bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel heat shock-induced long non-coding RNA in human cells
Authors: Onoguchi-Mizutani Rena , Kishi Yoshihiro , Ogura Yoko , Nishimura Yuuki , Imamachi Naoto , Suzuki Yutaka , Miyazaki Satoru , Akimitsu Nobuyoshi 
Published: October 2020

Abstract
The heat-shock response is a crucial system for survival of organisms under heat stress. During heat-shock stress, gene expression is globally suppressed, but expression of some genes, such as chaperone genes, is selectively promoted. These selectively activated genes have critical roles in the heat-shock response, so it is necessary to discover heat-inducible genes to reveal the overall heat-shock response picture. The expression profiling of heat-inducible protein-coding genes has been well-studied, but that of non-coding genes remains unclear in mammalian systems. Here, we used RNA-seq analysis of heat shock-treated A549 cells to identify seven novel long non-coding RNAs that responded to heat shock. We focussed on CTD-2377D24.6 RNA, which is most significantly induced by heat shock, and found that the promoter region of CTD-2377D24.6 contains the binding site for transcription factor HSF1 (heat shock factor 1), which plays a central role in the heat-shock response. We confirmed that HSF1 knockdown cancelled the induction of CTD-2377D24.6 RNA upon heat shock. These results suggest that CTD-2377D24.6 RNA is a novel heat shock-inducible transcript that is transcribed by HSF1.
Status Pivoting
Authors: Goor Dafna , Keinan Anat , Ordabayeva Nailya 
Published: October 2020

AbstractPrior research has established that status threat leads consumers to display status-related products such as luxury brands. While compensatory consumption within the domain of the status threat (e.g., products associated with financial and professional success) is the most straightforward way to cope with comparisons to high-status individuals, we examine when, why, and how consumers cope with status threat by choosing to “pivot” and display success and achievements in alternative domains. Using a mixed-method approach combining field and lab experiments, incentive-compatible designs, netnographic analysis, observational study, and qualitative interviews, we show that consumers cope with status threat by signaling their status and success in alternative domains. We conceptualize this behavior as “status pivoting” and show that it occurs because experiencing status threat motivates consumers to adopt beliefs about tradeoffs across domains; that is, to believe that status acquisition requires tradeoffs and hence others’ success in one domain comes at the cost of success in another domain. We compare the prevalence and appeal of status pivoting to restoring status within the domain of the threat. We further examine when consumers are likely to engage in status pivoting and show that this effect is attenuated when high status within the domain of the threat is attainable.
Banks Grass Mite (Acari: Tetranychidae) Suppression May Add to the Benefit of Drought-Tolerant Corn Hybrids Exposed to Water Stress
Authors: Ruckert Alice , Golec Julian R , Barnes Cody L , Ramirez Ricardo A 
Published: October 2020

Abstract
Spider mite (Acari: Tetranychidae) outbreaks are common on corn grown in the arid West. Hot and dry conditions reduce mite development time, increase fecundity, and accelerate egg hatch. Climate change is predicted to increase drought incidents and produce more intense temperature patterns. Together, these environmental shifts may cause more frequent and severe spider mite infestations. Spider mite management is difficult as many commercially available acaricides are ineffective due to the development of resistance traits in field mite populations. Therefore, alternative approaches to suppress outbreaks are critically needed. Drought-tolerant plant hybrids alleviate the challenges of growing crops in water-limited environments; yet, it is unclear if drought-tolerant hybrids exposed to water stress affect mite outbreaks under these conditions. We conducted a greenhouse experiment to evaluate the effect of drought-tolerant corn hybrids on Banks grass mite [Oligonychus pratensis Banks (Acari: Tetranychidae)], a primary pest of corn, under optimal irrigation and water-stress irrigation. This was followed by a 2-yr field study investigating the effect of drought-tolerant corn hybrids exposed to the same irrigation treatments on Banks grass mite artificially infested on hybrids and resident spider mite populations. Results showed that water-stressed drought-tolerant hybrids had significantly lower Banks grass mite and resident spider mite populations than water-stressed drought-susceptible hybrids. Interestingly, water-stressed drought-tolerant hybrids had equal Banks grass mite populations to drought-susceptible and drought-tolerant hybrids under optimal irrigation. We posit that planting drought-tolerant hybrids may suppress spider mite outbreaks in water-challenged areas.
Immunotherapy for advanced melanoma: current situation in Japan
Authors: Kato Junji , Uhara Hisashi 
Published: October 2020

Abstract
Treatment with immune checkpoint inhibitors provides long-term survival for patients with advanced melanoma. Improvements in the overall survival of advanced melanoma patients have been achieved with anti-PD-1 monotherapy and anti-PD-1+ CTLA4 combination therapy, but there are still many issues to resolve. Acral, mucosal and uveal melanoma have been less responsive to immune checkpoint inhibitors than cutaneous melanoma. For patients who have achieved a good response, it is still not known how long the anti-PD-1 therapy should be administered. Moreover, there is limited treatment for patients who relapse during or after adjuvant anti-PD-1 therapy. Here, we review the current evidence regarding the clinical effects of immunotherapy for advanced melanoma. Moreover, we review previous studies of acral, mucosal and uveal melanoma, and we discuss the recent findings regarding durable response after the cessation of anti-PD-1 therapy, and treatment options for recurrence after adjuvant therapy.
Syzygium samarangense Leaf Infusion as Aedes albopictus (Diptera: Culicidae) Ovitrap Bait
Authors: Shu Ching-Yu , Shelomi Matan 
Published: October 2020

Abstract
Adding lures can improve the efficiency of mosquito ovitraps used for monitoring or in attract-and-kill pest management. Easily produced, low-to-no cost bait would be ideal for remote field sites and community-run vector management. Plant infusions are popular ovitrap baits for their low cost and potent attractiveness, attributed either to the plants or their microbiomes. We tested fermented leaf infusions of the wax apple tree, Syzygium samarangense (Blume) Merr. & Perry, as bait in lethal ovitraps in urban Taipei with Bti larvicide. All trapped insects were inferred to be Asian tiger mosquito, Aedes albopictus (Skuse). The bait significantly increased the yield of the traps, with no negative interactions with the larvicide in either direction. Syzgium samarangense leaves are readily available across Taiwan, making their infusion an easy bait to greatly improve ovitrap efficiency.
Effect of 10-Valent Pneumococcal Conjugate Vaccine on Streptococcus pneumoniae Nasopharyngeal Carriage Among Children Less Than 5 Years Old: 3 Years Post-10-Valent Pneumococcal Conjugate Vaccine Introduction in Mozambique
Authors: Valenciano Sandra J , Moiane Benild , Lessa Fernanda C , Chaúque Alberto , Massora Sergio , Pimenta Fabiana C , Mucavele Helio , Verani Jennifer R , da Gloria Carvalho Maria , Whitney Cynthia G , Tembe Nelson , Sigaúque Betuel 
Published: October 2020

Abstract

Background
Mozambique introduced 10-valent pneumococcal conjugate vaccine (PCV10) in 2013 with doses at ages 2, 3, and 4 months and no catch-up or booster dose. We evaluated PCV10 impact on the carriage of vaccine-type (VT), non-VT, and antimicrobial non-susceptible pneumococci 3 years after introduction.

Methods
We conducted cross-sectional carriage surveys among HIV-infected and HIV-uninfected children aged 6 weeks to 59 months: 1 pre-PCV10 (2012–2013 [Baseline]) and 2 post-PCV10 introductions (2014–2015 [Post1] and 2015–2016 [Post2]). Pneumococci isolated from nasopharyngeal swabs underwent Quellung serotyping and antimicrobial susceptibility testing. Non-susceptible isolates (intermediate or resistant) were defined using Clinical and Laboratory Standards Institute 2018 breakpoints. We used log-binomial regression to estimate changes in the pneumococcal carriage between survey periods. We compared proportions of non-susceptible pneumococci between Baseline and Post2.

Results
We enrolled 720 children at Baseline, 911 at Post1, and 1208 at Post2. Baseline VT carriage was similar for HIV-uninfected (36.0%, 110/306) and HIV-infected children (34.8%, 144/414). VT carriage was 36% (95% confidence interval [CI]: 19%–49%) and 27% (95% CI: 11%–41%) lower in Post1 vs baseline among HIV-uninfected and HIV-infected children, respectively. VT carriage prevalence declined in Post2 vs Post1 for HIV-uninfected but remained stable for HIV-infected children. VT carriage prevalence 3 years after PCV10 introduction was 14.5% in HIV-uninfected and 21.0% in HIV-infected children. Pneumococcal isolates non-susceptible to penicillin declined from 66.0% to 56.2% (P= .0281) among HIV-infected children.

Conclusions
VT and antimicrobial non-susceptible pneumococci carriage dropped after PCV10 introduction, especially in HIV-uninfected children. However, VT carriage remained common, indicating ongoing VT pneumococci transmission.
The transcription factor ZmNAC49 reduces stomatal density and improves drought tolerance in maize
Authors: Xiang Yang , Sun Xiujuan , Bian Xiangli , Wei Tianhui , Han Tong , Yan Jingwei , Zhang Aying 
Published: October 2020

AbstractDrought stress severely limits the growth, development, and productivity of crops, and therefore understanding the mechanisms by which plants respond to drought is crucial. In this study, we cloned a maize NAC transcription factor, ZmNAC49, and identified its function in response to drought stress. We found that ZmNAC49 is localized in the nucleus and has transcriptional activation activity. ZmNAC49 expression is rapidly and strongly induced by drought stress, and overexpression enhances stress tolerance in maize. Overexpression also significant decreases the transpiration rate, stomatal conductance, and stomatal density in maize. Detailed study showed that ZmNAC49 overexpression affects the expression of genes related to stomatal development, namely ZmTMM, ZmSDD1, ZmMUTE, and ZmFAMA. In addition, we found that ZmNAC49 can directly bind to the promoter of ZmMUTE and suppress its expression. Taken together, our results show that the transcription factor ZmNAC49 represses ZmMUTE expression, reduces stomatal density, and thereby enhances drought tolerance in maize.
Multifaceted roles of nitric oxide in tomato fruit ripening: NO-induced metabolic rewiring and consequences for fruit quality traits
Authors: Zuccarelli Rafael , Rodríguez-Ruiz Marta , Lopes-Oliveira Patrícia J , Pascoal Grazieli B , Andrade Sónia C S , Furlan Cláudia M , Purgatto Eduardo , Palma José M , Corpas Francisco J , Rossi Magdalena , Freschi Luciano 
Published: October 2020

AbstractNitric oxide (NO) has been implicated as part of the ripening regulatory network in fleshy fruits. However, very little is known about the simultaneous action of NO on the network of regulatory events and metabolic reactions behind ripening-related changes in fruit color, taste, aroma and nutritional value. Here, we performed an in-depth characterization of the concomitant changes in tomato (Solanum lycopersicum) fruit transcriptome and metabolome associated with the delayed-ripening phenotype caused by NO supplementation at the pre-climacteric stage. Approximately one-third of the fruit transcriptome was altered in response to NO, including a multilevel down-regulation of ripening regulatory genes, which in turn restricted the production and tissue sensitivity to ethylene. NO also repressed hydrogen peroxide-scavenging enzymes, intensifying nitro-oxidative stress and S-nitrosation and nitration events throughout ripening. Carotenoid, tocopherol, flavonoid and ascorbate biosynthesis were differentially affected by NO, resulting in overaccumulation of ascorbate (25%) and flavonoids (60%), and impaired lycopene production. In contrast, the biosynthesis of compounds related to tomato taste (sugars, organic acids, amino acids) and aroma (volatiles) was slightly affected by NO. Our findings indicate that NO triggers extensive transcriptional and metabolic rewiring at the early ripening stage, modifying tomato antioxidant composition with minimal impact on fruit taste and aroma.
Variation in LOD Across SARS-CoV-2 Assay Systems: Need for Standardization
Authors: Sohni Youvraj 
Published: October 2020

Abstract
Multiple SARS-CoV-2 emergency use authorization (EUA) tests are being used for clinical testing across various clinical testing laboratories for meeting the diagnostic challenges of the ongoing pandemic. However, cross-assay variations in performance characteristics need to be recognized. A better understanding is needed of the clinical implications of cross-assay variation in performance characteristics, particularly in the limit of detection (LOD) of the SARS-CoV-2 assays used for clinical testing. Herein, a snapshot of the diversity of SARS-CoV-2 EUA analytical assay systems including methodologies, assay designs, and technology platforms is presented. Factors affecting the variations in LOD are discussed. Potential measures that may standardize across the various assay systems are suggested. Development of international standards and reference materials for the establishment of performance characteristics may substantially alleviate potential clinical decision-making challenges. Finally, cross-assay variation in LODs among the diverse SARS-CoV-2 diagnostic assays impacts clinical decision-making with multiple assay systems in use and lack of standardization across platforms. International standards in parallel with continued cross-platform studies and collaborative efforts across pertinent healthcare entities will help mitigate some of the clinical decision-making challenges.
How biased are halo properties in cosmological simulations?
Authors: Mansfield Philip , Avestruz Camille 
Published: October 2020

ABSTRACT
Cosmological N-body simulations have been a major tool of theorists for decades, yet many of the numerical issues that these simulations face are still unexplored. This paper measures numerical biases in these large, dark matter-only simulations that affect the properties of their dark matter haloes. We compare many simulation suites in order to provide several tools for simulators and analysts which help mitigate these biases. We summarize our comparisons with practical ‘convergence limits’ that can be applied to a wide range of halo properties, including halo properties which are traditionally overlooked by the testing literature. We also find that the halo properties predicted by different simulations can diverge from one another at unexpectedly high resolutions. We demonstrate that many halo properties depend strongly on force softening scale and that this dependence leads to much of the measured divergence between simulations. We offer an empirical model to estimate the impact of such effects on the rotation curves of a halo population. This model can serve as a template for future empirical models of the biases in other halo properties.
SDSS-IV MaNGA: when is morphology imprinted on galaxies?
Authors: Peterken Thomas , Merrifield Michael , Aragón-Salamanca Alfonso , Avila-Reese Vladimir , Boardman Nicholas F , Drory Niv , Lane Richard R 
Published: October 2020

ABSTRACT
It remains an open question as to how long ago the morphology that we see in a present-day galaxy was typically imprinted. Studies of galaxy populations at different redshifts reveal that the balance of morphologies has changed over time, but such snapshots cannot uncover the typical time-scales over which individual galaxies undergo morphological transformation, nor which are the progenitors of today’s galaxies of different types. However, these studies also show a strong link between morphology and star formation rate (SFR) over a large range in redshift, which offers an alternative probe of morphological transformation. We therefore derive the evolution in SFR and stellar mass of a sample of 4342 galaxies in the SDSS-IV MaNGA survey through a stellar population ‘fossil record’ approach, and show that the average evolution of the population shows good agreement with known behaviour from previous studies. Although the correlation between a galaxy’s contemporaneous morphology and SFR is strong over a large range of lookback times, we find that a galaxy’s present-day morphology only correlates with its relatively recent ($\sim \! 2\, \textrm {Gyr}$) star formation history. We therefore find strong evidence that morphological transitions to galaxies’ current appearance occurred on time-scales as short as a few billion years.
Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People
Authors: Lo Yun-Hua , Cheng Hsueh-Chien , Hsiung Chia-Ni , Yang Show-Ling , Wang Han-Yu , Peng Chia-Wei , Chen Chun-Yu , Lin Kung-Ping , Kang Mei-Ling , Chen Chien-Hsiun , Chu Hou-Wei , Lin Chiao-Feng , Lee Mei-Hsuan , Liu Quintin , Satta Yoko , Lin Cheng-Jui , Lin Marie , Chaw Shu-Miaw , Loo Jun-Hun , Shen Chen-Yang , Ko Wen-Ya 
Published: October 2020

Abstract
The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.
Antibiotic Treatment Regimes as a Driver of the Global Population Dynamics of a Major Gonorrhea Lineage
Authors: Osnes Magnus N , Dorp Lucy van , Brynildsrud Ola B , Alfsnes Kristian , Schneiders Thamarai , Templeton Kate E , Yahara Koji , Balloux Francois , Caugant Dominique A , Eldholm Vegard 
Published: October 2020

Abstract
The Neisseria gonorrhoeae multilocus sequence type (ST) 1901 is among the lineages most commonly associated with treatment failure. Here, we analyze a global collection of ST-1901 genomes to shed light on the emergence and spread of alleles associated with reduced susceptibility to extended-spectrum cephalosporins (ESCs).
The genetic diversity of ST-1901 falls into a minor and a major clade, both of which were inferred to have originated in East Asia. The dispersal of the major clade from Asia happened in two separate waves expanding from ∼1987 and 1996, respectively. Both waves first reached North America, and from there spread to Europe and Oceania, with multiple secondary reintroductions to Asia.
The ancestor of the second wave acquired the penA 34.001 allele, which significantly reduces susceptibility to ESCs. Our results suggest that the acquisition of this allele granted the second wave a fitness advantage at a time when ESCs became the key drug class used to treat gonorrhea. Following its establishment globally, the lineage has served as a reservoir for the repeated emergence of clones fully resistant to the ESC ceftriaxone, an essential drug for effective treatment of gonorrhea.
We infer that the effective population sizes of both clades went into decline as treatment schemes shifted from fluoroquinolones via ESC monotherapy to dual therapy with ceftriaxone and azithromycin in Europe and the United States. Despite the inferred recent population size decline, the short evolutionary path from the penA 34.001 allele to alleles providing full ceftriaxone resistance is a cause of concern.
A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages
Authors: Dellicour Simon , Durkin Keith , Hong Samuel L , Vanmechelen Bert , Martí-Carreras Joan , Gill Mandev S , Meex Cécile , Bontems Sébastien , André Emmanuel , Gilbert Marius , Walker Conor , Maio Nicola De , Faria Nuno R , Hadfield James , Hayette Marie-Pierre , Bours Vincent , Wawina-Bokalanga Tony , Artesi Maria , Baele Guy , Maes Piet 
Published: October 2020

Abstract
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analyzed with gold-standard phylogeographic approaches. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to analyze the spatiotemporal dispersal history and dynamics of SARS-CoV-2 lineages. As a proof of concept, we focus on the Belgian epidemic, which has had one of the highest spatial densities of available SARS-CoV-2 genomes. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.