bluuebunny/crossref_metadata_2025 huggingface dataset:
Quartz‐Hosted Melt Inclusions as Windows Into Magma Assembly and Storage Processes in the Youngest Toba Tuff
Authors: Tierney C. R. , Reid M. R.
Published: July 2021

Quartz‐hosted melt inclusions are windows into the assembly and storage of compositionally zoned magmas systems like the giant magma body responsible for the 2,800 km3 Youngest Toba Tuff (YTT), Indonesia. Feldspar‐sensitive element concentrations and interelement ratios in YTT quartz‐hosted melt inclusions are found to cluster into three discrete melt inclusion populations. Each population represents a small fraction of the overall range in YTT melt compositions and no more than ∼12% to ∼21% fractional crystallization at mostly eutectoid conditions accounts for the trace elements variations within them. Kinships between host matrix glasses and co‐hosted phases are interpreted as evidence of spatially discrete chemical domains of magma within a more broadly zoned magma system. Quartz growth in the dominant portion of the system apparently occurred after extraction of melt from mush, whereas chemically distinct crystal cores in the more crystal‐rich, low‐silica magmas may have been derived from mush during extraction or remobilized by mush rejuvenation. Collectively, the chemical zoning of the YTT appears to have developed prior to most quartz growth, likely “bottom‐up” due to mush‐derived melt heterogeneity.
Wintertime Water Mass Transformation in the Western Iceland and Greenland Seas
Authors: Huang Jie , Pickart Robert S. , Bahr Frank , McRaven Leah T. , Xu Fanghua
Published: July 2021

Hydrographic and velocity data from a 2018 winter survey of the western Iceland and Greenland Seas are used to investigate the ventilation of overflow water feeding Denmark Strait. We focus on the two general classes of overflow water: warm, saline Atlantic‐origin Overflow Water (AtOW) and cold, fresh Arctic‐origin Overflow Water (ArOW). The former is found predominantly within the East Greenland Current (EGC), while the latter resides in the interior of the Iceland and Greenland Seas. Progressing north to south, the properties of AtOW in the EGC are modified diapycnally during the winter, in contrast to summer when along‐isopycnal mixing dominates. The water column response to a 10‐days cold‐air outbreak was documented using repeat observations. During the event, the northerly winds pushed the freshwater cap of the EGC onshore, and convection modified the water at the seaward edge of the current. Lateral transfer of heat and salt from the core of AtOW in the EGC appears to have influenced some of this water mass transformation. The long‐term evolution of the mixed layers in the interior was investigated using a 1‐D mixing model. This suggests that, under strong atmospheric forcing, the densest component of ArOW can be ventilated in this region. Numerous anti‐cyclonic eddies spawned from the EGC were observed during the winter survey, revealing that these features can play differing roles in modifying/prohibiting the open‐ocean convection.
Biotic Response to Early Eocene Warming Events: Integrated Record From Offshore Zealandia, North Tasman Sea
Authors: Alegret L. , Harper D. T. , Agnini C. , Newsam C. , Westerhold T. , Cramwinckel Marlow J. , Dallanave E. , Dickens G. R. , Sutherland R.
Published: July 2021

Environmental and biotic responses to early Eocene hyperthermal events in the southwest Pacific are critical for global paleoclimate reconstructions during Cenozoic greenhouse intervals, but detailed multidisciplinary studies are generally missing from this time and location. Eocene carbonate sediments were recovered during International Ocean Discovery Program Expedition 371 at Site U1510 on southern Lord Howe Rise in the Tasman Sea. Part of the Early Eocene Climatic Optimum (EECO; 53.26–49.14 Ma) and superimposed hyperthermal events have been identified based on refined calcareous nannofossil biostratigraphic data and carbon stable isotope records on bulk sediment and benthic foraminifera. Four negative carbon isotope excursions (CIEs) associated with negative oxygen isotope excursions are recognized within the EECO. Comparison with a global compilation of sites indicates these CIEs correlate to the K event (Eocene Thermal Maximum 3), and tentatively to the S, T, and U events. Sediments with a high carbonate content throughout the EECO provide an excellent opportunity to examine these CIEs, as carbonate dissolution often impacts correlative records elsewhere. Benthic foraminifera and calcareous nannoplankton taxa indicative of warm waters are most abundant during the K event, the most prominent hyperthermal of the EECO. Eutrophication of surface waters during the K event did not lead to increased trophic conditions at the seafloor, whereas a coupled response is observed during smaller hyperthermals. The biotic turnover sheds new light on the paleoenvironmental consequences of hyperthermal events.
Body‐Wave Tomographic Imaging of the Turkana Depression: Implications for Rift Development and Plume‐Lithosphere Interactions
Authors: Kounoudis R. , Bastow I. D. , Ebinger C. J. , Ogden C. S. , Ayele A. , Bendick R. , Mariita N. , Kianji G. , Wigham G. , Musila M. , Kibret B.
Published: July 2021

The Turkana Depression, a topographically subdued, broadly rifted zone between the elevated East African and Ethiopian plateaus, disrupts the N–S, fault‐bounded rift basin morphology that characterizes most of the East African Rift. The unusual breadth of the Turkana Depression leaves unanswered questions about the initiation and evolution of rifting between the Main Ethiopian Rift (MER) and Eastern Rift. Hypotheses explaining the unusually broad, low‐lying area include superposed Mesozoic and Cenozoic rifting and a lack of mantle lithospheric thinning and dynamic support. To address these issues, we have carried out the first body‐wave tomographic study of the Depression's upper mantle. Seismically derived temperatures at 100 km depth exceed petrological estimates, suggesting the presence of mantle melt, although not as voluminous as the MER, contributes to velocity anomalies. A NW–SE‐trending high wavespeed band in southern Ethiopia at 200 km depth is interpreted as refractory Proterozoic lithosphere which has likely influenced the localization of both Mesozoic and Cenozoic rifting. At 100 km depth below the central Depression, a single localized low wavespeed zone is lacking. Only in the northernmost Eastern Rift and southern Lake Turkana is there evidence for focused low wavespeeds resembling the MER, that bifurcate below the Depression and broaden approaching southern Ethiopia further north. These low wavespeeds may be attributed to melt‐intruded mantle lithosphere or ponded asthenospheric material below lithospheric thin‐spots induced by the region's multiple rifting phases. Low wavespeeds persist to the mantle transition zone suggesting the Depression may not lack mantle dynamic support in comparison to the two plateaus.
Multi‐Decadal Change in Western US Nighttime Vapor Pressure Deficit
Authors: Chiodi Andrew M. , Potter Brian E. , Larkin Narasimhan K.
Published: July 2021

Amid reports from western US wildland fire managers that, compared to when many started their careers, fires are burning longer throughout the day before reducing in intensity overnight, we examined decadal changes in nighttime vapor pressure deficits over the western United States with a focus on the summer fire season. We calculated changes using a recently updated observation‐assimilating reanalysis (ERA5) available at hourly resolution over the 1980–2019 period. Analysis identifies the proximate cause (atmospheric temperature vs. moisture content) of the observed changes and the extent to which they have been captured in climate model simulations. Increases in nighttime vapor pressure deficits of >50% in 40 years are evident over foothills of mountains ranges adjacent to arid plateaus. The largest observed increases greatly exceed the forced climate‐model response. Correlation analysis reveals a broad link between the variability of western US summer‐nighttime vapor pressure deficit and the Pacific Decadal Oscillation.
Plate Boundary and Triple Junction Control of Shatsky Rise Formation and Implications for Other Ocean Plateaus
Authors: Georgen Jennifer E. , Shotorban A. Katrina
Published: July 2021

In the study of marine large igneous provinces, investigations often focus on the importance of mantle plumes in generating excess magmatism. Few studies, however, have addressed the role of plate boundary processes in promoting widespread and extensive mantle melting. This study investigates how spreading center geometry may have facilitated the emplacement of Shatsky Rise, an oceanic plateau in the western Pacific Ocean. The largest structure within Shatsky Rise, Tamu Massif, was created ∼140–150 Ma at the Pacific‐Izanagi‐Farallon (PIF) ridge‐ridge‐ridge triple junction. Moreover, the PIF triple junction was one of three triple junctions operating in close proximity at the time, as the nascent Pacific Plate (NPP) began to expand in size. This study suggests that the thermal conditions of the NPP, which likely resulted in a large area of thin lithosphere, could have significantly facilitated widespread mantle melting as well as the magmatic expression of any nearby mantle plume.
Sources of Uncertainty in Multimodel Large Ensemble Projections of the Winter North Atlantic Oscillation
Authors: McKenna C. M. , Maycock A. C.
Published: July 2021

Projections of the winter North Atlantic circulation exhibit large spread. Coupled Model Intercomparison Project archives typically provide only a few ensemble members per model, rendering it difficult to quantify reducible model structural uncertainty and irreducible internal variability (IV) in projections. We estimate using the Multimodel Large Ensemble Archive that model structural differences explain two‐thirds of the spread in late 21st century (2080–2099) projections of the winter North Atlantic Oscillation (NAO). This estimate is biased by systematic model errors in the forced NAO response and IV. Across the North Atlantic, the NAO explains a substantial fraction of the spread in mean sea level pressure (MSLP) projections due to IV, except in the central North Atlantic. Conversely, the spread in North Atlantic MSLP projections associated with model differences is largely unexplained by the NAO. Therefore, improving understanding of the NAO alone may not constrain the reducible uncertainty in North Atlantic MSLP projections.
Interseismic Deformation From Sentinel‐1 Burst‐Overlap Interferometry: Application to the Southern Dead Sea Fault
Authors: Li Xing , Jónsson Sigurjón , Cao Yunmeng
Published: July 2021

Interferometric Synthetic Aperture Radar (InSAR) data are increasingly being used to map interseismic deformation with ascending and descending‐orbit observations allowing for resolving the near‐east and vertical displacement components. The north component has, however, been difficult to retrieve due to the limited sensitivity of standard InSAR observations in that direction. Here, we address this problem by using time‐series analysis of along‐track interferometric observations in burst‐overlap areas of the Terrain Observation with Progressive Scan imaging mode of the Sentinel‐1 radar satellites. We apply this method to the southern part of the near‐north striking Dead Sea transform fault to show that the ∼5 mm/year relative motion is well recovered. Furthermore, the results indicate the locking depth of the fault decreases toward the south as it enters the transtensional Gulf of Aqaba basin. Our results show that time‐series analysis of burst‐overlap interferometric observations can be used to obtain meaningful interseismic deformation rates of slow‐moving and northerly striking faults.
Fluxes of Carbon Dioxide From Managed Ecosystems Estimated by National Inventories Compared to Atmospheric Inverse Modeling
Authors: Chevallier Frédéric
Published: July 2021

The UNFCCC reporting guidelines on annual emission inventories have been encouraging comparison of national inventory reports with atmospheric measurements or atmospheric inverse modeling. We have initiated a framework to compare two CO2 atmospheric inversions with the net agricultural, forestry and other land use (AFOLU) fluxes reported by 10 parties to the UNFCCC. Our study highlights large conceptual differences or ambiguities (temporal support, spatial perimeter, scope of the processes) between inventory reports and between these reports and what the atmosphere sees. We recommend that more effort be invested into documenting the inventories in order to allow unambiguous conversion between reported values and the way they are seen by the atmosphere. We also highlight the potential of Bayesian atmospheric inversion products generated in quasi‐near‐real time with robust error bars and consistently across the world, to directly inform international CO2 flux accounting for the AFOLU sector in large countries or groups of countries.
North American East Coast Sea Level Exhibits High Power and Spatiotemporal Complexity on Decadal Timescales
Authors: Little Christopher M. , Piecuch Christopher G. , Ponte Rui M.
Published: July 2021

Tide gauges provide a rich, long‐term, record of the amplitude and spatiotemporal structure of interannual to multidecadal coastal sea‐level variability, including that related to North American east coast sea level “hotspots.” Here, using wavelet analyses, we find evidence for multidecadal epochs of enhanced decadal (10–15 year period) sea‐level variability at almost all long (70 years) east coast tide gauge records. Within this frequency band, large‐scale spatial covariance is time‐dependent; notably, coastal sectors north and south of Cape Hatteras exhibit multidecadal epochs of coherence (1960–1990) and incoherence (1990‐present). Results suggest that previous interpretations of along coast covariance, and its underlying physical drivers, are clouded by time‐dependence and frequency‐dependence. Although further work is required to clarify the mechanisms driving sea‐level variability in this frequency band, we highlight potential associations with the North Atlantic sea surface temperature tripole and Atlantic Multidecadal Variability.
Formation of Horizontally Deflected Slabs in the Mantle Transition Zone Caused by Spinel‐to‐Post‐Spinel Phase Transition, Its Associated Grainsize Reduction Effects, and Trench Retreat
Authors: Mao Wei , Zhong Shijie
Published: July 2021

Seismic observations indicate accumulation of subducted slabs in the mantle transition zone in many subduction zones. By systematically conducting 2‐D numerical experiments, we demonstrate that a weak layer or zone beneath the spinel‐to‐post‐spinel phase transition leads to horizontally deflected (stagnant) slab structures in the mantle transition zone, which is consistent with recent studies of 3‐D global mantle convection models. Trench retreat velocity, Clapeyron slope and the viscosity contrast between the lower mantle and mantle transition zone also affect horizontally deflected slab formation. By considering grain size dependent viscosity and grainsize evolution for slabs going through the phase change in the lower mantle, our models with a dynamically generated weak zone beneath the phase boundary indicate that the geometry and viscosity reduction of the weak zone is strongly affected by grain growth rate. A smaller grain growth rate results in a thicker and wider weak zone that promotes deflected slab formation.
Quantifying the Imprints of Stratospheric Contributions to Interhemispheric Differences in Tropospheric CFC‐11, CFC‐12, and N2O Abundances
Authors: Lickley Megan , Solomon Susan , Kinnison Doug , Krummel Paul , Mühle Jens , O'Doherty Simon , Prinn Ronald , Rigby Matthew , Stone Kane A. , Wang Peidong , Weiss Ray , Young Dickon
Published: July 2021

For trace gases destroyed in the stratosphere, mass flux across the tropopause can substantially influence observed surface hemispheric differences (NH‐SH). Here, we quantify associations between observed stratospheric and tropospheric NH‐SH growth rate anomalies of CFC‐11, CFC‐12, and N2O. We employ a chemistry climate model along with satellite and global surface station observations. Our model explains 60% of observed N2O NH‐SH growth rate variability from 2005 to 2019, compared to 30% for CFC‐11% and 40% for CFC‐12, supporting evidence that unexpected anthropogenic emissions caused sustained positive NH‐SH anomalies in these CFCs from 2012 to 2017. Between 2012 and 2015, the observed CFC‐11 NH‐SH difference grew by 1.7 ppt; our model explains 0.5 ± 0.1 ppt of this growth, but not the duration. Our model suggests that in the absence of further emission anomalies, new NH‐SH positive tracer anomalies should have occurred in 2020, and predicts small negative anomalies in 2021.
Ion Scattering and Energization in Filamentary Structures Through Earth's Magnetosheath
Authors: Chaston C. C. , Travnicek P.
Published: July 2021

Multi‐point measurements on kinetic scales through Earth's magnetosheath have revealed a spectrum of filamentary currents and vortical flows advected with the shocked plasmas outside the magnetopause. The spectral energy density in these structures is correlated with enhanced ion temperatures. Using an empirically derived statistical model based on fluid‐kinetic theory for these structures we demonstrate how they act to scatter magnetosheath ions. Through the combined action of energization in the direction perpendicular to the background magnetic field along chaotic orbits, and pitch‐angle scattering into the parallel direction appreciable ion energization occurs. These dynamics drive heating while generating non‐thermal energetic tails similar to that observed. It is shown how the operation of this process depends on the field topology with deviations from planar form and counter‐propagation required to drive significant energization. This process will modulate ion anisotropies through the magnetosheath independent of both adiabatic effects and the action of anisotropy instabilities.
Ground Observation of Negative Sprites Over a Tropical Thunderstorm as the Embryo of Hurricane Harvey (2017)
Authors: Wang Yongping , Lu Gaopeng , Cummer Steven A. , Lucena Frankie , Cohen Morris B. , Ren Huan , Li Jiagen , Cheng Zhengwei , Zhang Shoubao
Published: July 2021

We report on the observation of six red sprites produced by negative cloud‐to‐ground (CG) lightning strokes in a tropical thunderstorm that later evolved into Hurricane Harvey (2017). Most of these sprites conformed to the morphological characteristics of typical negative sprites previously observed over continental thunderstorms. The sprite‐producing CG strokes were located in or near the deep convection region and their impulse charge moment changes all exceeded −500 C‐km. During the sprite generation stage, the CG lightning stroke rate declined and the tropical thunderstorm structure appeared stable. Our analysis suggests that tropical marine meteorological systems, such as tropical disturbances, depressions, and thunderstorms are more likely to be main production systems of negative sprites. The frequent occurrence of 18 gigantic jets produced by the same thunderstorm further indicates that the thundercloud charge structures of sprite‐producing oceanic thunderstorms are significantly different from that of continental thunderstorms.
Gravity Wave Observations by the Mars Science Laboratory REMS Pressure Sensor and Comparison With Mesoscale Atmospheric Modeling With MarsWRF
Authors: Guzewich Scott D. , de la Torre Juárez Manuel , Newman Claire E. , Mason Emily , Smith Michael D. , Miller Nina , Khayat Alain S. J. , Kahanpää Henrik , Viúdez‐Moreiras Daniel , Richardson Mark I.
Published: July 2021

Surface pressure measurements on Mars have revealed a wide variety of atmospheric phenomena. The Mars Science Laboratory Rover Environmental Monitoring Station pressure sensor data set is now the longest duration record of surface pressure on Mars. We use the first 2580 Martian sols, nearly 4 Mars years, of measurements to identify atmospheric pressure waves with periods of tens of minutes to hours using wavelet analysis on residual pressure after the tidal harmonics are removed. We find these waves have a clear diurnal cycle with strongest activity in the early morning and late evening and a seasonal cycle with the strongest waves in the second half of the martian year (Ls = 180–360°). The strongest such waves of the entire mission occurred during the Mars Year 34 global dust storm. Comparable atmospheric waves are identified using atmospheric modeling with the MarsWRF general circulation model in a “nested” high spatial resolution mode. With the support of the modeling, we find these waves best fit the expected properties of inertia‐gravity waves with horizontal wavelengths of O(100s) of km.
Evolution of Ocean Productivity in the Sub‐Tropical West Pacific Ocean Across the Last Deglaciation
Authors: Hu Bangqi , Zhang Handan , Ouyang Siqi , Zhao Jingtao , Wang Feifei , Li Qing , Jaccard Samuel L. , Luo Yiming
Published: July 2021

Changes in marine export productivity may have played a prominent role in the atmospheric CO2 rise and associated warming of the last deglaciation, via their impact on the air‐sea partitioning of CO2. To study the evolution of marine export production in the western subtropical Pacific Ocean during the last deglaciation and the mechanisms governing these changes, 230Th‐normalization has been applied on a sediment core retrieved from the Okinawa Trough. The reconstructed export productivity record shows two prominent peaks, centered around 14 and 17 ka. Given that phytoplankton growth at our study site is limited by the availability of nutrients today, elevated macro‐nutrient supply must have been responsible for sustaining the two deglacial productivity peaks. Specifically, higher nutrient supply originating from the subpolar gyre via subsurface water advection, with enhanced vertical mixing in the subpolar gyre during early HS1 and enhanced wind‐driven upwelling during the B/A, would have fueled phytoplankton productivity and export. In contrast, reduced nutrient supply to the euphotic zone caused by gyre circulation changes would have lead to decreased export production during the Holocene. These observations lend support to a predominant control of nutrient availability on the evolution of the marine carbon cycle in the subtropical west Pacific Ocean across the last deglaciation.
Retracted: Control of Multiple Detachments on Structural Development in the Southern Junggar Fold‐and‐Thrust Belt, Northern Tian Shan: Implications for Seismic Hazard Assessment
Authors: Qiu Jianhua , Rao Gang , Yu Yangli , Wang Xin , Peng Zhenyu , Gao Lin , Yang Disheng , Xiao Lixin , Yao Qi
Published: July 2021

As large earthquakes in contractional fold‐and‐thrust belts are usually associated with complex ruptures along multiple faults or fault splays, the evaluation of potential rupture extent and relevant hazards continues to be challenging. We present a case study on the geometry and kinematic evolution of the southern Junggar fold‐and‐thrust belt, northern Tian Shan, where the 1906 M 8 Manas earthquake occurred. Our interpretations of seismic reflection profiles acquired during oil and gas exploration demonstrate that multiple detachments played significant roles in controlling the structural segmentation. We speculate that seismic potential in active fold‐and‐thrust belts can be under‐estimated by relying on the mapped surface fault traces. Structural analysis of subsurface images in sufficient detail may provide important insights into seismic hazard evaluation and hence complement traditional paleo‐seismic studies, particularly in densely populated regions such as the city of Urumqi.
Microplastics accumulate fungal pathogens in terrestrial ecosystems
Authors: Gkoutselis Gerasimos , Rohrbach Stephan , Harjes Janno , Obst Martin , Brachmann Andreas , Horn Marcus A. , Rambold Gerhard
Published: July 2021

Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely neglected in this context, despite their affinity for plastics and their impact as pathogens. To unravel the role of MP as a carrier of fungal pathogens in terrestrial ecosystems and the immediate human environment, epiplastic mycobiomes from municipal plastic waste from Kenya were deciphered using ITS metabarcoding as well as a comprehensive meta-analysis, and visualised via scanning electron as well as confocal laser scanning microscopy. Metagenomic and microscopic findings provided complementary evidence that the terrestrial plastisphere is a suitable ecological niche for a variety of fungal organisms, including important animal and plant pathogens, which formed the plastisphere core mycobiome. We show that MPs serve as selective artificial microhabitats that not only attract distinct fungal communities, but also accumulate certain opportunistic human pathogens, such as cryptococcal and Phoma-like species. Therefore, MP must be regarded a persistent reservoir and potential vector for fungal pathogens in soil environments. Given the increasing amount of plastic waste in terrestrial ecosystems worldwide, this interrelation may have severe consequences for the trans-kingdom and multi-organismal epidemiology of fungal infections on a global scale.
Isolation, characterization, anti-MRSA evaluation, and in-silico multi-target anti-microbial validations of actinomycin X2 and actinomycin D produced by novel Streptomyces smyrnaeus UKAQ_23
Authors: Qureshi Kamal A. , Bholay Avinash D. , Rai Pankaj K. , Mohammed Hamdoon A. , Khan Riaz A. , Azam Faizul , Jaremko Mariusz , Emwas Abdul-Hamid , Stefanowicz Piotr , Waliczek Mateusz , Kijewska Monika , Ragab Ehab A. , Rehan Medhat , Elhassan Gamal O. , Anwar Md Jamir , Prajapati Dinesh K.
Published: July 2021

Streptomyces smyrnaeus UKAQ_23, isolated from the mangrove-sediment, collected from Jubail,Saudi Arabia, exhibited substantial antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), including non-MRSA Gram-positive test bacteria. The novel isolate, under laboratory-scale conditions, produced the highest yield (561.3 ± 0.3 mg/kg fermented agar) of antimicrobial compounds in modified ISP-4 agar at pH 6.5, temperature 35 °C, inoculum 5% v/w, agar 1.5% w/v, and an incubation period of 7 days. The two major compounds, K1 and K2, were isolated from fermented medium and identified as Actinomycin X2 and Actinomycin D, respectively, based on their structural analysis. The antimicrobial screening showed that Actinomycin X2 had the highest antimicrobial activity compared to Actinomycin D, and the actinomycins-mixture (X2:D, 1:1, w/w) against MRSA and non-MRSA Gram-positive test bacteria, at 5 µg/disc concentrations. The MIC of Actinomycin X2 ranged from 1.56–12.5 µg/ml for non-MRSA and 3.125–12.5 µg/ml for MRSA test bacteria. An in-silico molecular docking demonstrated isoleucyl tRNA synthetase as the most-favored antimicrobial protein target for both actinomycins, X2 and D, while the penicillin-binding protein-1a, was the least-favorable target-protein. In conclusion, Streptomyces smyrnaeus UKAQ_23 emerged as a promising source of Actinomycin X2 with the potential to be scaled up for industrial production, which could benefit the pharmaceutical industry.
Collagen and elastic fibres in acute and chronic liver injury
Authors: Hall Andrew , Cotoi Corina , Luong Tu Vinh , Watkins Jennifer , Bhathal Prithi , Quaglia Alberto
Published: July 2021

The histological distinction between acute and chronic liver injury is a challenging aspect of liver histopathology. It is traditionally based on the interpretation of morphological changes to the extracellular matrix (ECM) at sites of hepatocyte loss using histochemical stains. Our aim was to investigate whether immunohistochemistry and multiplexing for collagen type (I & III) and elastic fibres and a modified Victoria blue method could be helpful. We studied 43 livers removed at transplantation for acute liver failure (ALF, 20 cases) or cirrhosis (23) plus 8 normal controls. In ALF the periportal ECM was normal in 2 cases, contained mainly collagen I associated with a ductular reaction in 6 cases, and delicate elastic strands in 11 cases. Periportal deposition of mainly collagen I and mature elastic fibres was observed in cirrhosis. In ALF the perisinusoidal ECM was intact in 4 cases, collapsed or condensed but of normal composition (predominantly collagen III) in 2 cases, and collapsed and condensed containing mostly collagen I in 17 cases (7 including delicate immature elastic strands). In contrast, bridging fibrous septa of cirrhosis contained abundant collagen 1 and bundles of mature elastin. We propose the use of a scale and the use of immunohistochemistry and multiplexing in additional to histochemical stains to characterise the ECM changes in acute and chronic liver injury.
Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states
Authors: Chen Xueqing , Emerson Mark M.
Published: July 2021

Notch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
A fuzzy rank-based ensemble of CNN models for classification of cervical cytology
Authors: Manna Ankur , Kundu Rohit , Kaplun Dmitrii , Sinitca Aleksandr , Sarkar Ram
Published: July 2021

Cervical cancer affects more than 0.5 million women annually causing more than 0.3 million deaths. Detection of cancer in its early stages is of prime importance for eradicating the disease from the patient’s body. However, regular population-wise screening of cancer is limited by its expensive and labour intensive detection process, where clinicians need to classify individual cells from a stained slide consisting of more than 100,000 cervical cells, for malignancy detection. Thus, Computer-Aided Diagnosis (CAD) systems are used as a viable alternative for easy and fast detection of cancer. In this paper, we develop such a method where we form an ensemble-based classification model using three Convolutional Neural Network (CNN) architectures, namely Inception v3, Xception and DenseNet-169 pre-trained on ImageNet dataset for Pap stained single cell and whole-slide image classification. The proposed ensemble scheme uses a fuzzy rank-based fusion of classifiers by considering two non-linear functions on the decision scores generated by said base learners. Unlike the simple fusion schemes that exist in the literature, the proposed ensemble technique makes the final predictions on the test samples by taking into consideration the confidence in the predictions of the base classifiers. The proposed model has been evaluated on two publicly available benchmark datasets, namely, the SIPaKMeD Pap Smear dataset and the Mendeley Liquid Based Cytology (LBC) dataset, using a 5-fold cross-validation scheme. On the SIPaKMeD Pap Smear dataset, the proposed framework achieves a classification accuracy of 98.55% and sensitivity of 98.52% in its 2-class setting, and 95.43% accuracy and 98.52% sensitivity in its 5-class setting. On the Mendeley LBC dataset, the accuracy achieved is 99.23% and sensitivity of 99.23%. The results obtained outperform many of the state-of-the-art models, thereby justifying the effectiveness of the same. The relevant codes of this proposed model are publicly available on GitHub.
A new charophyte habitat with a stabilized good ecological potential of mine water
Authors: Napiórkowska-Krzebietke Agnieszka , Skrzypczak Andrzej Robert
Published: July 2021

Each newly-created pond which is supplied with mine water gives the opportunity to study a unique ecosystem in context of possible conditions for biotic live. Therefore, this research aimed to assess a phytoplankton-based ecological potential against the trophic conditions and the risk of contamination with trace elements, and demonstrate the possibility to stabilize at least good water quality of a clarification pond. The gradual decrease in turbidity-related variables (including suspended solids and iron) and nutrients, on the one hand, and an increase in phytoplankton-related indicators, on the other hand, were the most evident. Besides, relative stability in trace elements (the best water quality class), trophic level (slightly eutrophic level) and ecological potential (maximum potential), and relative instability in sulfates and calcium were also recorded. The final stabilization of water habitat resulted in abundant growth of charophyte Nitella mucronata. This all suggested a new ecological opportunity for settlement of a rare species and important for biodiversity enhancement. Furthermore, the study revealed that a clarification pond did not pose any toxic risk from the elevated content of trace elements or the growth of toxic or potentially toxic cyanobacteria which is essential for proper functioning and management of water ecosystems.
The association between serum selenium concentration and prognosis in patients with heart failure in a Chinese population
Authors: Zhang Zhiliang , Chang Chao , Zhang Yuxin , Chai Zhiyong , Li Jinbei , Qiu Chunguang
Published: July 2021

Whether Selenium (Se) deficiency relates with adverse prognosis in Chinese patients with heart failure (HF) is still unknown. This study aimed to investigate the association of serum Se level and the outcomes of patients with HF in a Chinese population. Patients with HF and serum Se examination were retrospectively included. Baseline information were collected at patient’s first admission. The primary and secondary outcomes were all-cause mortality and rehospitalization for HF during follow-up, respectively. The study participants were divided into quartiles according to their serum Se concentrations. The Cox proportional hazard models were adopted to estimate the association of serum Se levels with observed outcomes. A total of 411 patients with HF with a mean age of 62.5 years were included. The mean serum level of Se was 68.3 ± 27.7 µg/L. There was nonsignificant difference of baseline characterizes between the four quartile groups. In comparison with patients in the highest quartile, those with the lowest quartile (17.40–44.35 µg/L) were associated with increased risk of all-cause mortality [adjusted hazard ratios (95% CI) 2.32 (1.43–3.77); Ptrend = 0.001]. Our study suggested that a lower serum Se level was significantly associated with increased risk of all-cause mortality in patients with HF.
Type 1 diabetes patients increase CXCR4+ and CXCR7+ haematopoietic and endothelial progenitor cells with exercise, but the response is attenuated
Authors: Taylor Guy S. , Shaw Andy , Smith Kieran , Capper Tess E. , Scragg Jadine H. , Cronin Michael , Bashir Ayat , Flatt Anneliese , Campbell Matthew D. , Stevenson Emma J. , Shaw James A. , Ross Mark , West Daniel J.
Published: July 2021

Exercise mobilizes angiogenic cells, which stimulate vascular repair. However, limited research suggests exercise-induced increase of endothelial progenitor cell (EPCs) is completely lacking in type 1 diabetes (T1D). Clarification, along with investigating how T1D influences exercise-induced increases of other angiogenic cells (hematopoietic progenitor cells; HPCs) and cell surface expression of chemokine receptor 4 (CXCR4) and 7 (CXCR7), is needed. Thirty T1D patients and 30 matched non-diabetes controls completed 45 min of incline walking. Circulating HPCs (CD34+, CD34+CD45dim) and EPCs (CD34+VEGFR2+, CD34+CD45dimVEGFR2+), and subsequent expression of CXCR4 and CXCR7, were enumerated by flow cytometry at rest and post-exercise. Counts of HPCs, EPCs and expression of CXCR4 and CXCR7 were significantly lower at rest in the T1D group. In both groups, exercise increased circulating angiogenic cells. However, increases was largely attenuated in the T1D group, up to 55% lower, with CD34+(331 ± 437 Δcells/mL vs. 734 ± 876 Δcells/mLp = 0.048), CD34+VEGFR2+(171 ± 342 Δcells/mL vs. 303 ± 267 Δcells/mL,p = 0.006) and CD34+VEGFR2+CXCR4+(126 ± 242 Δcells/mL vs. 218 ± 217 Δcells/mL,p = 0.040) significantly lower. Exercise-induced increases of angiogenic cells is possible in T1D patients, albeit attenuated compared to controls. Decreased mobilization likely results in reduced migration to, and repair of, vascular damage, potentially limiting the cardiovascular benefits of exercise.

Trial registration: ISRCTN63739203.
Plastome evolution and organisation in the Hoya group (Apocynaceae)
Authors: Rodda Michele , Niissalo Matti A.
Published: July 2021

The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.
Detection and analysis of photo-acoustic emission in Direct Laser Interference Patterning
Authors: Steege Tobias , Alamri Sabri , Lasagni Andrés Fabián , Kunze Tim
Published: July 2021

Functional laser texturing by means of Direct Laser Interference Patterning is one of the most efficient approaches to fabricate well-defined micro textures which mimic natural surfaces, such as the lotus effect for self-cleaning properties or shark skin for reduced friction. While numerous technical and theoretical improvements have been demonstrated, strategies for process monitoring are yet to be implemented in DLIP, for instance aiming to treat complex and non-plane surfaces. Over the last 35 years, it has been shown that the sound pressure generated by a laser beam hitting a surface and producing ablation can be detected and analysed using simple and commercially available transducers and microphones. This work describes the detection and analysis of photo-acoustic signals acquired from airborne acoustic emission during DLIP as a direct result of the laser–material interaction. The study includes the characterization of the acoustic emission during the fabrication of line-like micro textures with different spatial periods and depths, the interpretation the spectral signatures deriving from single spot and interference ablation, as well as a detailed investigation of the vertical extent of the interference effect based on the ablated area and its variation with the interference period. The results show the possibility to develop an autofocusing system using only the signals from the acoustic emission for 3D processing, as well as the possibility to predict deviations in the DLIP processing parameters.
Predictability of COVID-19-related morbidity and mortality based on model estimations to establish proactive protocols of countermeasures
Authors: Svensson Göran , Rodriguez Rocio , Padin Carmen
Published: July 2021

The COVID-19 pandemic (SARS-CoV-2) has revealed the need for proactive protocols to react and act, imposing preventive and restrictive countermeasures on time in any society. The extent to which confirmed cases can predict the morbidity and mortality in a society remains an unresolved issue. The research objective is therefore to test a generic model’s predictability through time, based on percentage of confirmed cases on hospitalized patients, ICU patients and deceased. This study reports the explanatory and predictive ability of COVID-19-related healthcare data, such as whether there is a spread of a contagious and virulent virus in a society, and if so, whether the morbidity and mortality can be estimated in advance in the population. The model estimations stress the implementation of a pandemic strategy containing a proactive protocol entailing what, when, where, who and how countermeasures should be in place when a virulent virus (e.g. SARS-CoV-1, SARS-CoV-2 and MERS) or pandemic strikes next time. Several lessons for the future can be learnt from the reported model estimations. One lesson is that COVID-19-related morbidity and mortality in a population is indeed predictable. Another lesson is to have a proactive protocol of countermeasures in place.
Salt-tolerance screening in Limonium sinuatum varieties with different flower colors
Authors: Xu Xiaojing , Zhou Yingli , Mi Ping , Wang Baoshan , Yuan Fang
Published: July 2021

Limonium sinuatum, a member of Plumbaginaceae commonly known as sea lavender, is widely used as dried flower. Five L. sinuatum varieties with different flower colors (White, Blue, Pink, Yellow, and Purple) are found in saline regions and are widely cultivated in gardens. In the current study, we evaluated the salt tolerance of these varieties under 250 mmol/L NaCl (salt-tolerance threshold) treatment to identify the optimal variety suitable for planting in saline lands. After the measurement of the fresh weight (FW), dry weight (DW), contents of Na+, K+, Ca2+, Cl−, malondialdehyde (MDA), proline, soluble sugars, hydrogen peroxide (H2O2), relative water content, chlorophyll contents, net photosynthetic rate, and osmotic potential of whole plants, the salt-tolerance ability from strongest to weakest is identified as Pink, Yellow, Purple, White, and Blue. Photosynthetic rate was the most reliable and positive indicator of salt tolerance. The density of salt glands showed the greatest increase in Pink under NaCl treatment, indicating that Pink adapts to high-salt levels by enhancing salt gland formation. These results provide a theoretical basis for the large-scale planting of L. sinuatum in saline soils in the future.
Oncological and functional outcomes of supratotal resection of IDH1 wild-type glioblastoma based on 11C-methionine PET: a retrospective, single-center study
Authors: Hirono Seiichiro , Ozaki Ko , Kobayashi Masayoshi , Hara Ayaka , Yamaki Tomohiro , Matsutani Tomoo , Iwadate Yasuo
Published: July 2021

The oncological and functional outcomes in glioblastoma (GBM) patients following supratotal resection (SupTR), involving complete resection of contrast-enhancing enhanced (CE) tumors and areas of methionine (Met) uptake on 11C-met positron emission tomography (Met-PET), are unknown. We conducted a retrospective review in newly diagnosed, IDH1 wild-type GBM patients, comparing SupTR with gross total resection (GTR), in which only CE tumor tissue was resected. All patients underwent standard radiotherapy and temozolomide treatment, and were followed for tumor recurrence and overall survival (OS). Among the 30 patients included in this study, 7 underwent SupTR and 23 underwent GTR. Awake craniotomy with cortical and subcortical mapping was more frequently performed in the SupTR group than in the GTR group. During the follow-up period, significantly different patterns of disease progression were observed between groups. Although more than 80% of recurrences were local in the GTR group, all recurrences in the SupTR group were distant. Median OS in the GTR and SupTR groups was 18.5 months (95% confidence interval [CI] 14.2–35.1) and not reached (95% CI 30.5-not estimable), respectively; this difference was statistically significant (p = 0.03 by log-rank test). No postoperative neurocognitive decline was evident in patients who underwent SupTR. Compared to GTR alone, aggressive resection of both CE tumors and areas with Met uptake (SupTR) under awake craniotomy with functional mapping results in a survival benefit associated with better local control and neurocognitive preservation.
Polarization-insensitive GaN metalenses at visible wavelengths
Authors: Chen Meng-Hsin , Yen Cheng-Wei , Guo Chia-Chun , Su Vin-Cent , Kuan Chieh-Hsiung , Lin Hoang Yan
Published: July 2021

The growth of wide-bandgap materials on patterned substrates has revolutionized the means with which we can improve the light output power of gallium nitride (GaN) light-emitting diodes (LEDs). Conventional patterned structure inspection usually relies on an expensive vacuum-system-required scanning electron microscope (SEM) or optical microscope (OM) with bulky objectives. On the other hand, ultra-thin metasurfaces have been widely used in widespread applications, especially for converging lenses. In this study, we propose newly developed, highly efficient hexagon-resonated elements (HREs) combined with gingerly selected subwavelength periods of the elements for the construction of polarization-insensitive metalenses of high performance. Also, the well-developed fabrication techniques have been employed to realize the high-aspect-ratio metalenses working at three distinct wavelengths of 405, 532, and 633 nm with respective diffraction-limited focusing efficiencies of 93%, 86%, and 92%. The 1951 United States Air Force (USAF) test chart has been chosen to characterize the imaging capability. All of the images formed by the 405-nm-designed metalens show exceptional clear line features, and the smallest resolvable features are lines with widths of 870 nm. To perform the inspection capacity for patterned substrates, for the proof of concept, a commercially available patterned sapphire substrate (PSS) for the growth of the GaN LEDs has been opted and carefully examined by the high-resolution SEM system. With the appropriately chosen metalenses at the desired wavelength, the summits of structures in the PSS can be clearly observed in the images. The PSS imaging qualities taken by the ultra-thin and light-weight metalenses with a numerical aperture (NA) of 0.3 are comparable to those seen by an objective with the NA of 0.4. This work can pioneer semiconductor manufacturing to choose the polarization-insensitive GaN metalenses to inspect the patterned structures instead of using the SEM or the bulky and heavy conventional objectives.
Curcumin induced the cell death of immortalized human keratinocytes (HaCaT) through caspase-independent and caspase-dependent pathways
Authors: Song Wei , Ren Yuan-Jing , Liu Lu-Lu , Zhao Ya-Ying , Li Qi-Fu , Yang Hai-Bo
Published: July 2021

Curcumin from turmeric has good anti-proliferation ability for human keratinocytes (HaCaT). Curcumin-induced apoptosis of HaCaT cells occurs not only through the caspase-dependent pathway but also through the caspase-independent pathway.
Development of a multifunctional neoglycoside auxiliary for applications in glycomics research
Authors: Cheewawisuttichai Thamrongsak , Brichacek Matthew
Published: July 2021

A novel, multifunctional, tetrazine-containing neoglycoside auxiliary has been synthesized in three steps and 28% overall yield.