenue from retail seed sales exceeded the costs associated with establishing and maintaining wildflower strips after the second growing season. A wholesale approach, in contrast, resulted in considerable net economic losses. We provide proof-of-concept that, under retail scenarios, the sale of native wildflower seeds may provide an alternative economic benefit that, to our knowledge, remains unexplored. The retail seed-sales approach could encourage greater farmer adoption of wildflower strips as a pollinator-conservation strategy in agroecosystems. The approach could also fill a need for regionally produced, native wildflower seed for habitat restoration and landscaping aimed at conserving native plants and pollinators.
Toxicities of Insecticidal Toxic Baits to Control Ceratitis capitata (Diptera: Tephritidae): Implications for Field Management
Authors: Baronio Cléber Antonio , Bernardi Daniel , Schutze Inana Xavier , Baldin Morgana Mattiello , Machota Ruben , Garcia Flávio Roberto Mello , Botton Marcos 
Published: June 2019

Abstract
Ceratitis capitata (Wiedemann, 1824) is a significant insect pest of fruits produced worldwide and is capable of causing direct and indirect damage to fruit. Chemical control is the most frequently used management strategy, mainly involving organophosphate insecticides. However, the frequent use of this chemical group has resulted in unacceptable chemical residues on fruits. In this study, the toxicity of 18 insecticides was evaluated in adults and larvae of C. capitata in a laboratory. The organophosphate insecticides chlorpyrifos (Lorsban 480BR), phosmet (Imidan 500WP), and malathion (Malathion 1000EC); the spinosyns spinetoram (Delegate 250WG) and spinosad (Tracer); and the pyrethroid alpha-cypermethrin (Fastac 100SC) caused high mortality (>80%) in C. capitata adults in topical application bioassays and by ingestion when mixed with Biofruit 5% food lures. However, the insecticides chlorfenapyr (Pirate), spinetoram and chlorpyrifos produced a significant reduction in larval infestation of the fruits (67, 74, and 84% larval mortality, respectively). Insecticides based on spinosyns, alpha-cypermethrin, and cyantraniliprole are alternatives that can replace organophosphates in the management of C. capitata in the field.
The Myth of Diversification: The Destabilizing Impact of Diversification on Financial Institutions
Authors: Jin Kwon-Yong 
Published: June 2019

Abstract
This article analyses the impact of asset and activity diversification on the stability of major financial institutions. Diversification is typically viewed as a positive element in risk management. However, examining recent examples concerning diversified multinational financial institutions and a theoretical model of failure risk facing them, this article demonstrates that under certain conditions, diversification can actually increase systemic risk. Financial conglomerates can be ‘too big to manage’, they can become too similar to each other and susceptible to coordinated failure, and, most importantly, catastrophic losses in one part of the firm can overwhelm the whole firm. Based on this finding, this article proposes a number of mitigation measures to limit intra-firm spillover and to make the resolution of troubled financial institutions smoother.
A Rare Case of Pseudomyiasis in a Dog by Hermetia illucens (Diptera: Stratiomyidae)
Authors: Mulieri P R , Patitucci L D , Scolaro A 
Published: June 2019

Abstract
Hermetia illucens (L.) (Diptera: Stratiomyidae), commonly known as black soldier fly is a dipterous species which can produce enteric pseudomyiasis in humans and domestic animals. Veterinary cases of intestinal myiasis caused by H. illucens in dogs have not been reported previously. We present this rare pseudomyiasis (= accidental myiasis) produced by infestation with several larvae of the intestinal tract in a dog inhabiting a city in the province of Buenos Aires, Argentina.
Cardiomyopathy in Thalassemia: Quick Review from Cellular Aspects to Diagnosis and Current Treatments
Authors: Ghanavat Majid , Haybar Habib , Pezeshki Seyed Mohammad Sadegh , Shahjahani Mohammad , Jodat Hosein , Elyasi Milad , Saki Najmaldin 
Published: June 2019

Abstract

Background
Cardiomyopathic manifestations induced by continuous blood transfusion are the leading cause of death among patients with thalassemia major (TM). Despite introduction of chelation therapy, heart failure after cardiomyopathic manifestations is still a major threat to patients.

Methods
We performed a search of relevant English-language literature, retrieving publications from the PubMed database and the Google Scholar search engine (2005–2018). We used “thalassemia major”, “cardiomyopathy”, “iron overload”, “cardiac magnetic resonance T2” “chelation therapy”, and “iron burden” as keywords.

Results
The results of the studies we found suggest that cardiac hepcidin is a major regulator of iron homeostasis in cardiac tissue. Unlike previous assumptions, the heart appears to have a limited regeneration capability, originating from a small population of hypoxic cardiomyocytes.

Conclusions
Oxygen levels determine cardiomyocyte gene-expression patterns. Upregulation of cardiac hepcidin in hypoxia preserves cardiomyocytes from forming out of reactive oxygen species catalyzed by free cellular iron in cardiomyocytes. Using the limited regeneration capacity of cardiac cells and gaining further understanding of the cellular aspects of cardiomyopathic manifestations may help health care professionals to develop new therapeutic strategies.
ALMA observations of A0620–00: fresh clues on the nature of quiescent black hole X-ray binary jets
Authors: Gallo Elena , Teague Richard , Plotkin Richard M , Miller-Jones James C A , Russell David M , Dinçer Tolga , Bailyn Charles , Maccarone Thomas J , Markoff Sera , Fender Rob P 
Published: June 2019

ABSTRACT
We report on Atacama Large Millimeter Array (ALMA) continuum observations of the black hole X-ray binary A0620–00 at an X-ray luminosity nine orders of magnitude sub-Eddington. The system was significantly detected at 98 GHz (at 44 ± 7 $\mu$Jy) and only marginally at 233 GHz (20 ± 8 $\mu$Jy), about 40 d later. These results suggest either an optically thin sub-mm synchrotron spectrum, or highly variable sub-mm jet emission on month time-scales. Although the latter appears more likely, we note that, at the time of the ALMA observations, A0620–00 was in a somewhat less active optical-IR state than during all published multiwavelength campaigns when a flat-spectrum, partially self-absorbed jet has been suggested to extend from the radio to the mid-IR regime. Either interpretation is viable in the context of an internal shock model, where the jet’s spectral shape and variability are set by the power density spectrum of the shells’ Lorentz factor fluctuations. While strictly simultaneous radio–mm-IR observations are necessary to draw definitive conclusions for A0620–00, the data presented here, in combination with recent radio and sub-mm results from higher luminosity systems, demonstrate that jets from black hole X-ray binaries exhibit a high level of variability – either in flux density or intrinsic spectral shape, or both – across a wide spectrum of Eddington ratios. This is not in contrast with expectations from an internal shock model, where lower jet power systems can be expected to exhibit larger fractional variability owing to an overall decrease in synchrotron absorption.
Possible evolution of the circum-galactic medium around QSOs with QSO age and cosmic time revealed by Ly α haloes
Authors: Momose Rieko , Goto Tomotsugu , Utsumi Yousuke , Hashimoto Tetsuya , Chiang Chia-Ying , Kim Seong-Jin , Kashikawa Nobunari , Shimasaku Kazuhiro , Miyazaki Satoshi 
Published: June 2019

ABSTRACT
We first present new Subaru narrow-band observations of the Ly α halo around the quasi-stellar object (QSO) CFHQ J232908−030158 at z = 6.42, which appears the most luminous and extended halo at z > 5 (LLy α = 9.8 × 1043 erg s−1 within 37 pkpc diameter). Then, combining these measurements with available data in the literature, we find two different evolutions of QSOs’ Ly α haloes. First is a possible short-term evolution with QSO age seen in four z > 6 QSOs. We find the anticorrelation between the Ly α halo scales with QSOs’ infrared (IR) luminosity, with J2329−0301’s halo being the brightest and largest. It indicates that ionizing photons escape more easily out to circum-galactic regions when host galaxies are less dusty. We also find a positive correlation between IR luminosity and black hole mass (MBH). Given MBH as an indicator of QSO age, we propose a hypothesis that a large Ly α halo mainly exists around QSOs in the young phase of their activity due to a small amount of dust. The second is an evolution with cosmic time seen over z ∼ 2–5. We find the increase of surface brightness towards lower redshift with a similar growth rate to that of dark matter haloes (DHs) that evolve to MDH = 1012–1013 M⊙ at z = 2. The extent of Ly α haloes is also found to increase at a rate scaling with the virial radius of growing DHs, $r_\text{vir} \propto M_\text{DH}^{1/3}(1+z)^{-1}$. These increases are consistent with a scenario that the circum-galactic medium around QSOs evolves in mass and size keeping pace with hosting DHs.
3D optical spectroscopic study of NGC 3344 with SITELLE: I. Identification and confirmation of supernova remnants
Authors: Moumen I , Robert C , Devost D , Martin R P , Rousseau-Nepton L , Drissen L , Martin T 
Published: June 2019

ABSTRACT
We present the first optical identification and confirmation of a sample of supernova remnants (SNRs) in the nearby galaxy NGC 3344. Using high spectral and spatial resolution data, obtained with the CFHT imaging Fourier transform spectrograph SITELLE, we identified about 2200 emission line regions, many of which are H ii regions, diffuse ionized gas regions, and also SNRs. Considering the stellar population and diffuse ionized gas background, which are quite important in NGC 3344, we have selected 129 SNR candidates based on four criteria for regions where the emission lines flux ratio [S ii]/H α ≥ 0.4. Emission lines of [O ii] λ3727, H β, [O iii] λλ4959,5007, H α, [N ii] λλ6548,6583, and [S ii] λλ6716,6731 have been measured to study the ionized gas properties of the SNR candidates. We adopted a self-consistent spectroscopic analysis, based on Sabbadin plots and Baldwin, Phillips & Terlevich diagrams, to confirm the shock-heated nature of the ionization mechanism in the candidates sample. With this analysis, we end up with 42 Confirmed SNRs, 45 Probable SNRs, and 42 Less likely SNRs. Using shock models, the confirmed SNRs seem to have a metallicity ranging between Large Magellanic Cloud and 2×solar. We looked for correlations between the size of the confirmed SNRs and their emission lines ratios, their galaxy environment, and their galactocentric distance: We see a trend for a metallicity gradient among the SNR population, along with some evolutionary effects.