bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis and Characterization of Ordered Mesoporous MCM-41 From Natural Chlorite and its Application in Methylene Blue Adsorption
Authors: Wang Zhizeng , Zhao Qinyi , Wang Dongyun , Cui Chong
Published: June 2021

Mesoporous materials have a wide range of applications in the fields of nanotechnology, biotechnology, information technology, and medicine, but historically, the resource materials used for their synthesis have been expensive. Natural silicate minerals are characterized by their abundance, low cost, and large SiO2 contents, making them an alternative silicon source for mesoporous silica. The objective of the present study was to determine the utility of natural chlorite as the source of Si for synthesizing hexagonal mesoporous silica materials (MCM-41). The natural chlorite was pretreated by acid leaching and calcination, followed by a hydrothermal reaction with cetyltrimethylammonium bromide (CTAB) as the template, and subsequent calcination to prepare MCM-41. The structures and the porosity of MCM-41 were characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), 29Si magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (29Si MAS NMR), and N2 adsorption–desorption measurements. The mechanism of structural evolution from natural chlorite to MCM-41 was investigated using these techniques. Calcination of chlorite results in amorphization and partial structural breakdown, while subsequent acid leaching dissolves the Mg and Al in the octahedral sheets to leave the Si–O framework as a silicon source. 29Si MAS NMR results revealed that the ratio of Q4/Q3 increased from 0.91 to 1.21 after hydrothermal synthesis of MCM-41 from leached chlorite, demonstrating more polymerization of the Si–O structure in MCM-41. The final MCM-41 products were amorphous SiO2, with a large surface area of 630 m2/g, a pore volume of 0.46 mL/g, and a narrow pore-size distribution of 2.8 nm. MCM-41 showed favorable adsorption toward methylene blue (MB) with a monolayer adsorption capacity of up to 302 mg/g, indicating potential for application in adsorption.
PRENEX NORMAL FORM THEOREMS IN SEMI-CLASSICAL ARITHMETIC
Authors: FUJIWARA MAKOTO , KURAHASHI TAISHI
Published: June 2021

Akama et al. [1] systematically studied an arithmetical hierarchy of the law of excluded middle and related principles in the context of first-order arithmetic. In that paper, they first provide a prenex normal form theorem as a justification of their semi-classical principles restricted to prenex formulas. However, there are some errors in their proof. In this paper, we provide a simple counterexample of their prenex normal form theorem [1, Theorem 2.7], then modify it in an appropriate way which still serves to largely justify the arithmetical hierarchy. In addition, we characterize a variety of prenex normal form theorems by logical principles in the arithmetical hierarchy. The characterization results reveal that our prenex normal form theorems are optimal. For the characterization results, we establish a new conservation theorem on semi-classical arithmetic. The theorem generalizes a well-known fact that classical arithmetic is
$\Pi _2$
-conservative over intuitionistic arithmetic.
A “Common Spectacle” of the Race: Garveyism’s Visual Politics of Founding
Authors: GETACHEW ADOM
Published: June 2021

The questions of what makes a people a people and how they are endowed with political power are central to political founding. Through the Universal Negro Improvement Association’s first annual convention, this essay reconstructs the central role of aesthetic practices to the constitution of a new people. The convention’s spectacular performances were a vehicle through which participants came to understand themselves as constituting the Universal Negro—a transnational and empowered political subject. Founding was tied to the development of “reverential self-regard,” which was a process rather than a singular moment. Central to this process was both the gaze of spectators whose affective responses confirmed the power of the people and the political leader who served as the people’s mirror. Focusing on a mass movement rather than canonical instances of constituting republics brings into sharp relief the reiterative labors of staging, enacting, and viewing necessary to the practice of founding.
Sowing the Seeds of a Future Crisis: The SEC and the Emergence of the Nationally Recognized Statistical Rating Organization (NRSRO) Category, 1971–1975
Authors: Smith Andrew , Wright Robert E.
Published: June 2021

Since 2008, academics and policymakers have frequently debated why bond rating agencies such as Moody's, S&P, and Fitch enjoy considerable power and influence. The 2008 financial crisis focused our attention on the bond rating agencies that had previously categorized mortgage-backed securities as investment grade. Scholars have attributed the power enjoyed by the rating agencies to regulations that confer a privileged status on those agencies that are designated as nationally recognized statistical rating organizations (NRSROs) by the U.S. Securities and Exchange Commission (SEC). While these authors mention in passing that the relevant regulation went into effect in 1975, none has conducted archival research to examine why this regulation was introduced at that time. This article is the first historical investigation of the creation of this crucial regulation, which entrenched the concept of the NRSRO in federal securities law. It shows that the SEC mandated the use of NRSRO-created ratings even though SEC officials vigorously debated whether it was wise for the commission to endorse ratings produced by agencies that operate on the basis of the controversial issuer-pay model. This article contributes to our understanding of the SEC's role in the development of the distinctive features of American capitalism.
The African Adoption of the Portuguese Crusade during the Fifteenth and Sixteenth Centuries
Authors: Simmons Adam
Published: June 2021

The Portuguese engagement with the continent of Africa following the conquest of Ceuta in 1415 was framed, among numerous conditions, as a crusade (Portuguese: cruzada). However, crusading influences on Portuguese expansion are often sidelined in favour of economic motives. Unlike North and north-east Africa's connected histories with the Crusades (1095–1291) and the continual role of crusading in the following centuries, the fifteenth century offered a new arena. Kongo's adoption of Christianity in the late fifteenth century was the first time that an African power can be viewed as engaging in crusading ideology as a Latin Christian power. Significantly, Kongo was converted by Portuguese missionaries who were undertaking their own crusade. Yet, the crusading influence on Kongo's early development of its Christianity has hitherto been overlooked in Africanist scholarship. Similarly, the situation in Kongo remains a lacuna in Crusades scholarship too. This article calls for a closer discussion between the histories of Africa and the Crusades through the case of Kongo and comparative African examples, such as Benin and Ndongo, to highlight the need to better connect these histories.
The Evolution of Tunisian Salafism after the Revolution: FromLa Maddhabiyyato Salafi-Malikism
Authors: Merone Fabio , Blanc Théo , Sigillò Ester
Published: June 2021

What shape does Salafism take in Tunisia after the ban of the Salafi-Jihadi group Ansar al-Shari‘a and the wave of securitization carried out by national authorities? This article argues that a constraining legal context put Salafism's doctrinal rigidity in tension with its survival and ultimately prompted a residual current of Salafi actors to accommodate their stance toward Malikism, the prevalent school (madhhab) in the country. This adaptation is at odds with contemporary Salafism, which traditionally dismisses all four law schools (lā madhabiyya), rejects their blind imitation (taqlῑd), and claims the superiority of the Qur'an, hadith, and consensus of thesalaf(pious predecessors) over jurisprudence (fiqh). To account for this puzzle, this article scrutinizes the historical development of Salafism and the evolution of its stance toward Malikism across three generational waves. It notably shows how religious securitization associated with the promotion of a “moderate” Islam pushed Salafi actors to redefine their ideology to preserve their preaching and teaching activities. We call Salafi-Malikism the outcome of this adaptive strategy. Drawing on the Tunisian case, we argue that, despite its purist claims, Salafism is not an immutable religious current, but can take different trajectories to survive in constraining environments.
Model-based yield gap analysis and constraints of rainfed sorghum production in Southwest Ethiopia
Authors: Habte Abera , Worku Walelign , Gayler Sebastian , Ayalew Dereje , Mamo Girma
Published: June 2021

For ensuring food demand of the fast growing population in developing countries, quantification of crop yield gaps and exploring production constraints are very crucial. Sorghum is one of the most important climate change resilient crops in the rainfed farming systems of semi-arid tropics. However, there is little information about yield gaps and production constraints. This study aimed at analysing existing yield gaps and exploring major constraints of sorghum production in Southwest Ethiopia. A crop simulation model approach using AquaCrop and DSSAT was used to estimate potential yield and analyse the yield gaps. Model calibration and evaluation was performed using data from field experiments conducted in 2018 and 2019. Sorghum production constraints were assessed using a survey. The actual and water-limited yield of sorghum ranged from 0.58 to 2.51 and 3.6 to 6.47 t/ha, respectively for the period 2003–17. The regional yield gaps of sorghum for the targeted period were 3.02–3.95 t/ha with a mean value of 3.51 t/ha. Majority of respondent farmers considered seasonal rainfall risk (98%), poor soil fertility (86%), lack of improved varieties (78%) and inadequate weed management (56%) as major factors responsible for the existing yield gaps. The mean exploitable yield gap (2.5 t/ha) between water-limited and actual yield showed the level of existing opportunity for improvement in the actual productivity of sorghum. The gaps also call for introduction of proper interventions such as adoption of improved varieties, planting date adjustment, conservation tillage, fertilizer application and on time weed management.
Improving the monitoring of conservation programmes: lessons from a grant-making initiative for threatened species
Authors: Badalotti Alessandro , van Galen Laura , Vié Jean-Christophe , Stephenson P. J.
Published: June 2021

Many conservation projects have weak capacity to monitor their target species and the threats they face, compromising adaptive management. We assessed 74 vertebrate and plant conservation projects worldwide that were supported by the SOS–Save Our Species Programme (now IUCN Save Our Species) during 2012–2015. Our aim was to determine how and where monitoring efforts were focused, identify trends in data availability and make recommendations for improvement. Project managers reported more of a decrease in threats (73%) and improved habitat conditions (68%) than positive population changes (19%), primarily because of the focus of their objectives and limited time to collect population data. More population data were collected on reptiles and amphibians than mammals and birds, contrary to global trends. This probably reflects a greater focus of mammal and bird projects on improving habitats or reducing threats. There were geographical differences in data availability. Lessons learnt that could be applied to future project portfolios include: a common strategic framework should be developed, along with a set of common indicators against which projects can align and demonstrate their contributions; more guidance and capacity building support should be provided to grantees; and a greater allocation of project budgets should be dedicated to monitoring.
A coin hoard from Ayasuluk and the arrival of silver gigliati from Mediterranean Europe in early 14th-century western Anatolia
Authors: Baker Julian , Pancar Lale
Published: June 2021

In 1972 a hoard of eight fine silver coins was discovered in or near the baptistery of the basilica of St John in Ayasuluk. It is now conserved at the Ephesus Archaeological Museum in Selçuk. The coins were minted in southern France, southern Italy and on the island of Rhodes, between ca AD 1303 and 1319 or perhaps a little later. Accordingly, a concealment date of ca 1320 or a bit later is proposed. While the currency which they represent (the gigliato) is well known from other finds of the area, the present hoard is relatively early and from a particularly significant location. This currency found great success in commercial contexts in the eastern Aegean and western Anatolia during the period ca 1325 to ca 1370. By contrast, this study reveals two initial phases in the establishment and further dissemination of the gigliato in a concentrated part of western Anatolia, one in 1304 and another before and after ca 1317. On both occasions the Catalans were instrumental in shaping these processes: initially as conquerors on behalf of the Byzantine emperors and then, from their new base in Greece, as allies of the Aydinogullari rulers of Ayasuluk. Additionally, it is proposed that this new gigliato currency might have been minted at Rhodes from the summer of 1319, after which it rapidly reached the Ephesus area in a military context.
Early Australian rabbit-proof fences: paling, slab and stub fences, modified dry stone walls, and wire netting
Authors: Pickard John
Published: June 2021

Fences were critical in the fight against rabbits in colonial Australia. Initially, domestic rabbits were farmed in pens or paddocks fenced with paling fences or walls. Wild-caught rabbits imported from England escaped and became serious pests from the 1850s. As their status changed from protected private property to a major pest, the functions of fences changed to fencing rabbits out. Legislation requiring or specifying rabbit-proof fences lagged several years behind recognition of rabbits as a problem. Most log and brush fences in infested districts were burnt to destroy rabbit harbour. Dry stone walls were modified in many ways; paling, slab, picket and stub fences were all tried, but were unsuccessful, and by 1886 netting was standard. Using examples from the rich agricultural Western District and the considerably poorer Mallee Region of Victoria, this article describes the many forms of rabbit fences used between the 1850s and the mid-1880s. All of the experimentation with different structures was by individual landholders, with colonial governments conspicuous by their lack of involvement until they erected rabbit-proof barrier fences.
Card guessing with partial feedback
Authors: Diaconis Persi , Graham Ron , He Xiaoyu , Spiro Sam
Published: June 2021

Consider the following experiment: a deck with m copies of n different card types is randomly shuffled, and a guesser attempts to guess the cards sequentially as they are drawn. Each time a guess is made, some amount of ‘feedback’ is given. For example, one could tell the guesser the true identity of the card they just guessed (the complete feedback model) or they could be told nothing at all (the no feedback model). In this paper we explore a partial feedback model, where upon guessing a card, the guesser is only told whether or not their guess was correct. We show in this setting that, uniformly in n, at most
$m+O(m^{3/4}\log m)$
cards can be guessed correctly in expectation. This resolves a question of Diaconis and Graham from 1981, where even the
$m=2$
case was open.
Lexical borrowing in the Middle English period: a multi-domain analysis of semantic outcomes
Authors: SYLVESTER LOUISE , TIDDEMAN MEGAN , INGHAM RICHARD
Published: June 2021

The Middle English period is well known as one of widespread lexical borrowing from French and Latin, and scholarly accounts traditionally assume that this influx of loanwords caused many native terms to shift in sense or to drop out of use entirely. The study analyses an extensive dataset, tracking patterns in lexical retention, replacement and semantic change, and comparing long-term outcomes for both native and non-native words. Our results challenge the conventional view of competition between existing terms and foreign incomers. They show that there were far fewer instances of relexification, and far more of synonymy, during the Middle English period than might have been expected. When retention rates for words first attested between 1100 and 1500 are compared, it is loanwords, not native terms, which are more likely to become obsolete at any point up to the nineteenth century. Furthermore, proportions of outcomes involving narrowing and broadening (often considered common outcomes following the arrival of a co-hyponym in a semantic space) were low in the Middle English period, regardless of language of origin.
Evolution of Japanese security policy and the House of Councilors
Authors: Takenaka Harukata
Published: June 2021

Japanese security policy has undergone a significant degree of evolution since the early 1990s. As a result, the range of responses Japan can make in international crisis has significantly expanded. The gradual evolution and expansion of the Japanese security policy culminated in the legislation of security-related bills under the second Abe administration in September 2015. The security-related bills dramatically transformed Japanese security policy as it allowed Japan to exercise the right of collective defense when certain conditions are met. The gradual change of Japanese security policy has so far gathered much academic attention. There is a strong claim in the existing literature on Japanese security policy that changes in security policies became possible because of reforms in domestic institutions, which had expanded the Japanese prime minister's power. It is the contention of this article that the Japanese prime minister is still faced with severe constraints from the Diet, in particular from the House of Councilors even after a series of institutional reforms has empowered Japanese prime ministers to significantly alter Japanese security policy. It demonstrates that as the House of Councilors has significant power in the Japanese political system, some Japanese prime ministers had to have the implementation of some security policies delayed or was driven to revise some policies they had originally envisioned through several case studies.
China in medieval Indian imagination: “China”-inspired images in medieval South Asia
Authors: Kim Jinah
Published: June 2021

Cross-cultural exchanges between India and China during the first millennium are often understood through a Buddhist lens; by investigating the impact of Indian Buddhist sources, be they literary, doctrinal, or artistic, to receiving Chinese communities. In these cultural transactions, instigated by traveling pilgrim-monks and enacted by imperial power players in China, India emerges as a remote, idealized, and perhaps “hollow” center. Imagined or real, the importance of images of India in medieval Chinese Buddhist landscape has been established beyond doubt. What seems to be missing in this unidirectional looking is the impact of these cultural communications in India. What were the Indian responses to Chinese Buddhists' demands and their physical presence? How was China imagined and translated in medieval India? This essay proposes to locate the activities of Chinese monks in India and the iconographies of China-inspired Indian Buddhist images within the larger historical context of shifting cultural and political geography of the medieval Buddhist world. By exploring different types of evidence from borderlands, vis-à-vis the monolithic concepts of China and India, the essay also complicates the China–India studies' comparative model.
Introducing NARCliM1.5: Evaluating the Performance of Regional Climate Projections for Southeast Australia for 1950–2100
Authors: Nishant Nidhi , Evans Jason P. , Di Virgilio Giovanni , Downes Stephanie M. , Ji Fei , Cheung Kevin K. W. , Tam Eugene , Miller Joseph , Beyer Kathleen , Riley Matthew L.
Published: June 2021

The NARCliM project contributes to the CORDEX initiative for Australasia. The first generation of NARCliM (N1.0) used CMIP3 global climate models (GCMs) and provided near and far future estimates of climate change across Australasia at 50‐km and southeast Australia at 10‐km resolution under a business‐as‐usual climate scenario. However, multiple sets of 20‐year periods in N1.0 did not permit analysis of long‐term, inter‐annual to decadal trends across the 21st century. Feedback on user needs for regional climate information revealed the desire for multiple emission scenarios and use of newer CMIP5 GCMs for dynamical downscaling. These limitations led to development of the second iteration of NARCliM, namely NARCliM1.5 (N1.5). The N1.5 downscaling exercise uses CMIP5 GCMs and is temporally expanded to cover 150 years (1950–2100) for two future Representative Concentration Pathways (RCP4.5 and RCP8.5). N1.5 simulations remain at the 50‐km and 10 km resolutions over the same domains as N1.0, thus producing an expanded and complementary data set for regional climate change. N1.5 simulations substantially improve over N1.0 in capturing the seasonal patterns and magnitudes of precipitation, including improvements in overall bias. Conversely, N1.5 shows similar results to N1.0 for maximum and minimum temperature, with no substantial improvement in overall bias. N1.5 projections project a hotter and drier future relative to N1.0. The combined N1.0 and N1.5 ensemble provides a wider spread of future climates more representative of that found in the full CMIP5 ensemble. Together, N1.0 and N1.5 ensembles provide an improved, more comprehensive data set for studying climate change.
Origin, Variability, and Pathways of East Sea Intermediate Water in a High‐Resolution Ocean Reanalysis
Authors: Kim Sang‐Yeob , Park Young‐Gyu , Kim Young Ho , Seo Seongbong , Jin Hyunkeun , Pak Gyundo , Lee Ho Jin
Published: June 2021

The East Sea Intermediate Water (ESIW) is the subsurface salinity minimum layer in the depth range 200–400 m in the East/Japan Sea. The origin, variability, and pathways of the ESIW were investigated using a 4‐year‐long (2015–2018) high‐resolution (1/24°) ocean reanalysis and Lagrangian particle modeling. A backward particle tracking analysis revealed that the ESIW was formed south of Vladivostok and shows strong interannual variability. In 2018, owing to strong northwesterly winds, heat loss to the air intensified, and freshwater transport from the northern East/Japan Sea was simultaneously decreased by about 18% compared with the previous year. Furthermore, there was increased formation of water masses heavier than that of the typical ESIW, and the volume of the ESIW was reduced. A forward particle tracking analysis showed that the contribution of the particles originated from the northern end of the East/Japan Sea was about two times greater than those from the southern end. The major portion of the ESIW's freshwater came from the northern East/Japan Sea, where sea ice melted and the Amur River discharged. The remaining portion was from the Changjiang River, which came through the Korea Strait. The ESIW reached the Ulleung Basin over the course of a year mainly through the deep channel, the Ulleung Trough, located to the north of the basin. The diapycnal diffusivity of 1.0 × 10−4 m2 s−1 could erode away the low salinity core in about 27 years.
A New Method for Connecting the Radiation Sources of Lightning Discharge Extension Channels
Authors: Li YuRui , Zhang Yang , Zhang YiJun , Krehbiel Paul R.
Published: June 2021

The connections of lightning radiation sources along channels are greatly affected by the radiation source density, and the channel length is geometrically scaled when neglecting repeated discharges in the same channel. Based on lightning mapping array (LMA) three‐dimensional radiation source location data of two lightning flashes, this study presents a radiation source connection method considering the source density and repeated discharges in channels that includes two steps: the connection of radiation sources and the connection of segments. After increasing the spatial connection threshold determined by the source density, the stability of the channel scale under different detection capabilities (source densities) is improved compared with that of the traditional fixed spatial threshold method. The channel growth rate of the low‐density case reaches 120.99%, which is close to the real situation, and the connection shape is consistent with the real situation. For repeated discharge paths, by limiting the time interval of the radiation source connection, the optimized threshold obtained in this paper can distinguish between discharges occurring in the same channel at different times. Compared with the geometric scale, the discharge scale is significantly larger (∼2.8 times the geometric scale in one case) and can better characterize both the lightning discharge process and the affected area. These comprehensive results show that the proposed method can reduce the number of incorrect connections, increase the channel length, and obtain a more realistic discharge scale.
Liver fat storage is controlled by HNF4α through induction of lipophagy and is reversed by a potent HNF4α agonist
Authors: Lee Seung-Hee , Veeriah Vimal , Levine Fred
Published: June 2021

We report the discovery of strong HNF4α agonists and their use to uncover a previously unknown pathway by which HNF4α controls the level of fat storage in the liver. This involves the induction of lipophagy by dihydroceramides, the synthesis and secretion of which is controlled by genes induced by HNF4α. The HNF4α activators are N-trans caffeoyltyramine (NCT) and N-trans feruloyltyramine (NFT), which are structurally related to the known drugs alverine and benfluorex, which we previously showed to be weak HNF4α activators. In vitro, NCT and NFT induced fat clearance from palmitate-loaded cells. In DIO mice, NCT led to recovery of hepatic HNF4α expression and reduction of steatosis. Mechanistically, increased dihydroceramide production and action downstream of HNF4α occurred through increased expression of HNF4α downstream genes, including SPNS2 and CYP26A1. NCT was completely nontoxic at the highest dose administered and so is a strong candidate for an NAFLD therapeutic.
Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa
Authors: Morton Ben , Barnes Kayla G. , Anscombe Catherine , Jere Khuzwayo , Matambo Prisca , Mandolo Jonathan , Kamng’ona Raphael , Brown Comfort , Nyirenda James , Phiri Tamara , Banda Ndaziona P. , Van Der Veer Charlotte , Mndolo Kwazizira S. , Mponda Kelvin , Rylance Jamie , Phiri Chimota , Mallewa Jane , Nyirenda Mulinda , Katha Grace , Kambiya Paul , Jafali James , Mwandumba Henry C. , Gordon Stephen B. ,   Blantyre COVID-19 Consortium,   Clinical, Phulusa Jacob , Mkandawire Mercy , Kaimba Sylvester , Thole Herbert , Nthala Sharon , Nsomba Edna , Keyala Lucy , Mandala Peter , Chinoko Beatrice , Gmeiner Markus , Kaudzu Vella , Lissauer Samantha , Freyne Bridget , MacPherson Peter , Swarthout Todd D. , Iroh Tam Pui-Ying ,   Laboratory, Sichone Simon , Ahmadu Ajisa , Kanjewa Oscar , Nyasulu Vita , Chinyama End , Zuza Allan , Denis Brigitte , Storey Evance , Bondera Nedson , Matchado Danford , Chande Adams , Chingota Arthur , Ntwea Chimenya , Mkandawire Langford , Mhango Chimwemwe , Lakudzala Agness , Chaponda Mphatso , Mwenechanya Percy , Mvaya Leonard , Tembo Dumizulu ,   Data and statistics, Henrion Marc Y. R. , Chirombo James , Masesa Clemens , Gondwe Joel , Cornick Jennifer , Jambo Kondwani C.
Published: June 2021

Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we characterise patients hospitalised with suspected (PCR-negative/IgG-positive) or confirmed (PCR-positive) COVID-19, and healthy community controls (PCR-negative/IgG-negative). PCR-positive COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-negative/IgG-positive and PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants exhibited a nasal and systemic cytokine signature analogous to PCR-positive COVID-19 participants, predominated by chemokines and neutrophils and distinct from PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants had increased propensity forStaphylococcus aureusandStreptococcus pneumoniaecolonisation. PCR-negative/IgG-positive individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.
Dynamic control of Purcell enhanced emission of erbium ions in nanoparticles
Authors: Casabone Bernardo , Deshmukh Chetan , Liu Shuping , Serrano Diana , Ferrier Alban , Hümmer Thomas , Goldner Philippe , Hunger David , de Riedmatten Hugues
Published: June 2021

The interaction of single quantum emitters with an optical cavity enables the realization of efficient spin-photon interfaces, an essential resource for quantum networks. The dynamical control of the spontaneous emission rate of quantum emitters in cavities has important implications in quantum technologies, e.g., for shaping the emitted photons’ waveform or for driving coherently the optical transition while preventing photon emission. Here we demonstrate the dynamical control of the Purcell enhanced emission of a small ensemble of erbium ions doped into a nanoparticle. By embedding the nanoparticles into a fully tunable high finesse fiber based optical microcavity, we demonstrate a median Purcell factor of 15 for the ensemble of ions. We also show that we can dynamically control the Purcell enhanced emission by tuning the cavity on and out of resonance, by controlling its length with sub-nanometer precision on a time scale more than two orders of magnitude faster than the natural lifetime of the erbium ions. This capability opens prospects for the realization of efficient nanoscale quantum interfaces between solid-state spins and single telecom photons with controllable waveform, for non-destructive detection of photonic qubits, and for the realization of quantum gates between rare-earth ion qubits coupled to an optical cavity.
Analysis of the genomic landscape of yolk sac tumors reveals mechanisms of evolution and chemoresistance
Authors: Zong Xuan , Zhang Ying , Peng Xinxin , Cao Dongyan , Yu Mei , Wang Jinhui , Li Hongyue , Guo Xuejiao , Liang Han , Yang Jiaxin
Published: June 2021

Yolk sac tumors (YSTs) are a major histological subtype of malignant ovarian germ cell tumors with a relatively poor prognosis. The molecular basis of this disease has not been thoroughly characterized at the genomic level. Here we perform whole-exome and RNA sequencing on 41 clinical tumor samples from 30 YST patients, with distinct responses to cisplatin-based chemotherapy. We show that microsatellite instability status and mutational signatures are informative of chemoresistance. We identify somatic driver candidates, including significantly mutated genesKRASandKITand copy-number alteration drivers, including deletedARID1AandPARK2, and amplifiedZNF217,CDKN1B, andKRAS. YSTs have very infrequentTP53mutations, whereas the tumors from patients with abnormal gonadal development contain bothKRASandTP53mutations. We further reveal a role ofOVOL2overexpression in YST resistance to cisplatin. This study lays a critical foundation for understanding key molecular aberrations in YSTs and developing related therapeutic strategies.
Defect and strain engineering of monolayer WSe2 enables site-controlled single-photon emission up to 150 K
Authors: Parto Kamyar , Azzam Shaimaa I. , Banerjee Kaustav , Moody Galan
Published: June 2021

In recent years, quantum-dot-like single-photon emitters in atomically thin van der Waals materials have become a promising platform for future on-chip scalable quantum light sources with unique advantages over existing technologies, notably the potential for site-specific engineering. However, the required cryogenic temperatures for the functionality of these sources has been an inhibitor of their full potential. Existing methods to create emitters in 2D materials face fundamental challenges in extending the working temperature while maintaining the emitter’s fabrication yield and purity. In this work, we demonstrate a method of creating site-controlled single-photon emitters in atomically thin WSe2 with high yield utilizing independent and simultaneous strain engineering via nanoscale stressors and defect engineering via electron-beam irradiation. Many of the emitters exhibit biexciton cascaded emission, single-photon purities above 95%, and working temperatures up to 150 K. This methodology, coupled with possible plasmonic or optical micro-cavity integration, furthers the realization of scalable, room-temperature, and high-quality 2D single- and entangled-photon sources.
Real-time imaging of cellular forces using optical interference
Authors: Meek Andrew T. , Kronenberg Nils M. , Morton Andrew , Liehm Philipp , Murawski Jan , Dalaka Eleni , Booth Jonathan H. , Powis Simon J. , Gather Malte C.
Published: June 2021

Important dynamic processes in mechanobiology remain elusive due to a lack of tools to image the small cellular forces at play with sufficient speed and throughput. Here, we introduce a fast, interference-based force imaging method that uses the illumination of an elastic deformable microcavity with two rapidly alternating wavelengths to map forces. We show real-time acquisition and processing of data, obtain images of mechanical activity while scanning across a cell culture, and investigate sub-second fluctuations of the piconewton forces exerted by macrophage podosomes. We also demonstrate force imaging of beating neonatal cardiomyocytes at 100 fps which reveals mechanical aspects of spontaneous oscillatory contraction waves in between the main contraction cycles. These examples illustrate the wider potential of our technique for monitoring cellular forces with high throughput and excellent temporal resolution.
Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases
Authors: Lloréns-Rico Verónica , Vieira-Silva Sara , Gonçalves Pedro J. , Falony Gwen , Raes Jeroen
Published: June 2021

While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.
The functional organization of excitatory synaptic input to place cells
Authors: Adoff Michael D. , Climer Jason R. , Davoudi Heydar , Marvin Jonathan S. , Looger Loren L. , Dombeck Daniel A.
Published: June 2021

Hippocampal place cells contribute to mammalian spatial navigation and memory formation. Numerous models have been proposed to explain the location-specific firing of this cognitive representation, but the pattern of excitatory synaptic input leading to place firing is unknown, leaving no synaptic-scale explanation of place coding. Here we used resonant scanning two-photon microscopy to establish the pattern of synaptic glutamate input received by CA1 place cells in behaving mice. During traversals of the somatic place field, we found increased excitatory dendritic input, mainly arising from inputs with spatial tuning overlapping the somatic field, and functional clustering of this input along the dendrites over ~10 µm. These results implicate increases in total excitatory input and co-activation of anatomically clustered synaptic input in place firing. Since they largely inherit their fields from upstream synaptic partners with similar fields, many CA1 place cells appear to be part of multi-brain-region cell assemblies forming representations of specific locations.
Experimental warming differentially affects vegetative and reproductive phenology of tundra plants
Authors: Collins Courtney G. , Elmendorf Sarah C. , Hollister Robert D. , Henry Greg H. R. , Clark Karin , Bjorkman Anne D. , Myers-Smith Isla H. , Prevéy Janet S. , Ashton Isabel W. , Assmann Jakob J. , Alatalo Juha M. , Carbognani Michele , Chisholm Chelsea , Cooper Elisabeth J. , Forrester Chiara , Jónsdóttir Ingibjörg Svala , Klanderud Kari , Kopp Christopher W. , Livensperger Carolyn , Mauritz Marguerite , May Jeremy L. , Molau Ulf , Oberbauer Steven F. , Ogburn Emily , Panchen Zoe A. , Petraglia Alessandro , Post Eric , Rixen Christian , Rodenhizer Heidi , Schuur Edward A. G. , Semenchuk Philipp , Smith Jane G. , Steltzer Heidi , Totland Ørjan , Walker Marilyn D. , Welker Jeffrey M. , Suding Katharine N.
Published: June 2021

Rapid climate warming is altering Arctic and alpine tundra ecosystem structure and function, including shifts in plant phenology. While the advancement of green up and flowering are well-documented, it remains unclear whether all phenophases, particularly those later in the season, will shift in unison or respond divergently to warming. Here, we present the largest synthesis to our knowledge of experimental warming effects on tundra plant phenology from the International Tundra Experiment. We examine the effect of warming on a suite of season-wide plant phenophases. Results challenge the expectation that all phenophases will advance in unison to warming. Instead, we find that experimental warming caused: (1) larger phenological shifts in reproductive versus vegetative phenophases and (2) advanced reproductive phenophases and green up but delayed leaf senescence which translated to a lengthening of the growing season by approximately 3%. Patterns were consistent across sites, plant species and over time. The advancement of reproductive seasons and lengthening of growing seasons may have significant consequences for trophic interactions and ecosystem function across the tundra.
Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories
Authors: Friedrich Corinna , Schallenberg Simon , Kirchner Marieluise , Ziehm Matthias , Niquet Sylvia , Haji Mohamed , Beier Christin , Neudecker Jens , Klauschen Frederick , Mertins Philipp
Published: June 2021

Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
Stacking fault energy in concentrated alloys
Authors: Shih Mulaine , Miao Jiashi , Mills Michael , Ghazisaeidi Maryam
Published: June 2021

We revisit the meaning of stacking fault energy (SFE) and the assumptions of equilibrium dissociation of lattice dislocations in concentrated alloys. SFE is a unique value in pure metals. However, in alloys beyond the dilute limit, SFE has a distribution of values depending on the local atomic environment. Conventionally, the equilibrium distance between partial dislocations is determined by a balance between the repulsive elastic interaction between the partial dislocations and a unique value for SFE. This assumption is used to determine SFE from experimental measurements of dislocation splitting distances in metals and alloys, often contradicting computational predictions. We use atomistic simulations in a model NiCo alloy to study the dislocation dissociation process in a range of compositions with positive, zero, and negative average SFE and surprisingly observe a stable, finite splitting distance in all cases at low temperatures. We then compute the decorrelation stress and examine the balance of forces on the partial dislocations, considering the local effects on SFE, and observe that even the upper bound of SFE distribution alone cannot satisfy the force balance in some cases. Furthermore, we show that in concentrated solid solutions, the resisting force caused by interaction of dislocations with the local solute environment becomes a major force acting on partial dislocations. Here, we show that the presence of a high solute/dislocation interaction, which is not easy to measure and neglected in experimental measurements of SFE, renders the experimental values of SFE unreliable.
Cas9 targeted enrichment of mobile elements using nanopore sequencing
Authors: McDonald Torrin L. , Zhou Weichen , Castro Christopher P. , Mumm Camille , Switzenberg Jessica A. , Mills Ryan E. , Boyle Alan P.
Published: June 2021

Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on-targeted signals and exhibiting a 13.4-54x enrichment over whole-genome approaches. We show an individual flow cell can recover most MEIs (97% L1Hs, 93%AluYb, 51%AluYa, 99% SVA_F, and 65% SVA_E). We identify seventeen non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.
In situ decoration of Au NPs over polydopamine encapsulated GO/Fe3O4 nanoparticles as a recyclable nanocatalyst for the reduction of nitroarenes
Authors: Hemmati Saba , Heravi Majid M. , Karmakar Bikash , Veisi Hojat
Published: June 2021

A new and efficient catalyst has been designed and prepared via in situ immobilization of Au NPs fabricated polydopamine (PDA)-shelled Fe3O4 nanoparticle anchored over graphene oxide (GO) (GO/Fe3O4@PDA/Au). This novel, architecturally interesting magnetic nanocomposite was fully characterized using different analytical techniques such as Field Emission Scanning Electron Microscopy, Energy Dispersive X-ray Spectroscopy, elemental mapping, Transmission Electron Microscopy, Fourier Transformed Infrared Spectroscopy, X-ray Diffraction and Inductively Coupled Plasma-Atomic Electron Spectroscopy. Catalytic activity of this material was successfully explored in the reduction of nitroarenes to their corresponding substituted anilines, using NaBH4 as reducing agent at ambient conditions. The most significant merits for this protocol were smooth and clean catalysis at room temperature with excellent productivity, sustainable conditions, ease of separation of catalyst from the reaction mixture by using a magnetic bar and most importantly reusability of the catalyst at least 8 times without any pre-activation, minimum loss of activity and considerable leaching.
Publisher Correction: Identification of type III effectors modulating the symbiotic properties of Bradyrhizobium vignae strain ORS3257 with various Vigna species
Authors: Songwattana Pongpan , Chaintreuil Clémence , Wongdee Jenjira , Teulet Albin , Mbaye Mamadou , Piromyou Pongdet , Gully Djamel , Fardoux Joel , Zoumman Alexandre Mahougnon Aurel , Camuel Alicia , Tittabutr Panlada , Teaumroong Neung , Giraud Eric
Published: June 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Identification of damage development in the core of steel cord belts with the diagnostic system
Authors: Blazej Ryszard , Jurdziak Leszek , Kirjanow-Blazej Agata , Kozlowski Tomasz
Published: June 2021

Belt conveyors are used for transporting bulk materials over distances. The core of the belt, by transferring the longitudinal stresses and ensuring proper frictional coupling of the belt, enables belt movement and transportation of materials on its surface. As the belt cover and edges are used, the belt becomes abraded, and the core is subject to fatigue. The result is the development of cracks in rubber covers across the belt, which leads to the development of damage not only along the cables (the natural direction of water migration and corrosion) but also in the direction transverse to the belt axis. Conducting a series of scans of the St-type belt operating in one of the underground copper ore mines in Poland allowed identifying the number of failures as well as their size and changes over time. These data were in turn used to determine the measures defining the condition of the belt such as the density of defects (the number of defects per 1 m of the belt), the density of the area of damage (the area of damage per 1 m of the belt) and the change in the average area of a single defect over time. By determining the regression of these measures in time and the rate of damage development in both directions (along the axis of the belt and across the belt), it was possible to forecast future states of the belt, as well as to evaluate the costs of different belt replacement strategies and the economic rationalization of the decision to replace them. This research has become possible owing to the development of the DiagBelt system for two-dimensional imaging of the damage to the core of steel-cord belts with resolution sufficiently high to allow tracking the development of single core defects.