bluuebunny/crossref_metadata_2025 huggingface dataset:
What is Iran?
Authors: Adib-Moghaddam Arshin
Published: March 2021

What is Iran? What are its domestic politics? Its history? Its international relations? Here, Arshin Adib-Moghaddam sheds fresh light on these questions, offering a general introduction to everything there is to know about this country. Uniquely, he uses musical pieces as a way to offer a holistic understanding of the full spectrum of Iranian affairs. As a result, even the general reader is invited to traverse a wide array of topics in an interactive format which merges approaches from the social sciences with philosophy, poetry and art. These topics include a variety of themes, issues and personalities: from Trump, Khomeini, the Shah, Saddam Hussein and Qasem Soleimani, to Israel, Syria, Latin America, China and the Gulf monarchies. Ultimately, this book demonstrates in clear and accessible prose the impact of Iranian politics on a global scale, and offers solutions to the various crises enveloping the country in the region and beyond.
Removal of SARS-CoV-2 bioaerosols using ultraviolet air filtration
Authors: Barnewall Roy E. , Bischoff Werner E.
Published: March 2021

Engineering controls play an important role in reducing the spread of severe acute respiratory coronavirus virus 2 (SARS-CoV-2).1 Established technologies such as air filtration, and novel approaches such as ultraviolet (UV)-C light or plasma air ionization, have the potential to support the fight against the coronavirus disease 2019 (COVID-19) pandemic.2 We tested the efficacy of an air purification system (APS) combining UV-C light and high-efficiency particulate air (HEPA) filtration in a controlled environment using SARS-CoV-2 as test organism. The APS successfully removed the virus from the air using UV-C light by itself and in combination with HEPA air filtration.
Benthic foraminifera from the Albian shallow-marine limestones in the Geyik Dağı area (Central Taurides), southern Turkey
Authors: Solak Cemile , Taslı Kemal , Koç Hayati
Published: March 2021

Cretaceous carbonates in the Geyik Dağı area (Central Taurides, southern Turkey) are represented by two successions with different paleoenvironmental settings: open shelf to slope succession of Cenomanian to Danian age and inner platform succession of Albian to Maastrichtian age, which is interrupted by a post-Cenomanian disconformity. Outcropped lowermost part of the platform-type one is composed of rudistid limestones corresponding to the Urgonian-type carbonates and belongs to the Geyik Dağı Unit (=Anamas-Akseki Carbonate Platform). It contains a rich assemblage of larger benthic foraminifera including orbitolinid, chrysalidinid, cuneolinid, nezzazatid, and miliolid taxa, which has been illustrated and documented here for the first time from the upper Albian of the Tauride Carbonate Platform. The occurrence of such a diversified foraminiferal fauna indicates a prominent high diversity that took place in the Tauride Carbonate Platform during the late Albian time, which corresponds to a major emersion period in some parts of the platform.
Timing and nature of intracontinental deformation at the northwestern margin of the Sichuan Basin, China: evidence from structural analysis and detrital zircon U–Pb ages
Authors: Liu Songnan , Wang Yu , Ma Huimin , Qian Tao
Published: March 2021

The theory of plate tectonics suggests that deformation occurs mainly along plate boundaries; however, compression can result in the formation of orogens and basins within intracontinental settings. During these two tectonic processes, the sedimentation and environmental changes occur in response to marginal and intracontinental deformation. Early Jurassic – Early Cretaceous deformation and basin formation along the Qinling orogenic belt and the northwestern Sichuan Basin in central–SW China are ideal for investigating a reactivated tectonic belt and basin formation. We studied the Lower Jurassic – Lower Cretaceous sedimentary sequences and structures along the northwestern margin of the Sichuan Basin, and obtained detrital zircon U–Pb ages for these rocks. The structures show that deformation migrated SE-wards and S-wards into the Sichuan Basin along the Longmen Shan, Micang Shan and Daba Shan tectonic belts during middle–late Mesozoic time. The Lower Jurassic oligomictic conglomerates have a smaller grain size and thicken towards the south, indicating protracted transport from a northern source. The conglomerates deposited near-source record post-orogenic south-vergent thrusting during the Late Triassic – Early Jurassic epochs. The Lower Cretaceous conglomerates and sandstones have multiple sources, which indicate that they were rapidly deposited near their source, synchronous with thrusting that occurred in response to coeval SE-wards and S-wards thrusting in the Longmen Shan and Daba Shan tectonic belts during the Late Jurassic – Early Cretaceous epochs. Detrital zircon grains from the Lower Jurassic – Lower Cretaceous sedimentary rocks yielded age peaks of 2600–2200, 1850–1600, 850–700, 540–400, 250–180 and 180–140 Ma. A comparison of these ages with those of surrounding exposed rocks indicates that the sediments in the northwestern Sichuan Basin were supplied from the Qinling orogenic belt, the northwestern Yangtze Block, the south margin of the North China Block and the Songpan–Garzê Terrane. The youngest peaks of detrital zircon U–Pb ages at 207 and 159 Ma constrain the two stages of intracontinental shortening and highlight the link between intracontinental deformation and sedimentation.
Privatizing the Commons: Protest and the Moral Economy of National Resources in Jordan
Authors: Lacouture Matthew
Published: March 2021

This article interrogates the social impact of one aspect of structural adjustment in the Hashemite Kingdom of Jordan: privatization. In the mid-2000s, King Abdullah II privatized Jordan's minerals industry as part of the regime's accelerated neoliberal project. While many of these privatizations elicited responses ranging from general approval to ambivalence, the opaque and seemingly corrupt sale of the Jordan Phosphate Mines Company (JPMC) in 2006 was understood differently, as an illegitimate appropriation of Jordan's national resources and, by extension, an abrogation of the state's (re-) distributive obligations. Based on interviews with activists, I argue that a diverse cross-section of social movement constituencies – spanning labour and non-labour movements (and factions within and across those movements) – perceived such illegitimate privatizations as a moral violation, which, in turn, informed transgressive activist practices and discourses targeting the neoliberal state. This moral violation shaped the rise and interaction of labour and non-labour social movements in Jordan's “Arab uprisings”, peaking in 2011–2013. While Jordan's uprisings were largely demobilized after 2013, protests in 2018 and 2019 demonstrate the continued relevance of this discourse. In this way, the 2011–2013 wave of protests – and their current reverberations – differ qualitatively from Jordan's earlier wave of “food riots” in 1989 (and throughout the 1990s), which I characterize as primarily restorative in nature.
Buy them out before they are built: evaluating the proactive acquisition of vacant land in flood-prone areas
Authors: Atoba Kayode , Newman Galen , Brody Samuel , Highfield Wesley , Kim Youjung , Juan Andrew
Published: March 2021

Rising flood damages have prompted local communities to implement buyout and property acquisition programmes to eliminate repetitive losses for at-risk properties. However, buyouts are often costly to implement and are reactionary solutions to flooding. This study quantifies the benefits of acquiring vacant private properties in flood-prone areas rather than acquiring such properties after they are built up. Using a geodesign framework that integrates concepts and analytical approaches derived from geographical, spatial and statistical-based disciplines, we analyse vacant properties with high development potential that intersect current and future floodplain areas in Houston (TX, USA). We use geospatial proximity analysis to select candidate properties, land-use prediction modelling to estimate future development and sea-level rise and benefit–cost analysis to assess the economic viability of buyouts. The results indicate that cumulative avoided flood losses exceed the cost of vacant land acquisition by a factor of nearly two to one, and up to a factor of ten to one in selected areas. This study emphasizes the benefits of proactive property buyouts that focus on acquiring parcels before they are built up, while also avoiding the social and institutional problems associated with traditional buyout programmes.
Traumatic mitral annular avulsion and interventricular septum dissection
Authors: Ma Huibo , Zhang Haizhou , Ma Xiaochun
Published: March 2021

We presented a rare case of traumatic mitral annular avulsion and interventricular septum dissection after an unintentional falling injury in a 5-year-old female child. A successful surgical repair of mitral annulus and interventricular septum was performed to restore the haemodynamic stability.
Medicare for All, Some, or None? Testing the Effects of Ambiguity in the Context of the 2020 Presidential Election
Authors: Simas Elizabeth N.
Published: March 2021

Political scientists have long contemplated whether candidates are better off taking more ambiguous policy positions. Taking advantage of a lack of clarity in Senator Kamala Harris’s healthcare position, I use an original survey experiment to apply these theories to the case of the 2020 presidential election. I find that ambiguity offers Harris little to no advantage over two of her leading Democratic primary opponents and, among certain subjects, harms her relative to Senator Elizabeth Warren. I also find negative effects on Harris’s favorability relative to President Donald Trump. These results have interesting implications for both the 2020 election and the broader study of candidate rhetoric because they illustrate potential downsides to avoiding clear issue statements.
Learning through Peer Reviewing and Publishing in the Pi Sigma Alpha Undergraduate Journal of Politics: Twenty Years Later
Authors: Walker Christina P. , Towner Terri L. , Clawson Rosalee A. , Oxley Zoe M. , Nemacheck Christine L. , Rapoport Ronald
Published: March 2021

The Pi Sigma Alpha Undergraduate Journal of Politics (PSAJ), sponsored by the Pi Sigma Alpha National Honor Society, was founded in 2001 at Purdue University. After 20 years, much has changed in undergraduate research and publishing, but the benefits of producing a peer-reviewed journal remain the same. Undergraduate research has increased in prominence, and the journal has modernized to meet these transformations. This article describes the history, purpose, and operations of the PSAJ. Most important, a survey of former Editorial Board members, Pi Sigma Alpha Faculty Chapter Advisors, and published authors in the journal reveal attitudes toward operating an undergraduate journal, using undergraduate research in the college classroom, and publishing in a peer-reviewed journal, respectively. We conclude with calls to continue to encourage undergraduate research and to assign published undergraduate research in upper-level courses.
Cognitive analysis of specific threat beliefs and safety-seeking behaviours in generalised anxiety disorder: revisiting the cognitive theory of anxiety disorders
Authors: Gústavsson Sævar M. , Salkovskis Paul M. , Sigurðsson Jón F.
Published: March 2021

Background:

Generalised anxiety disorder (GAD) has been an uneasy member of the anxiety disorders group since its inclusion in the third edition of the DSM. Multiple theories and treatment protocols for GAD and its defining symptom, excessive worry, have comparable efficacy in treating GAD symptoms. Crucially, these theories of GAD and excessive worry fail to explain when and why worry is excessive and when it is adaptive.

Aims:

In this paper we propose a cognitive behavioural account of the difference between excessive and adaptive states of worry and explore the theme of threat and the function of safety-seeking behaviours as seen in GAD. Specifically, we incorporate the concept of inflated responsibility in a cognitive behavioural analysis of threat appraisal and safety-seeking behaviours in excessive worry and GAD.

Conclusion:

It is proposed that when worry is used as a strategy intended to increase safety from perceived social or physical threat then it should be conceptualised as a safety-seeking behaviour. However, when worry is used as a strategy to solve a problem which the person realistically can resolve or to deal explicitly with the feeling of anxiety then it functions as an adaptive coping behaviour. We also propose that the theme of threat in GAD centres on an inflated sense of responsibility for external everyday situations, and the function of safety-seeking behaviours is to attain certainty that responsibility has been fulfilled. The clinical implications of this cognitive behavioural analysis of excessive worry are discussed, as well as future research directions.
Perceptions of a food benefit programme that includes financial incentives for the purchase of fruits and vegetables and restrictions on the purchase of foods high in added sugar
Authors: Fagbenro Fatima A , Lasswell Tessa , Rydell Sarah A , Oakes J Michael , Elbel Brian , Harnack Lisa J
Published: March 2021

Objective:

To report perspectives of participants in a food benefit programme that includes foods high in added sugar (FAS) restrictions and FAS restrictions paired with fruits and vegetables (F/V) incentives.

Design:

Randomised experimental trial in which participant perspectives were an exploratory study outcome.

Setting:

Participants were randomised into one of three Supplemental Nutrition Assistance Program (SNAP)-like food benefit programme groups: (1) restriction: not allowed to buy FAS with benefits; (2) restriction paired with incentive: not allowed to buy FAS with benefits and 30 % financial incentive on eligible F/V purchased using benefits; or (3) control: same food purchasing rules as SNAP. Participants were asked questions to assess programme satisfaction.

Participants:

Adults in the Minneapolis-St. Paul, MN metropolitan area, eligible for but not currently participating in SNAP who completed baseline and follow-up study measures (n 254).

Results:

Among remaining households in each group, most found the programme helpful in buying nutritious foods (88·2 %–95·7 %) and were satisfied with the programme (89·1 %–93·0 %). Sensitivity analysis results indicate that reported helpfulness and satisfaction with the programme may in some instances be lower among the restriction and the restrictions paired with incentive groups in comparison to the control group.

Conclusions:

A food benefit programme that includes restriction on purchase of FAS or restriction paired with a financial incentive for F/V purchases may be acceptable to most SNAP-eligible households with children.
Institutional incentives and community policing
Authors: Fegley Tate
Published: March 2021

Most American police departments claim to practice community-oriented policing (COP). The stated goals are to build partnerships between the police and the community, maintain order and quality of life, and solve problems that contribute to crime and fear of crime. However, researchers have noted how most departments attempting to implement COP have fallen short in successfully adopting the recommended reforms. This paper argues that the institutional setting in which American public policing operates leads to this result. By contrast, the institutional features of private security make its operation more conducive to achieving the goals of COP. These institutional differences include whether economic calculation is possible, the domain that is policed, and which rules are enforced.
Graphene-based wide band semi-flexible array antenna with parasitic patch for smart wireless devices
Authors: Vashi Ronak , Upadhyaya Trushit , Desai Arpan
Published: March 2021

In this paper, a semi-flexible 2 × 1 array antenna is proposed with epoxy glass fiber and graphene as patch and ground, respectively. Microstrip patch antenna with a center parasitic patch of half-wavelength and slot in the radiating patch have been incorporated for the bandwidth enhancement in order of 79.56% (2.21–5.13 GHz). The antenna has an overall size of 0.30λ × 0.24λ at a lower frequency of operation (2.45 GHz). The incorporation of slotted Graphene in radiating element leads to a wideband regime with satisfactory gain values of 2.73 and 3.744 dBi at 2.40 and 4.0 GHz, respectively. Antenna radiation efficiency in the range of 78% with linear polarization makes the antenna appropriate for WLAN band and smart wireless devices application.
Depression and increased risk of non-alcoholic fatty liver disease in individuals with obesity
Authors: Cho In Young , Chang Yoosoo , Sung Eunju , Kang Jae-Heon , Wild Sarah H. , Byrne Christopher D. , Shin Hocheol , Ryu Seungho
Published: March 2021

Abstract

Aims

The longitudinal relationship between depression and the risk of non-alcoholic fatty liver disease is uncertain. We examined: (a) the association between depressive symptoms and incident hepatic steatosis (HS), both with and without liver fibrosis; and (b) the influence of obesity on this association.

Methods

A cohort of 142 005 Korean adults with neither HS nor excessive alcohol consumption at baseline were followed for up to 8.9 years. The validated Center for Epidemiologic Studies-Depression score (CES-D) was assessed at baseline, and subjects were categorised as non-depressed (a CES-D < 8, reference) or depression (CES-D ⩾ 16). HS was diagnosed by ultrasonography. Liver fibrosis was assessed by the fibrosis-4 index (FIB-4). Parametric proportional hazards models were used to estimate the adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs).

Results

During a median follow-up of 4.0 years, 27 810 people with incident HS and 134 with incident HS plus high FIB-4 were identified. Compared with the non-depressed category, the aHR (95% CIs) for incident HS was 1.24 (1.15–1.34) for CES-D ⩾ 16 among obese individuals, and 1.00 (0.95–1.05) for CES-D ⩾ 16 among non-obese individuals (p for interaction with obesity <0.001). The aHR (95% CIs) for developing HS plus high FIB-4 was 3.41 (1.33–8.74) for CES-D ⩾ 16 among obese individuals, and 1.22 (0.60–2.47) for CES-D ⩾ 16 among non-obese individuals (p for interaction = 0.201).

Conclusions

Depression was associated with an increased risk of incident HS and HS plus high probability of advanced fibrosis, especially among obese individuals.
UAVSAR Observations of InSAR Polarimetric Phase Diversity: Implications for NISAR Ionospheric Phase Estimation
Authors: Brancato V. , Fattahi H.
Published: March 2021

The NASA‐ISRO Synthetic Aperture Radar (NISAR) is a repeat‐pass radar mission that will acquire fully polarimetric SAR data in an innovative acquisition mode known as quasi‐quad pol (QQP). It consists of simultaneously operating a HH/HV and a VH/VV dual‐pol modes in the lowest and upper parts of the transmitted frequency spectrum. Compared to more traditional acquisition modes, the ionospheric phase estimation algorithms for QQP repeat‐pass data will likely exploit the difference of two sub‐band SAR interferograms acquired not only at distinct center frequencies but also at different polarizations (e.g., HH/VV), making the ionospheric phase estimation vulnerable to possible bias caused by polarimetric interferometric scattering phase components. Using UAVSAR airborne data, we show that temporal variations of the interferometric scattering phase may introduce spurious polarimetric‐dependent phase terms which may bias QQP ionospheric phase estimates. The magnitude of this bias depends on the type of observed land cover. For bare soil and forested areas, we detect HH‐VV interferometric phase discrepancies up to 30° over 12 days, corresponding to a 10 cm bias at L‐band. Over comparable time intervals, changes in vegetation vitality introduce HH‐VV interferometric phase inconsistencies beyond 90° for vertically oriented agricultural fields. We simulate the QQP ionospheric phase screen over the San Andreas Fault, USA, a region characterized by a mixture of vegetated and bare soil surfaces. Based on the results from the UAVSAR data analysis, we recommend using the same polarization on the main and side‐bands of the NISAR operational science modes (e.g., single‐pol or dual‐pol) to avoid potential biases in the ionospheric phase estimates.
Eruptive Cycle and Bubble Trap of Strokkur Geyser, Iceland
Authors: Eibl Eva P. S. , Müller Daniel , Walter Thomas R. , Allahbakhshi Masoud , Jousset Philippe , Hersir Gylfi Páll , Dahm Torsten
Published: March 2021

The eruption frequency of geysers can be studied easily on the surface. However, details of the internal structure including possible water and gas filled chambers feeding eruptions and the driving mechanisms often remain elusive. We used a multidisciplinary network of seismometers, video cameras, water pressure sensors and one tiltmeter to study the eruptive cycle, internal structure, and mechanisms driving the eruptive cycle of Strokkur geyser in June 2018. An eruptive cycle at Strokkur always consists of four phases: (1) Eruption, (2) post‐eruptive conduit refilling, (3) gas filling of the bubble trap, and (4) regular bubble collapse at shallow depth in the conduit. For a typical single eruption 19 ± 4 bubble collapses occur in Phase 3 and 8 ± 2 collapses in Phase 4 at a mean spacing of 1.52 ± 0.29 and 24.5 ± 5.9 s, respectively. These collapses release latent heat to the fluid in the bubble trap (Phase 3) and later to the fluid in the conduit (Phase 4). The latter eventually reaches thermodynamic conditions for an eruption. Single to sextuple eruptions have similar spacings between bubble collapses and are likely fed from the same bubble trap at 23.7 ± 4.4 m depth, 13–23 m west of the conduit. However, the duration of the eruption and recharging phase linearly increases likely due to a larger water, gas and heat loss from the system. Our tremor data provides documented evidence for a bubble trap beneath a pool geyser.
A 3D Full Stress Tensor Model for Oklahoma
Authors: Chai Chengping , Delorey Andrew A. , Maceira Monica , Levandowski Will , Guyer Robert A. , Zhang Haijiang , Coblentz David , Johnson Paul A.
Published: March 2021

The stress tensor is an important property for upper crustal studies such as those that involve pore fluids and earthquake hazards. At tectonic plate scale, plate boundary forces and mantle convection are the primary drivers of the stress field. In many local settings (10–100 s of km and <10 km depth) in tectonic plate interiors, we can simplify by assuming a constant background stress field that is perturbed by local heterogeneity in density and elasticity. Local stress orientation and sometimes magnitude can be estimated from earthquake and borehole‐based observations when available. Modeling of the local stress field often involves interpolating sparse observations. We present a new method to estimate the 3D stress field in the upper crust and demonstrate it for Oklahoma. We created a 3D material model by inverting multiple types of geophysical observations simultaneously. Integrating surface‐wave dispersion, local travel times and gravity observations produces a model of P‐wave velocity, S‐wave velocity, and density. The stress field can then be modeled using finite element simulations. The simulations are performed using our simplified view of the local stress field as the sum of a constant background stress field that is perturbed by local density and elasticity heterogeneity and gravitational body forces. An orientation of N82°E, for the maximum compressive tectonic force, best agrees with previously observed stress orientations and faulting types in Oklahoma. The gravitational contribution of the horizontal stress field has a magnitude comparable to the tectonic contribution for the upper 5 km of the subsurface.
Experimental Insights on the Propagation of Fine‐Grained Geophysical Flows Entering Water
Authors: Bougouin Alexis , Roche Olivier , Paris Raphaël , Huppert Herbert E.
Published: March 2021

Granular flows that propagate down a mountainside, then reach the sea, a lake or a river and finally, travel underwater, is a common event on the Earth's surface. To help the description of such events, laboratory experiments on gas‐fluidized granular flows entering water are performed, analyzed, and compared to those propagating in air. The originality of this study lies in the fluidization process, which improves the laboratory modeling of geophysical flows by taking their high mobility into account. Qualitatively, the presence of the water body promotes the generation of a granular jet over the water surface, a leading and largest wave, and a particle‐driven gravity current underwater. Hydrodynamic forces mainly play a dissipative role by slowing and reducing the spreading of the granular mass underwater, but a low amount of grains are still transported by the turbulent fluid as a gravity current far away. The temporal evolution of the granular jet and the particle‐driven gravity current are well described by ballistic motion theory and scaling laws of homogeneous gravity currents, respectively. Most currents propagate with a constant flow‐front velocity along the horizontal bottom, which is controlled by the flow height depending on the water depth. In contrast, the bulk volume concentration of particles in the current is estimated to be nearly constant, interpreted as a critical concentration above which the excess of particles cannot be maintained by the turbulent fluid. This experimental study highlights the complexity of the dynamics and deposits of granular masses when they encounter a water body.
Unexpected High Absorption of Atmospheric Aerosols Over a Western Tibetan Plateau Site in Summer
Authors: Zhang Lei , Tang Chenguang , Huang Jianping , Du Tao , Guan Xu , Tian Pengfei , Shi Jinsen , Cao Xianjie , Huang Zhongwei , Guo Qi , Zhang Haotian , Wang Min , Zeng Huiyu , Wang Feiyang , Dolkar Pema
Published: March 2021

The assessment of atmospheric aerosol radiative effects in the Tibetan Plateau (TP) suffers from large uncertainties due to limited understanding of aerosol physicochemical properties. To quantify aerosol optical properties, size distributions, and chemical compositions in the western TP, an intensive field campaign was carried out at Shiquanhe National Reference Climatological Station from July 8 to August 2, 2019. Unexpected low single scattering albedo (SSA) at 870 nm was found for the fine aerosols with an average value of 0.73 ± 0.18. SSA was even lower than 0.60 in the morning when fine aerosols peaked, indicating high absorption of the fine aerosols induced by anthropogenic activities. Coarse mode aerosols accounted for 70.58% ± 14.98% of the total volume concentration and mineral dust was the most abundant species in total suspended particles with a mass fraction of 48.7%. Fine mode aerosol concentrations showed little dependence on wind speed while coarse mode aerosols and metallic element concentrations exhibited strong positive correlations with wind speed, indicating the importance of wind‐blown dust particles. The present study for the first time quantified key aerosol parameters in the western TP and unexpected high absorption of atmospheric aerosols were found over the site in summer. Our results suggest the need to carefully consider the radiative effects caused by aerosol absorption in the TP region.
Machine learning powered ellipsometry
Authors: Liu Jinchao , Zhang Di , Yu Dianqiang , Ren Mengxin , Xu Jingjun
Published: March 2021

Ellipsometry is a powerful method for determining both the optical constants and thickness of thin films. For decades, solutions to ill-posed inverse ellipsometric problems require substantial human–expert intervention and have become essentially human-in-the-loop trial-and-error processes that are not only tedious and time-consuming but also limit the applicability of ellipsometry. Here, we demonstrate a machine learning based approach for solving ellipsometric problems in an unambiguous and fully automatic manner while showing superior performance. The proposed approach is experimentally validated by using a broad range of films covering categories of metals, semiconductors, and dielectrics. This method is compatible with existing ellipsometers and paves the way for realizing the automatic, rapid, high-throughput optical characterization of films.
Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
Authors: Beckmann Sabrina , Farag Ibrahim F , Zhao Rui , Christman Glenn D , Prouty Nancy G , Biddle Jennifer F
Published: March 2021

Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by seven different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcrA gene sequencing coupled with metagenomic analyses. Based on 16S rRNA gene amplicon analyses, these sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and -2 archaeal clades were abundant in the carbonates yet their typical syntrophic partners, sulfate-reducing bacteria, were not significantly present. Based on mcrA amplicon analyses, the Candidatus Methanoperedens clades were also highly abundant. Our metagenome analysis indicated that methane oxidizers affiliated to the ANME-1 and -2, may be capable of performing complete methane- and potentially short-chain alkane oxidation independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds and may be involved in syntrophy with methane-oxidizing archaea. Carbonate structures represent a window for a more diverse utilization of electron acceptors for anaerobic methane oxidation along the Atlantic and Pacific Margin.
Evidences for lipid involvement in SARS-CoV-2 cytopathogenesis
Authors: Nardacci Roberta , Colavita Francesca , Castilletti Concetta , Lapa Daniele , Matusali Giulia , Meschi Silvia , Del Nonno Franca , Colombo Daniele , Capobianchi Maria Rosaria , Zumla Alimuddin , Ippolito Giuseppe , Piacentini Mauro , Falasca Laura
Published: March 2021

The pathogenesis of SARS-CoV-2 remains to be completely understood, and detailed SARS-CoV-2 cellular cytopathic effects requires definition. We performed a comparative ultrastructural study of SARS-CoV-1 and SARS-CoV-2 infection in Vero E6 cells and in lungs from deceased COVID-19 patients. SARS-CoV-2 induces rapid death associated with profound ultrastructural changes in Vero cells. Type II pneumocytes in lung tissue showed prominent altered features with numerous vacuoles and swollen mitochondria with presence of abundant lipid droplets. The accumulation of lipids was the most striking finding we observed in SARS-CoV-2 infected cells, both in vitro and in the lungs of patients, suggesting that lipids can be involved in SARS-CoV-2 pathogenesis. Considering that in most cases, COVID-19 patients show alteration of blood cholesterol and lipoprotein homeostasis, our findings highlight a peculiar important topic that can suggest new approaches for pharmacological treatment to contrast the pathogenicity of SARS-CoV-2.
Autophagy, an accomplice or antagonist of drug resistance in HCC?
Authors: Wu Yafei , Zhang Jigang , Li Qin
Published: March 2021

Hepatocellular carcinoma (HCC) is a highly lethal malignancy characterized by poor prognosis and a low 5-year survival rate. Drug treatment is proving to be effective in anti-HCC. However, only a small number of HCC patients exhibit sensitive responses, and drug resistance occurs frequently in advanced patients. Autophagy, an evolutionary process responsible for the degradation of cellular substances, is closely associated with the acquisition and maintenance of drug resistance for HCC. This review focuses on autophagic proteins and explores the intricate relationship between autophagy and cancer stem cells, tumor-derived exosomes, and noncoding RNA. Clinical trials involved in autophagy inhibition combined with anticancer drugs are also concerned.
Cullin-5 neddylation-mediated NOXA degradation is enhanced by PRDX1 oligomers in colorectal cancer
Authors: Xu Shoufang , Ma Yilei , Tong Qingchao , Yang Jun , Liu Jia , Wang Yanzhong , Li Guoli , Zeng Jin , Fang Sining , Li Fengying , Xie Xinyou , Zhang Jun
Published: March 2021

NOXA, a BH3-only proapoptotic protein involved in regulating cell death decisions, is highly expressed but short-lived in colorectal cancer (CRC). Neddylated cullin-5 (CUL5)-mediated ubiquitination and degradation of NOXA is crucial to prevent its overaccumulation and maintain an appropriate action time. However, how this process is manipulated by CRC cells commonly exposed to oxidative stress remain unknown. The peroxiredoxin PRDX1, a conceivable antioxidant overexpressed in CRC tissues, has been shown to inhibit apoptosis and TRAF6 ubiquitin-ligase activity. In this study, we found that PRDX1 inhibits CRC cell apoptosis by downregulating NOXA. Mechanistically, PRDX1 promotes NOXA ubiquitination and degradation, which completely depend on CUL5 neddylation. Further studies have demonstrated that PRDX1 oligomers bind with both the Nedd8-conjugating enzyme UBE2F and CUL5 and that this tricomplex is critical for CUL5 neddylation, since silencing PRDX1 or inhibiting PRDX1 oligomerization greatly dampens CUL5 neddylation and NOXA degradation. An increase in reactive oxygen species (ROS) is not only a hallmark of cancer cells but also the leading driving force for PRDX1 oligomerization. As shown in our study, although ROS play a role in upregulating NOXA mRNA transcription, ROS scavenging in CRC cells by N-acetyl-L-cysteine (NAC) can significantly reduce CUL5 neddylation and extend the NOXA protein half-life. Therefore, in CRC, PRDX1 plays a key role in maintaining intracellular homeostasis under conditions of high metabolic activity by reinforcing UBE2F-CUL5-mediated degradation of NOXA, which is also evidenced in the resistance of CRC cells to etoposide treatment. Based on these findings, targeting PRDX1 could be an effective strategy to overcome the resistance of CRC to DNA damage-inducing chemotherapeutics.
Ultrafast non-excitonic valley Hall effect in MoS2/WTe2 heterobilayers
Authors: Lee Jekwan , Heo Wonhyeok , Cha Myungjun , Watanabe Kenji , Taniguchi Takashi , Kim Jehyun , Cha Soonyoung , Kim Dohun , Jo Moon-Ho , Choi Hyunyong
Published: March 2021

The valley Hall effect (VHE) in two-dimensional (2D) van der Waals (vdW) crystals is a promising approach to study the valley pseudospin. Most experiments so far have used bound electron-hole pairs (excitons) through local photoexcitation. However, the valley depolarization of such excitons is fast, so that several challenges remain to be resolved. We address this issue by exploiting a unipolar VHE using a heterobilayer made of monolayer MoS2/WTe2 to exhibit a long valley-polarized lifetime due to the absence of electron-hole exchange interaction. The unipolar VHE is manifested by reduced photoluminescence at the MoS2 A exciton energy. Furthermore, we provide quantitative information on the time-dependent valley Hall dynamics by performing the spatially-resolved ultrafast Kerr-rotation microscopy; we find that the valley-polarized electrons persist for more than 4 nanoseconds and the valley Hall mobility exceeds 4.49 × 103 cm2/Vs, which is orders of magnitude larger than previous reports.
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
Authors: Butler Daniel , Mozsary Christopher , Meydan Cem , Foox Jonathan , Rosiene Joel , Shaiber Alon , Danko David , Afshinnekoo Ebrahim , MacKay Matthew , Sedlazeck Fritz J. , Ivanov Nikolay A. , Sierra Maria , Pohle Diana , Zietz Michael , Gisladottir Undina , Ramlall Vijendra , Sholle Evan T. , Schenck Edward J. , Westover Craig D. , Hassan Ciaran , Ryon Krista , Young Benjamin , Bhattacharya Chandrima , Ng Dianna L. , Granados Andrea C. , Santos Yale A. , Servellita Venice , Federman Scot , Ruggiero Phyllis , Fungtammasan Arkarachai , Chin Chen-Shan , Pearson Nathaniel M. , Langhorst Bradley W. , Tanner Nathan A. , Kim Youngmi , Reeves Jason W. , Hether Tyler D. , Warren Sarah E. , Bailey Michael , Gawrys Justyna , Meleshko Dmitry , Xu Dong , Couto-Rodriguez Mara , Nagy-Szakal Dorottya , Barrows Joseph , Wells Heather , O’Hara Niamh B. , Rosenfeld Jeffrey A. , Chen Ying , Steel Peter A. D. , Shemesh Amos J. , Xiang Jenny , Thierry-Mieg Jean , Thierry-Mieg Danielle , Iftner Angelika , Bezdan Daniela , Sanchez Elizabeth , Campion Thomas R. , Sipley John , Cong Lin , Craney Arryn , Velu Priya , Melnick Ari M. , Shapira Sagi , Hajirasouliha Iman , Borczuk Alain , Iftner Thomas , Salvatore Mirella , Loda Massimo , Westblade Lars F. , Cushing Melissa , Wu Shixiu , Levy Shawn , Chiu Charles , Schwartz Robert E. , Tatonetti Nicholas , Rennert Hanna , Imielinski Marcin , Mason Christopher E.
Published: March 2021

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin–angiotensin–aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinctACE2expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
Structural and functional characterization of a putative de novo gene in Drosophila
Authors: Lange Andreas , Patel Prajal H. , Heames Brennen , Damry Adam M. , Saenger Thorsten , Jackson Colin J. , Findlay Geoffrey D. , Bornberg-Bauer Erich
Published: March 2021

Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.
Predicting gastric cancer outcome from resected lymph node histopathology images using deep learning
Authors: Wang Xiaodong , Chen Ying , Gao Yunshu , Zhang Huiqing , Guan Zehui , Dong Zhou , Zheng Yuxuan , Jiang Jiarui , Yang Haoqing , Wang Liming , Huang Xianming , Ai Lirong , Yu Wenlong , Li Hongwei , Dong Changsheng , Zhou Zhou , Liu Xiyang , Yu Guanzhen
Published: March 2021

N-staging is a determining factor for prognostic assessment and decision-making for stage-based cancer therapeutic strategies. Visual inspection of whole-slides of intact lymph nodes is currently the main method used by pathologists to calculate the number of metastatic lymph nodes (MLNs). Moreover, even at the same N stage, the outcome of patients varies dramatically. Here, we propose a deep-learning framework for analyzing lymph node whole-slide images (WSIs) to identify lymph nodes and tumor regions, and then to uncover tumor-area-to-MLN-area ratio (T/MLN). After training, our model’s tumor detection performance was comparable to that of experienced pathologists and achieved similar performance on two independent gastric cancer validation cohorts. Further, we demonstrate that T/MLN is an interpretable independent prognostic factor. These findings indicate that deep-learning models could assist not only pathologists in detecting lymph nodes with metastases but also oncologists in exploring new prognostic factors, especially those that are difficult to calculate manually.
Impacts of long-term temperature change and variability on electricity investments
Authors: Khan Zarrar , Iyer Gokul , Patel Pralit , Kim Son , Hejazi Mohamad , Burleyson Casey , Wise Marshall
Published: March 2021

Long-term temperature change and variability are expected to have significant impacts on future electric capacity and investments. This study improves upon past studies by accounting for hourly and monthly dynamics of electricity use, long-term socioeconomic drivers, and interactions of the electric sector with rest of the economy for a comprehensive analysis of temperature change impacts on cooling and heating services and their corresponding impact on electric capacity and investments. Using the United States as an example, here we show that under a scenario consistent with a socioeconomic pathway 2 (SSP2) and representative concentration pathway 8.5 (RCP 8.5), mean temperature changes drive increases in annual electricity demands by 0.5-8% across states in 2100. But more importantly, peak temperature changes drive increases in capital investments by 3-22%. Moreover, temperature-induced capital investments are highly sensitive to both long-term socioeconomic assumptions and spatial heterogeneity of fuel prices and capital stock characteristics, which underscores the importance of a comprehensive approach to inform long-term electric sector planning.
Digital logic gates in soft, conductive mechanical metamaterials
Authors: El Helou Charles , Buskohl Philip R. , Tabor Christopher E. , Harne Ryan L.
Published: March 2021

Integrated circuits utilize networked logic gates to compute Boolean logic operations that are the foundation of modern computation and electronics. With the emergence of flexible electronic materials and devices, an opportunity exists to formulate digital logic from compliant, conductive materials. Here, we introduce a general method of leveraging cellular, mechanical metamaterials composed of conductive polymers to realize all digital logic gates and gate assemblies. We establish a method for applying conductive polymer networks to metamaterial constituents and correlate mechanical buckling modes with network connectivity. With this foundation, each of the conventional logic gates is realized in an equivalent mechanical metamaterial, leading to soft, conductive matter that thinks about applied mechanical stress. These findings may advance the growing fields of soft robotics and smart mechanical matter, and may be leveraged across length scales and physics.
In-situ observation of trapped carriers in organic metal halide perovskite films with ultra-fast temporal and ultra-high energetic resolutions
Authors: Kobbekaduwa Kanishka , Shrestha Shreetu , Adhikari Pan , Liu Exian , Coleman Lawrence , Zhang Jianbing , Shi Ying , Zhou Yuanyuan , Bekenstein Yehonadav , Yan Feng , Rao Apparao M. , Tsai Hsinhan , Beard Matthew C. , Nie Wanyi , Gao Jianbo
Published: March 2021

We in-situ observe the ultrafast dynamics of trapped carriers in organic methyl ammonium lead halide perovskite thin films by ultrafast photocurrent spectroscopy with a sub-25 picosecond time resolution. Upon ultrafast laser excitation, trapped carriers follow a phonon assisted tunneling mechanism and a hopping transport mechanism along ultra-shallow to shallow trap states ranging from 1.72–11.51 millielectronvolts and is demonstrated by time-dependent and independent activation energies. Using temperature as an energetic ruler, we map trap states with ultra-high energy resolution down to < 0.01 millielectronvolt. In addition to carrier mobility of ~4 cm2V−1s−1 and lifetime of ~1 nanosecond, we validate the above transport mechanisms by highlighting trap state dynamics, including trapping rates, de-trapping rates and trap properties, such as trap density, trap levels, and capture-cross sections. In this work we establish a foundation for trap dynamics in high defect-tolerant perovskites with ultra-fast temporal and ultra-high energetic resolution.
PGC1/PPAR drive cardiomyocyte maturation at single cell level via YAP1 and SF3B2
Authors: Murphy Sean A. , Miyamoto Matthew , Kervadec Anaïs , Kannan Suraj , Tampakakis Emmanouil , Kambhampati Sandeep , Lin Brian Leei , Paek Sam , Andersen Peter , Lee Dong-Ik , Zhu Renjun , An Steven S. , Kass David A. , Uosaki Hideki , Colas Alexandre R. , Kwon Chulan
Published: March 2021

Cardiomyocytes undergo significant structural and functional changes after birth, and these fundamental processes are essential for the heart to pump blood to the growing body. However, due to the challenges of isolating single postnatal/adult myocytes, how individual newborn cardiomyocytes acquire multiple aspects of the mature phenotype remains poorly understood. Here we implement large-particle sorting and analyze single myocytes from neonatal to adult hearts. Early myocytes exhibit wide-ranging transcriptomic and size heterogeneity that is maintained until adulthood with a continuous transcriptomic shift. Gene regulatory network analysis followed by mosaic gene deletion reveals that peroxisome proliferator-activated receptor coactivator-1 signaling, which is active in vivo but inactive in pluripotent stem cell-derived cardiomyocytes, mediates the shift. This signaling simultaneously regulates key aspects of cardiomyocyte maturation through previously unrecognized proteins, including YAP1 and SF3B2. Our study provides a single-cell roadmap of heterogeneous transitions coupled to cellular features and identifies a multifaceted regulator controlling cardiomyocyte maturation.