bluuebunny/crossref_metadata_2025 huggingface dataset:
Digital Humanities and Nineteenth Century Music: Some Perspectives and Examples from Latin America
Authors: Izquierdo José Manuel , Vera Fernanda
Published: January 2020

The advent of digital resources, the Internet, and an interconnected globe has deeply affected the humanities and its research. Music scholars in Latin America, like everywhere else, have observed this explosion of digital information sharing, but not everyone has been able to take advantage of the new opportunities afforded by this technology. On the one hand, advantages of digitization are slowly becoming recognized as tools to fight the enormous size of the region (Latin America), especially through technology's ability to easily and promptly disperse sources across great distances. In addition, digitization acts as an aid in countering the endemic lack of economic resources, and more broadly offers a path towards making the academic world a more connected and equal place. On the other hand, it is undeniable that the digital revolution has not reached people across the globe equally. Digital segregation is a problem that deeply impacts numerous nations around world; and for Latin America and the Caribbean, it has meant a slower pace of incorporation into the digital era. Key databases like JSTOR and the various READEX products are still largely unavailable to scholars in Latin America, and, given the steep price of such resources, the fight for a world of open-source information is becoming increasingly political.
Policing Space and Defying the Mainstream: Gender and the Creation of a Traditional Music Public Sphere in Twentieth-Century Ireland
Authors: SLOMINSKI TES
Published: January 2020

Whether in Ireland or elsewhere, most people first encounter Irish traditional music in public spaces such as pub sessions or concerts, or through the recorded traces of music-making produced for a listening public.1For those who become more involved in the scene as players, dancers, or avid listeners, festivals, schools, non-profit organisations, archives, and other instruments of the public sphere of Irish traditional music shape perceptions of the genre’s style, history, and participants. But while public and semi-public music-making has been a vital part of the transnational Irish traditional music scene for at least a century, the genre’s self-understanding still relies on its associations with a domestic, private past. In this article, I locate the roots of this contradiction in the historiographical problems presented by the 1935 Public Dance Halls Act—a piece of legislation that has had profound effects on musical practice and discourse in Ireland.2I examine the ways this law and the frequent retrospective overemphasis of its effects have contributed to the idealisation of Irish traditional music as rooted in a domestic, rural, and lower-class past. Combined with social and governmental restrictions on the activities of women during most of the twentieth century, this alignment of domesticity with imagined “authenticity” has shaped the reception of women’s public Irish traditional musical performance in the twentieth and twenty-first centuries.
Contraculture: Bird Names and the Degendering of Contra Dance
Authors: SNYDER ANDREW
Published: January 2020

At Oakland’s Circle Left contra dance, I notice my hands fumbling as I take “hands four” with my partner and our neighbour couple to form one of many foursomes in a long line of contra dancers. My partner and I place our hands facing palm up expecting to find a hand to hold facing palm down. In “traditional” contra, it is the person in the “lady” role who places their hand palm down on the hand of the person in the “gent” role. But this time it is I, a cisgendered male,1 who am in the wrong, since we decided before the dance that I am dancing the “raven” part, traditionally the “lady,” and my partner is dancing the “lark,” traditionally the “gent.” I correct myself and place my hand upon theirs. When I adopt the “raven” role, thirty-three years of contra dancing, that is, thirty-three years of gendered behaviour that have contributed to how I have learned to be male, are slightly difficult, but, as it turns out, not too difficult to unlearn. As we advance down and back up the hall, I make other, less minute mistakes, some that have to do with the new role expectations and some that are just part of a customary failure at executing dance moves perfectly. Like “traditional” contra dance, Circle Left (Figure 1) is a communitarian, participatory activity, and forgiveness is quickly given with a smile.
Exploring Creativity in Traditional Music
Authors: YUNG BELL
Published: January 2020

The term “traditional music” is widely used in musicological discourse as well as in everyday conversations, and is, indeed, in the name of our organisation: the International Council for Traditional Music.1It was also used in the titles of classic studies of Asian music by our elders, such as Yi Hye-gu (1981), Kishibe Shigeo (1969), William Malm (1959), A. C. Scott (1967, 1969, 1975), David Morton (1976), Judith Becker (1980), Terry Miller (1985), and others, and in the titles of many journal articles. In short, the term is at the core of the discipline of ethnomusicology and for this organisation.
Aerosol Impacts on Mesoscale Convective Systems Forming Under Different Vertical Wind Shear Conditions
Authors: Chen Qian , Fan Jiwen , Yin Yan , Han Bin
Published: January 2020

Following our previous study of wind shear effect on mesoscale convective system (MCS) organization under a clean atmospheric condition using the Weather Research and Forecasting model coupled with spectral‐bin microphysics, we conduct sensitivity simulations by increasing cloud condensation nuclei concentration to investigate aerosol impacts on MCSs forming under different wind shear conditions. We find that increased aerosols induce stronger updrafts and downdrafts in all MCSs. The stronger updrafts and enlarged convective core area contribute to larger vertical mass fluxes and enhance precipitation. The enhanced updrafts and vertical mass fluxes indicate convective invigoration. Increased updraft speed below 8‐km altitude is attributed to enhanced condensational heating, except for the weak wind shear and strong low‐level shear cases in which the enhanced low‐level convergence is another contributing factor. Interestingly, above 8‐km altitude, we see reduced updraft speed by the increased aerosols due to reduced vertical pressure perturbation gradient force. The accumulated rainfall and mean rain rate are increased with a greater occurrence frequency of heavy rain. Larger rain rate is seen in both convective and stratiform regions. In general, we see a higher frequency of deep clouds in the polluted condition because of invigorated convection, and more stratiform/anvil clouds, but a lower frequency of shallow warm clouds, with a larger significance for more organized MCSs. The consistently invigorated MCSs by aerosols under various wind shear conditions revealed by this study have important implications to weather and climate in warm and humid regions that are influenced by pollution.
Citizen Scientists Discover a New Auroral Form: Dunes Provide Insight Into the Upper Atmosphere
Authors: Palmroth M. , Grandin M. , Helin M. , Koski P. , Oksanen A. , Glad M. A. , Valonen R. , Saari K. , Bruus E. , Norberg J. , Viljanen A. , Kauristie K. , Verronen P. T.
Published: January 2020

Auroral forms are like fingerprints linking optical features to physical phenomena in the near‐Earth space. While discovering new forms is rare, recently, scientists reported of citizens' observations of STEVE, a pinkish optical manifestation of subauroral ionospheric drifts that were not thought to be visible to the naked eye. Here, we present a new auroral form named “the dunes”. On 7 October 2018, citizen observers took multiple digital photographs of the same dunes simultaneously from different locations in Finland and Sweden. We develop a triangulation method to analyze the photographs and conclude that the dunes are a monochromatic wave field with a wavelength of about 45 km within a thin layer at 100 km altitude. Supporting data suggest that the dunes manifest atmospheric waves, possibly mesospheric bores, which are rarely detected, and have not previously been observed via diffuse aurora nor at auroral latitudes and altitudes. The dunes present a new opportunity to investigate the coupling of the lower/middle atmosphere to the thermosphere and ionosphere. Our paper adds to the growing body of work that illustrates the value of citizen scientist images in carrying out quantitative analysis of optical phenomena, especially at small scales at subauroral latitudes. Further, the dune project presents means to create general interest toward physics, emphasizing that citizens can take part in scientific work by helping to uncover new phenomena.
A Flood Damage Allowance Framework for Coastal Protection With Deep Uncertainty in Sea Level Rise
Authors: Rasmussen D. J. , Buchanan Maya K. , Kopp Robert E. , Oppenheimer Michael
Published: January 2020

Deep uncertainty describes situations when there is either ignorance or disagreement over (1) models used to describe key system processes and (2) probability distributions used to characterize the uncertainty of key variables and parameters. Future projections of Antarctic ice sheet (AIS) mass loss remain characterized by deep uncertainty. This complicates decisions on long‐lived coastal protection projects when determining what margin of safety to implement. If the chosen margin of safety does not properly account for uncertainties in sea level rise, the effectiveness of flood protection could decrease over time, potentially putting lives and properties at a greater risk. To address this issue, we develop a flood damage allowance framework for calculating the height of a flood protection strategy needed to ensure that a given level of financial risk is maintained. The damage allowance framework considers decision maker preferences such as planning horizons, protection strategies, and subjective views of AIS stability. We use Manhattan—with the population and built environment fixed in time—to illustrate how our framework could be used to calculate a range of damage allowances based on multiple plausible scenarios of AIS melt. Under high greenhouse gas emissions, we find that results are sensitive to the selection of the upper limit of AIS contributions to sea level rise. Design metrics that specify financial risk targets, such as expected flood damage, allow for the calculation of avoided flood damages (i.e., benefits) that can be combined with estimates of construction cost and then integrated into existing financial decision‐making approaches (e.g., benefit‐cost analysis).
Observations of Laboratory and Natural Slow Slip Events: Hikurangi Subduction Zone, New Zealand
Authors: Ikari Matt J. , Wallace Laura M. , Rabinowitz Hannah S. , Savage Heather M. , Hamling Ian J. , Kopf Achim J.
Published: January 2020

Slow slip events (SSEs) are recognized as an important component of plate boundary fault slip, and there is a need for laboratory friction data on natural samples to guide comparisons with natural SSEs. Here, we compile a comprehensive catalog of SSEs observed geodetically at the Hikurangi subduction zone offshore northern New Zealand, and compare it with results of laboratory friction experiments that produce laboratory SSEs under plate tectonic driving rates (5 cm/yr). We use samples from Ocean Drilling Program Site 1124 seaward of the Hikurangi subduction zone to represent the plate boundary that hosts shallow SSEs at Hikurangi. We find that laboratory SSEs exhibit a similar displacement record and range of stress drops as the natural SSEs. Results of velocity step tests, which can be used to evaluate frictional instability based on the critical stiffness criterion, indicate that the slow slip activity at Hikurangi is a form of stably‐accelerating slip. Our laboratory SSEs provide an alternative method of quantifying (in)stability by direct measurement of the unloading stiffness during the stress drop. The observed dependence of laboratory SSE parameters on effective normal stress is consistent with critical stiffness theory; however, depth‐increasing projections based on laboratory data do not match observations from natural SSEs. These differences are likely related to changing temperature and fault rock composition downdip but also complications related to scaling and/or limited sampling. Scientific drilling recently undertaken at the Hikurangi subduction zone should serve to improve and guide future studies of the role of frictional properties for the occurrence of SSEs.
VLF Transmitters and Lightning‐Generated Whistlers: 1. Modeling Waves From Source to Space
Authors: Starks M. J. , Albert J. M. , Ling A. G. , O'Malley S. , Quinn R. A.
Published: January 2020

Waves from nine major ground‐based very low frequency (VLF) transmitters are modeled from their sources to 660 km altitude with a full‐wave code, which reliably treats transionospheric attenuation, and then ray‐and‐power traced throughout the plasmasphere. Lightning‐generated whistlers, previously modeled at 660 km altitude, are ray‐and‐power traced throughout the plasmasphere as well. The resulting profiles of electric and magnetic fields, including wave normal angles, are organized by
value. Two versions of a realistic plasmaspheric density model are used, and ducted as well as nonducted propagation are treated. Results are compared to empirical models based on near‐equatorial measurements by Van Allen Probes. A companion paper will evaluate resonant interactions of these waves with radiation belt electrons.
VLF Transmitters and Lightning‐Generated Whistlers: 2. Diffusion of Radiation Belt Electrons
Authors: Albert J. M. , Starks M. J. , Selesnick R. S. , Ling A. G. , O'Malley S. , Quinn R. A.
Published: January 2020

In a companion paper, new models of waves from ground‐based very low frequency transmitters and from lightning were presented. Ray‐and‐power tracing provided wave amplitudes as well as trajectories and wave normal angles throughout the plasmasphere. Here, these are used to evaluate diffusion of radiation belt electrons. These are combined with recent models of hiss and Coulomb collisions to find lifetimes and particle distributions. Butterfly pitch angle distributions and near‐megaelectron volt electrons are produced, confirming the role of energy diffusion. Coulomb energy drag, while often omitted, is also found to be important and should not be neglected.
The Properties and Origins of Corotating Plasmaspheric Irregularities as Revealed Through a New Tomographic Technique
Authors: Helmboldt J. F. , Haiducek J. D. , Clarke T. E.
Published: January 2020

This paper describes insights into the nature of corotating plasmaspheric irregularities (CPIs) enabled by a newly developed method for range‐ and time‐resolved tomographic images of these structures. The method is based on high‐precision measurements of total electron content gradients measure toward cosmic radio sources using an interferometric radio telescope, the Very Large Array (VLA). Exploiting hundreds of hours of data from the VLA Low‐band Ionosphere and Transient Experiment, we confirm that CPIs are predominantly detected at night and at
shells
2–4. Combining this large data set with other ionospheric, atmospheric, and space weather databases, we have established that CPI detection rates are much higher when levels of solar and geomagnetic activity are low. We also demonstrate that higher detection rates coincide with drivers of perturbations in the ionospheric electric field, including sporadic E and gravity waves. The gravity wave sources most commonly associated with CPIs are jet stream bend/shear and substorm‐triggered atmospheric disturbances. We also show that simulations of the plasmaspheric impact of both gravity wave‐driven electric field perturbations and polarization electric fields associated with electrobuoyancy waves/sporadic E produce results that are very similar to what is observed with the VLA.
Physically Consistent Modeling of Dike‐Induced Deformation and Seismicity: Application to the 2014 Bárðarbunga Dike, Iceland
Authors: Heimisson Elías R. , Segall Paul
Published: January 2020

Dike intrusions are often associated with surface deformation and propagating swarms of earthquakes. These are understood to be manifestations of the same underlying physical process, although rarely modeled as such. We construct a physics‐based model of the 2014 Bárðarbunga dike, by far the best observed large dike (
0.5 km
) to date. We constrain the background stress state by the total dike deformation, the time‐dependent dike pressure from continuous GPS and the extent of the seismic swarm, and the spatial dependence of frictional properties via the space‐time evolution of seismicity. We find that the geodetic and earthquake data can be reconciled with a self‐consistent set of parameters. The complex spatial and temporal evolution of the Bárðarbunga seismicity can be explained by dike‐induced elastic stress changes on preexisting faults, constrained by observed focal mechanisms. In particular, the model captures the segmentation of seismicity, where only the newest dike segment is seismically active. Our results indicate that many features of the seismicity result from the interplay between time‐dependent magma pressure within the dike and stress memory effects. The spatial variability in seismicity requires heterogeneity in frictional properties and/or local initial stresses. Modeling suggests that the dike pressure drops during rapid advances and increases during pauses, which primarily causes the segmentation of the seismicity. Joint analysis of multiple data types could potentially lead to improved, physics‐based eruption forecasts.
Phase‐Coherent Amplification of Ocean Swells Over Submarine Canyons
Authors: Tamura Hitoshi , Kawaguchi Koji , Fujiki Takashi
Published: January 2020

Ocean swells can be a significant coastal hazard, potentially causing coastal disasters with costly damage to infrastructure and tragic loss of lives. We have observed this in the coastal region of Toyama Bay in the Sea of Japan, which has been devastated by severe winter swell events (the so‐called YoriMawari‐nami; YM wave). An extreme swell event was recorded in February 2008 in which the wave height at a site in the bay reached 9+ m, which corresponds to 16 times the local climatological average. Substantial efforts by the Japanese coastal engineering community have been expended to reproduce YM wave events with phase‐averaged wave models but, to our knowledge, with no success. During an archetype YM event, we found that the Noto peninsula filtered the incoming wavefield such that in the bay incident waves were quasi‐monochromatic. The swell then refracted over a submarine canyon resulting in a bimodal directional distribution of wave energy. This initiated conditions favorable for coherent interference, violating the assumptions of the phase‐averaged approach. Coherent interference is the key mechanism for understanding the formation of the large amplitudes and for matching observed high space‐time variability. Our results demonstrate the significance of the coherent interference for wave statistics over coastal bathymetry; only by accounting for phase‐resolving phenomena were we able to adequately reproduce the observations.
Contrasting Patterns of Labile and Semilabile Dissolved Organic Carbon From Continental Waters to the Open Ocean
Authors: LaBrie Richard , Lapierre Jean‐François  , Maranger Roxane
Published: January 2020

Marine and freshwater prokaryotes feed primarily on bioavailable labile dissolved organic carbon (BDOCL), as well as the bioavailable fraction of the semilabile DOC (BDOCSL) pool. These fractions are operationally defined here as the DOC consumed within a month and greater than a month to a year and a half, respectively. Organic matter from these different pools comes from various autochthonous and allochthonous sources, but their relative bioavailability is unknown across aquatic ecosystems. To fill this gap, we compiled literature information that included 653 batch culture DOC biodegradation experiments across eight aquatic ecosystem types over the past 20 years. We show that the proportion of BDOCL across all aquatic ecosystems was surprisingly consistent (6.1%) despite a 2 order of magnitude variation in initial DOC concentrations, suggesting an overall tight balance between carbon supply and consumption. A higher proportion of BDOCL, 16.3% on average, was observed in high productivity ecosystems. BDOCSL, on the other hand, gradually decreased from 16.0% in lakes to 7.2% in estuaries to undetectable in the open ocean, suggesting that terrestrial connectivity regulates BDOCSL across the continuum. Our results support that recent primary production fuels short‐term prokaryotic DOC needs with an increasing reliance on the abundant BDOCSL pool as ecosystems approach the land‐water interface. Batch culture experiments show that BDOCSL is metabolizable in freshwater and coastal environments but not in the open ocean. We estimate that BDOCSL can sustain 62% of total prokaryotic biomass in inland waters and coasts and an estimated total of 16.7% across aquatic biomes.
Success and efficiency of phase 2/3 adjunctive trials for MDD funded by industry: a systematic review
Authors: Salloum Naji C. , Fava Maurizio , Ball Sophia , Papakostas George I.
Published: January 2020

To review the success rate and efficiency of industry-sponsored phase 2/3 clinical trials for adjunctive therapies for antidepressant partial- and non-responders with major depressive disorder (MDD), a systematic search of Pubmed/Medline was conducted, in addition to abstracts of major psychiatric meeting held since 2010, of randomized, placebo-controlled adjunct oral pharmacotherapy trials in this patient population. Forty-six (n = 33,900; 70 drug compactor arms) trials were pooled, yielding only three approved drugs. Twenty-two (31.4%) drug-placebo comparisons were successful. Numerically, success rates for treatment arms from studies with one versus more than one drug-placebo comparison were higher (39.3% versus 26.2%). The antidepressant lead-in employing single-blind placebo and the sequential-parallel comparison design (SPCD) were successful in 50% and 40% of cases, respectively. The direct randomization (no lead-in) design yielded positive results in one third of cases. The success rate of open-label antidepressant lead-ins without placebo or using double-blind placebo was very poor (<15%). There was also a pronounced discrepancy in terms of efficiency across study designs. Accounting for sample size requirements, a phase 3 program using SPCD would have a higher cumulative chance of yielding two positive trials (50%) than a phase 3 program using a single-blind placebo lead-in (40%). Future programs should carefully weigh the need for a lead-in, which is time-consuming, expensive and, in some cases (i.e., open-label antidepressant without placebo or with double-blind placebo) nearly futile. Instead, more effort should involve the use of studies where patients are directly randomized, such as the SPCD, with more investment shifted towards the accurate and independent vetting of subject eligibility.
A psychiatric disease-related circular RNA controls synaptic gene expression and cognition
Authors: Zimmerman Amber J. , Hafez Alexander K. , Amoah Stephen K. , Rodriguez Brian A. , Dell’Orco Michela , Lozano Evelyn , Hartley Brigham J. , Alural Begüm , Lalonde Jasmin , Chander Praveen , Webster Maree J. , Perlis Roy H. , Brennand Kristen J. , Haggarty Stephen J. , Weick Jason , Perrone-Bizzozero Nora , Brigman Jonathan L. , Mellios Nikolaos
Published: January 2020

Although circular RNAs (circRNAs) are enriched in the mammalian brain, very little is known about their potential involvement in brain function and psychiatric disease. Here, we show that circHomer1a, a neuronal-enriched circRNA abundantly expressed in the frontal cortex, derived from Homer protein homolog 1 (HOMER1), is significantly reduced in both the prefrontal cortex (PFC) and induced pluripotent stem cell-derived neuronal cultures from patients with schizophrenia (SCZ) and bipolar disorder (BD). Moreover, alterations in circHomer1a were positively associated with the age of onset of SCZ in both the dorsolateral prefrontal cortex (DLPFC) and orbitofrontal cortex (OFC). No correlations between the age of onset of SCZ and linear HOMER1 mRNA were observed, whose expression was mostly unaltered in BD and SCZ postmortem brain. Using in vivo circRNA-specific knockdown of circHomer1a in mouse PFC, we show that it modulates the expression of numerous alternative mRNA transcripts from genes involved in synaptic plasticity and psychiatric disease. Intriguingly, in vivo circHomer1a knockdown in mouse OFC resulted in specific deficits in OFC-mediated cognitive flexibility. Lastly, we demonstrate that the neuronal RNA-binding protein HuD binds to circHomer1a and can influence its synaptic expression in the frontal cortex. Collectively, our data uncover a novel psychiatric disease-associated circRNA that regulates synaptic gene expression and cognitive flexibility.
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae
Authors: Leu Andy O , Cai Chen , McIlroy Simon J , Southam Gordon , Orphan Victoria J , Yuan Zhiguo , Hu Shihu , Tyson Gene W
Published: January 2020

Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names “Candidatus Methanoperedens manganicus” and “Candidatus Methanoperedens manganireducens” for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment.
Lipids and small metabolites provisioned by ambrosia fungi to symbiotic beetles are phylogeny-dependent, not convergent
Authors: Huang Yin-Tse , Skelton James , Hulcr Jiri
Published: January 2020

Long-term symbiotic associations often lead to reciprocal adaptation between the involved entities. One of the main challenges for studies of such symbioses is differentiating adaptation from neutral processes and phylogenetic background. Ambrosia fungi, cultivated by ambrosia beetles as their sole food source, provide an excellent model to study evolutionary adaptation in a comparative framework because they evolved many times, and each origin bears features seemingly convergently adapted to the symbiosis. We tested whether the symbiotic lifestyle of unrelated ambrosia fungi has led to convergence in the key feature of the symbiotic phenotype—nutrition provisioning to the vector beetles. We compared conidia and mycelium content in three phylogenetic pairs of ambrosia fungi and their closely related nonambrosia relatives using an untargeted metabolomic assay. Multivariate analysis of 311 polar metabolites and 14063 lipid features revealed no convergence of nutrient content across ambrosia lineages. Instead, most variation of the metabolome composition was explained by phylogenetic relationships among the fungi. Thus the overall metabolome evolution of each ambrosia fungus is mostly driven by its inherited metabolism rather than the transition toward symbiosis. We identified eight candidate lipid compounds with expression levels different between the swollen ambrosia spores and other tissues, but they were not consistently elevated across ambrosia fungi. We conclude that ambrosia provisions consist either of nonspecific nutrients in elevated amounts, or of metabolites that are specific to each of the ambrosia symbioses.
The long noncoding RNA TUG1 is required for TGF-β/TWIST1/EMT-mediated metastasis in colorectal cancer cells
Authors: Shen Xuning , Hu Xiu , Mao Jiayan , Wu Ying , Liu Hao , Shen Jian , Yu Jiayin , Chen Wei
Published: January 2020

Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide, and metastasis is the major cause of CRC-related mortality. Transforming growth factor-beta (TGF-β) has a central role not only in the regulation of the normal colon but also in the development and metastasis of CRC. However, TGF-β is not considered an ideal therapeutic target because it shows both pro-tumorigenic and anti-tumorigenic activity, depending on the tumor stage. Therefore, it is important to find a downstream signaling component of TGF-β that can be targeted to impair CRC metastasis. Here, we show that TGF-β promotes CRC migration and upregulates the expression of long-noncoding RNA Taurine Upregulated Gene 1 (TUG1). TUG1 knockdown inhibited migration, invasion, and epithelial–mesenchymal transition (EMT) of CRC cells in vitro, and reduced CRC lung metastasis in vivo. TGF-β induced metastasis, and TUG1 knockdown inhibited these effects. In addition, TGF-β could not reverse the anti-metastasis effects of TUG1 knockdown. These data demonstrate that TUG1 is a downstream molecular of TGF-β. Moreover, TWIST1 expression was increased with TGF-β treatment, and TUG1 knockdown decreased TWIST1 expression in CRC cells. TWIST1 knockdown inhibited invasion and EMT in CRC cells; these effects were not changed by simultaneous TUG1 knockdown, indicating that TWIST1 is a downstream mediator of TUG1. Moreover, TUG1 was significantly overexpressed in CRC patients. In conclusion, TGF-β promotes metastasis of CRC via a TUG1/TWIST1/EMT signaling pathway. TUG1 may be a promising drug target to inhibit TGF-β pathway activation in the treatment of CRC.
The transcription elongation factor TCEA3 induces apoptosis in rhabdomyosarcoma
Authors: Kazim Noor , Adhikari Abhinav , Oh Teak Jung , Davie Judith
Published: January 2020

TCEA3 is one of three genes representing the transcription elongation factor TFIIS family in vertebrates. TCEA3 is upregulated during skeletal muscle differentiation and acts to promote muscle specific gene expression during myogenesis. Rhabdomyosarcoma (RMS) is a pediatric cancer derived from the muscle lineage, but the expression or function of TCEA3 in RMS was uncharacterized. We found that TCEA3 expression was strongly inhibited in RMS cell lines representing both ERMS and ARMS subtypes of RMS. TCEA3 expression correlates with DNA methylation and we show that TBX2 is also involved in the repression of TCEA3 in RMS cell lines. Ectopic expression of TCEA3 inhibited proliferation of RMS cell lines and initiated apoptosis through both the intrinsic and extrinsic pathways. We found that only pan-caspase inhibitors could block apoptosis in the presence of TCEA3. While expression of TCEA3 is highest in skeletal muscle, expression has been detected in other tissues as well, including breast, ovarian and prostate. We found that ectopic expression of TCEA3 also promotes apoptosis in HeLa, MCF7, MDA-231, and PC3 cell lines, representing cervical, breast, and prostate cancer, respectively. Restoration of TCEA3 expression in RMS cell lines enhanced sensitivity to chemotherapeutic drugs, including TRAIL. Thus, TCEA3 presents a novel target for therapeutic strategies to promote apoptosis and enhance sensitivity to current chemotherapeutic drugs.
Lymphatic endothelial cells prime naïve CD8+ T cells into memory cells under steady-state conditions
Authors: Vokali Efthymia , Yu Shann S. , Hirosue Sachiko , Rinçon-Restrepo Marcela , V. Duraes Fernanda , Scherer Stefanie , Corthésy-Henrioud Patricia , Kilarski Witold W. , Mondino Anna , Zehn Dietmar , Hugues Stéphanie , Swartz Melody A.
Published: January 2020

Lymphatic endothelial cells (LECs) chemoattract naïve T cells and promote their survival in the lymph nodes, and can cross-present antigens to naïve CD8+ T cells to drive their proliferation despite lacking key costimulatory molecules. However, the functional consequence of LEC priming of CD8+ T cells is unknown. Here, we show that while many proliferating LEC-educated T cells enter early apoptosis, the remainders comprise a long-lived memory subset, with transcriptional, metabolic, and phenotypic features of central memory and stem cell-like memory T cells. In vivo, these memory cells preferentially home to lymph nodes and display rapid proliferation and effector differentiation following memory recall, and can protect mice against a subsequent bacterial infection. These findings introduce a new immunomodulatory role for LECs in directly generating a memory-like subset of quiescent yet antigen-experienced CD8+ T cells that are long-lived and can rapidly differentiate into effector cells upon inflammatory antigenic challenge.
Microscaled proteogenomic methods for precision oncology
Authors: Satpathy Shankha , Jaehnig Eric J. , Krug Karsten , Kim Beom-Jun , Saltzman Alexander B. , Chan Doug W. , Holloway Kimberly R. , Anurag Meenakshi , Huang Chen , Singh Purba , Gao Ari , Namai Noel , Dou Yongchao , Wen Bo , Vasaikar Suhas V. , Mutch David , Watson Mark A. , Ma Cynthia , Ademuyiwa Foluso O. , Rimawi Mothaffar F. , Schiff Rachel , Hoog Jeremy , Jacobs Samuel , Malovannaya Anna , Hyslop Terry , Clauser Karl R. , Mani D. R. , Perou Charles M. , Miles George , Zhang Bing , Gillette Michael A. , Carr Steven A. , Ellis Matthew J.
Published: January 2020

Cancer proteogenomics promises new insights into cancer biology and treatment efficacy by integrating genomics, transcriptomics and protein profiling including modifications by mass spectrometry (MS). A critical limitation is sample input requirements that exceed many sources of clinically important material. Here we report a proteogenomics approach for core biopsies using tissue-sparing specimen processing and microscaled proteomics. As a demonstration, we analyze core needle biopsies from ERBB2 positive breast cancers before and 48–72 h after initiating neoadjuvant trastuzumab-based chemotherapy. We show greater suppression of ERBB2 protein and both ERBB2 and mTOR target phosphosite levels in cases associated with pathological complete response, and identify potential causes of treatment resistance including the absence of ERBB2 amplification, insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification, and candidate resistance mechanisms including androgen receptor signaling, mucin overexpression and an inactive immune microenvironment. The clinical utility and discovery potential of proteogenomics at biopsy-scale warrants further investigation.
Global projections of future urban land expansion under shared socioeconomic pathways
Authors: Chen Guangzhao , Li Xia , Liu Xiaoping , Chen Yimin , Liang Xun , Leng Jiye , Xu Xiaocong , Liao Weilin , Qiu Yue’an , Wu Qianlian , Huang Kangning
Published: January 2020

Despite its small land coverage, urban land and its expansion have exhibited profound impacts on global environments. Here, we present the scenario projections of global urban land expansion under the framework of the shared socioeconomic pathways (SSPs). Our projections feature a fine spatial resolution of 1 km to preserve spatial details. The projections reveal that although global urban land continues to expand rapidly before the 2040s, China and many other Asian countries are expected to encounter substantial pressure from urban population decline after the 2050s. Approximately 50–63% of the newly expanded urban land is expected to occur on current croplands. Global crop production will decline by approximately 1–4%, corresponding to the annual food needs for a certain crop of 122–1389 million people. These findings stress the importance of governing urban land development as a key measure to mitigate its negative impacts on food production.
Nuthatches vary their alarm calls based upon the source of the eavesdropped signals
Authors: Carlson Nora V , Greene Erick , Templeton Christopher N
Published: January 2020

Animal alarm calls can contain detailed information about a predator’s threat, and heterospecific eavesdropping on these signals creates vast communication networks. While eavesdropping is common, this indirect public information is often less reliable than direct predator observations. Red-breasted nuthatches (Sitta canadensis) eavesdrop on chickadee mobbing calls and vary their behaviour depending on the threat encoded in those calls. Whether nuthatches propagate this indirect information in their own calls remains unknown. Here we test whether nuthatches propagate direct (high and low threat raptor vocalizations) or indirect (high and low threat chickadee mobbing calls) information about predators differently. When receiving direct information, nuthatches vary their mobbing calls to reflect the predator’s threat. However, when nuthatches obtain indirect information, they produce calls with intermediate acoustic features, suggesting a more generic alarm signal. This suggests nuthatches are sensitive to the source and reliability of information and selectively propagate information in their own mobbing calls.
Uncomputability and complexity of quantum control
Authors: Bondar Denys I. , Pechen Alexander N.
Published: January 2020

In laboratory and numerical experiments, physical quantities are known with a finite precision and described by rational numbers. Based on this, we deduce that quantum control problems both for open and closed systems are in general not algorithmically solvable, i.e., there is no algorithm that can decide whether dynamics of an arbitrary quantum system can be manipulated by accessible external interactions (coherent or dissipative) such that a chosen target reaches a desired value. This conclusion holds even for the relaxed requirement of the target only approximately attaining the desired value. These findings do not preclude an algorithmic solvability for a particular class of quantum control problems. Moreover, any quantum control problem can be made algorithmically solvable if the set of accessible interactions (i.e., controls) is rich enough. To arrive at these results, we develop a technique based on establishing the equivalence between quantum control problems and Diophantine equations, which are polynomial equations with integer coefficients and integer unknowns. In addition to proving uncomputability, this technique allows to construct quantum control problems belonging to different complexity classes. In particular, an example of the control problem involving a two-mode coherent field is shown to be NP-hard, contradicting a widely held believe that two-body problems are easy.
Clinical characteristics and visual outcomes of work-related open globe injuries in Japanese patients
Authors: Morikawa Shohei , Okamoto Fumiki , Okamoto Yoshifumi , Mitamura Yoshinori , Ishikawa Hiroto , Harimoto Kozo , Ueda Tetsuo , Sakamoto Taiji , Sugitani Kazuhiko , Sawada Osamu , Mori Junya , Takamura Yoshihiro , Oshika Tetsuro ,   Japan-Clinical Research of Study (J-CREST) group, Inomoto Naoki , Gomi Fumi , Takeuchi Masaru , Ogata Nahoko , Yamashita Toshifumi , Otsuka Hiroki , Sameshima Seiji , Shiihara Hideki , Hirano Yoshio , Yasukawa Tsutomu , Ohji Masahito , Kinoshita Takamasa
Published: January 2020

Purpose: To investigate the clinical characteristics and visual outcomes of patients with work-related open globe injuries (OGIs) and compare them with patients with non-work-related OGIs. Design: Retrospective, observational, multicentre, case-control study. Methods: A total of 374 patients with work-related OGIs and 170 patients with non-work-related OGIs who presented to hospitals that belong to the Japan-Clinical Research of Study group from 2005 to 2015 were included in this study. Clinical data including age, sex, initial and final visual acuity, type of open globe injury, lens status, zone of injury, wound length, and presence of proliferative vitreoretinopathy, retinal detachment, expulsive haemorrhage, and endophthalmitis were recorded. Main Outcome Measures: Visual acuity. Results Work-related OGIs were associated with younger age, male sex, better initial and final visual acuity, more laceration, smaller wounds, presence of retinal detachment, and expulsive haemorrhage, compared with non-work-related OGIs. Multiple regression analysis revealed that final visual acuity is significantly associated with initial visual acuity, wound length, and the presence of proliferative vitreoretinopathy in work-related OGIs. Conclusions: Work-related OGIs showed better visual outcomes than other OGIs. Initial visual acuity, wound length, and the presence of proliferative vitreoretinopathy are predictors of visual outcomes in patients with work-related OGIs.
Optical trapping reveals differences in dielectric and optical properties of copper nanoparticles compared to their oxides and ferrites
Authors: Purohit Pablo , Samadi Akbar , Bendix Poul Martin , Laserna J. Javier , Oddershede Lene B.
Published: January 2020

In a nanoplasmonic context, copper (Cu) is a potential and interesting surrogate to less accessible metals such as gold, silver or platinum. We demonstrate optical trapping of individual Cu nanoparticles with diameters between 25 and 70 nm and of two ionic Cu nanoparticle species, CuFe2O4 and CuZnFe2O4, with diameters of 90 nm using a near infrared laser and quantify their interaction with the electromagnetic field experimentally and theoretically. We find that, despite the similarity in size, the trapping stiffness and polarizability of the ferrites are significantly lower than those of Cu nanoparticles, thus inferring a different light-particle interaction. One challenge with using Cu nanoparticles in practice is that upon exposure to the normal atmosphere, Cu is spontaneously passivated by an oxide layer, thus altering its physicochemical properties. We theoretically investigate how the presence of an oxide layer influences the optical properties of Cu nanoparticles. Comparisons to experimental observations infer that oxidation of CuNPs is minimal during optical trapping. By finite element modelling we map out the expected temperature increase of the plasmonic Cu nanoparticles during optical trapping and retrieve temperature increases high enough to change the catalytic properties of the particles.
Adaptability, resilience and environmental buffering in European Refugia during the Late Pleistocene: Insights from La Riera Cave (Asturias, Cantabria, Spain)
Authors: Jones Jennifer R. , Marín-Arroyo Ana B. , Straus Lawrence G. , Richards Michael P.
Published: January 2020

The Upper Palaeolithic in Europe was a time of extensive climatic changes that impacted on the survival and distribution of human populations. During the Late Glacial Maximum (LGM), southern European peninsulas were refugia for flora, fauna, and human groups. One of these refugia, the Cantabrian region (northern Atlantic Spain), was intensively occupied throughout the Upper Palaeolithic. Characterising how climatic events were expressed in local environments is crucial to understand human and animal survival. La Riera Cave (Asturias) has a rich geo-cultural sequence dating between 20.5kyr BP to 6.5kyr BP and represents an ideal location in which to explore this. Stable isotope analysis of red deer and ibex is used alongside other environmental and climatic proxies to reconstruct Late Upper Palaeolithic conditions. Results show that during the LGM, ibex adapted their niche to survive, and became a major prey species for humans. The diverse environmental opportunities offered in the high-relief and coastal environs of La Riera may help to explain the high human population levels in the Cantabrian Region throughout the Late Upper Palaeolithic. Despite fluctuating conditions, herbivores and humans had the flexibility and resilience to adapt, demonstrating the importance of southern European refugia for the survival of different species.
Zika virus infection leads to mitochondrial failure, oxidative stress and DNA damage in human iPSC-derived astrocytes
Authors: Ledur Pítia Flores , Karmirian Karina , Pedrosa Carolina da Silva Gouveia , Souza Leticia Rocha Quintino , Assis-de-Lemos Gabriela , Martins Thiago Martino , Ferreira Jéssica de Cassia Cavalheiro Gomes , de Azevedo Reis Gabriel Ferreira , Silva Eduardo Santos , Silva Débora , Salerno José Alexandre , Ornelas Isis Moraes , Devalle Sylvie , Madeiro da Costa Rodrigo Furtado , Goto-Silva Livia , Higa Luiza Mendonça , Melo Adriana , Tanuri Amilcar , Chimelli Leila , Murata Marcos Massao , Garcez Patrícia Pestana , Filippi-Chiela Eduardo Cremonese , Galina Antonio , Borges Helena Lobo , Rehen Stevens Kastrup
Published: January 2020

Zika virus (ZIKV) has been extensively studied since it was linked to congenital malformations, and recent research has revealed that astrocytes are targets of ZIKV. However, the consequences of ZIKV infection, especially to this cell type, remain largely unknown, particularly considering integrative studies aiming to understand the crosstalk among key cellular mechanisms and fates involved in the neurotoxicity of the virus. Here, the consequences of ZIKV infection in iPSC-derived astrocytes are presented. Our results show ROS imbalance, mitochondrial defects and DNA breakage, which have been previously linked to neurological disorders. We have also detected glial reactivity, also present in mice and in post-mortem brains from infected neonates from the Northeast of Brazil. Given the role of glia in the developing brain, these findings may help to explain the observed effects in congenital Zika syndrome related to neuronal loss and motor deficit.
Fenugreek Counters the Effects of High Fat Diet on Gut Microbiota in Mice: Links to Metabolic Benefit
Authors: Bruce-Keller Annadora J. , Richard Allison J. , Fernandez-Kim Sun-Ok , Ribnicky David M. , Salbaum J. Michael , Newman Susan , Carmouche Richard , Stephens Jacqueline M.
Published: January 2020

Fenugreek (Trigonella foenum-graecum) is an annual herbaceous plant and a staple of traditional health remedies for metabolic conditions including high cholesterol and diabetes. While the mechanisms of the beneficial actions of fenugreek remain unknown, a role for intestinal microbiota in metabolic homeostasis is likely. To determine if fenugreek utilizes intestinal bacteria to offset the adverse effects of high fat diets, C57BL/6J mice were fed control/low fat (CD) or high fat (HFD) diets each supplemented with or without 2% (w/w) fenugreek for 16 weeks. The effects of fenugreek and HFD on gut microbiota were comprehensively mapped and then statistically assessed in relation to effects on metrics of body weight, hyperlipidemia, and glucose tolerance. 16S metagenomic analyses revealed robust and significant effects of fenugreek on gut microbiota, with alterations in both alpha and beta diversity as well as taxonomic redistribution under both CD and HFD conditions. As previously reported, fenugreek attenuated HFD-induced hyperlipidemia and stabilized glucose tolerance without affecting body weight. Finally, fenugreek specifically reversed the dysbiotic effects of HFD on numerous taxa in a manner tightly correlated with overall metabolic function. Collectively, these data reinforce the essential link between gut microbiota and metabolic syndrome and suggest that the preservation of healthy populations of gut microbiota participates in the beneficial properties of fenugreek in the context of modern Western-style diets.