bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining microenvironment normalization strategies to improve cancer immunotherapy
Authors: Mpekris Fotios , Voutouri Chrysovalantis , Baish James W. , Duda Dan G. , Munn Lance L. , Stylianopoulos Triantafyllos , Jain Rakesh K. 
Published: February 2020

Significance
Immunotherapy has changed the standard of care in cancer treatment, but an estimated 87% of patients currently do not derive long-term benefit from immune checkpoint blocker monotherapy. Therefore, new therapeutic strategies are needed to improve the response rates in patients who are resistant to immune checkpoint inhibition. We have developed a mathematical framework to determine how tumor microenvironment normalization strategies—specifically, vascular and stroma normalization—might improve immunotherapy efficacy. By incorporating complex interactions among various types of cancer cells, immune cells, stromal cells, and the vasculature, as well as physical mechanisms, we provide guidelines for designing effective combinatorial therapeutic strategies and point out areas for future investigation.
Translating narratives and counter-narratives in Ahmet Ümit’sWhen Pera Trees Whisper
Authors: Tekgül-Akın Duygu 
Published: February 2020

AbstractThis study analyzes the translation of political narratives inBeyoğlu’nun En Güzel Abisi, a 2013 detective novel by the best-selling Turkish author Ahmet Ümit. Translated into English by Elke Dixon asWhen Pera Trees Whisper(2014), the novel addresses the events of 6–7 September 1955 that led to the exodus of non-Muslim communities from Istanbul as well as the Gezi Park protests in 2013. The source text reproduces the competing public narratives on issues including ethnic diversity in Turkey, the public mobilization at Gezi, and police intervention during the protests. These narratives play a crucial role, particularly in light of the framing of the protagonist, Chief Inspector Nevzat, as a “good cop” in previous installments of the detective series. In the target text, Elke Dixon translates narratives and counter-narratives for an international readership, conveying the variety of narrative perspectives and framing choices through explicitations, shifts, and other strategies.
Holocene erosion and deposition within a small catchment of the northeastern Borisoglebsk Upland (Central European Russia)
Authors: Belyaev V R , Garankina E V , Shorkunov I G , Konstantinov E A , Rusakov A V , Shishkina Yu V , Andreev P V , Verlova T A 
Published: February 2020

Abstract
During the Holocene, interfluvial landscapes of European plains have experienced alternating periods of relative stability and significant shifts in climate, soil and geomorphological development. Assumed to be an arena of major transformation their evolutionary model is not entirely resolved yet. Based on lithostratigraphic, geomorphologic and soil survey, new results on the Holocene dynamics of fluvial and related processes including landscape stabilization phases for one of the gully catchments draining the Borisoglebsk Upland northeastern slope towards the Nero Lake are presented. Common absence of the early Holocene deposits can be explained by generally negative sediment budget of the catchment. Nevertheless, continuous erosion was not likely whether rare climatic extremes probably were the case. A series of middle Holocene dates obtained by analyzing total organic carbon from organic-accumulative layers of buried soils, lake gyttja and peats highlights strong evidence of the synchronous phase of landscape stabilization in both upper and lower parts of the Puzhbol catchment accompanied by active infilling of small erosion cuts in its middle part. The upper part of the Puzhbol Gully fan sediment shows clear evidence of synchronous accumulation of agrogenic colluvium and gully alluvium since XIIth Century on top of the lake terrace deposits.
Changes of vegetation in the eastern part of Khanka Plain (south of the Russian Far East) at the transition from the Late Pleistocene cryochron (MIS 2) to the Early Holocene
Authors: Belyanin P S , Belyanina N I 
Published: February 2020

Abstract
Reconstructions of the vegetation in the eastern part of the Khanka Plain have been performed for the time interval at the transition from the Late Pleistocene cryochron (MIS 2) to the Holocene. New evidence of considerable changes in the vegetation structure were provided by the palynological studies supplemented with radiocarbon dates on wood fragments and plant detritus recovered from alluvial, lacustrine and mires sediments. It has been found that at the glacial stage MIS 2 the Khanka Plain was dominated by open birch forests with larch and spruce, alternating with Sphagnum mires with shrub birch. Later, at the interstadial, formations typical of southern boreal dark coniferous (needle-leaved) taiga became widely spread. The Early Holocene was marked by wide expansion of broadleaf trees (and first of all, elm and Mongolian oak) in the Khanka Plain ecosystems. Mixed forests with Korean pine became widely spread in the mountains surrounding the lowland. Mires, patches of dark coniferous forests, and open forests of larch persisted on the plains adjoining the lake and on swampy valley floors.
Diachronic analysis of historical and modern landscapes of the Herakleian peninsula
Authors: Ergina E I , Malashina M C , Ergin S M , Melezhik K A 
Published: February 2020

Abstract
The Herakleian Peninsula has a unique geographical location and a long history of development. The methods of historical and geographical research of this territory have been considered. The historical landscapes development dynamics research of the Peninsula has been conducted with the use of cartographic material, satellite images interpretation and a field observations of the territory within the selected time slices. Map analysis of the economic subsystem of the anthropogenic landscapes of the Herakleian Peninsula has been made. Areas of the South -Western and North-Eastern parts of the Peninsula which preserve the historical features of the modern land use formation have been singled out with regard to the specifics of the arrangement of land allotments (klers) in the ancient system of agriculture.
Archaeological sites in the Katynka river basin (Smolensk Region): Paleogeographic study
Authors: Ershova E G , Krenke N A , Kittel P , Lavrenov N G 
Published: February 2020

Abstract
The first results of paleogeographic study at estuary of the Katynka river allow to reconstruct the dynamics of vegetation in this part of the Dnieper floodplain for about 5 millennia and identify some traces of Neolithic, Early Iron Age and Medieval human activity. The most prominent anthropogenic transformation of landscapes (signs of slash-and-burn agriculture) was associated with the late Holocene «Gnezdovo» buried soil dated 2-5 centuries AD.
Late Holocene malacofauna-based paleoenvironmental reconstruction for the Bazaikha River and Tartat River valleys (Krasnoyark Depression, Central Siberia)
Authors: Makarchuk D E , Yamskikh G Yu , Lebedeva N V , Brungardt V O , Bochka V V 
Published: February 2020

Abstract
The results of malacofauna-based palaeoenvironment reconstructions for the Late Holocene in the valleys of Bazaikha and Tartat rivers (Krasnoyarsk depression) are presented. Palynological analyses of the flood-plain deposits and radiocarbon dating complemented malacofaunal analysis. Biodiversity of malacofauna is represented by 7 freshwater species and 15 land species. Species belonging to the Valloniidae Morse, 1864 and Lymnaeidae Rafinesque, 1815 families are dominant in the fossil assemblages. The finding of Gastrocopta theeli shell in the Late Holocene deposits of the Bazaikha section is the first one in the territory of Krasnoyarsk depression. This finding supports the relic, spotted character of the geographic range of this species. Emploting malacofauna proxies and the Eleneva Cave reference section palynological record enabled reconstructing Late Holocene palaeoenvironmental conditions in the area. Malacofauna in the valleys of Bazaikha and Tartat rivers developed under the conditions of gradual increase in heat availability and decreasing annual precipitation and warm-period precipitation during the last 2500 years. A reduction of malacofauna diversity 950 years ago was caused by a change in the precipitation regime.
A 10 000-year pollen and plant macrofossil record from the Losiny Ostrov National Park (Moscow, Russia)
Authors: Miagkaia A , Ershova E 
Published: February 2020

Abstract
The paper presents the first results of pollen and macrofossil analysis of a peat bog located near the Moscow city within the territory of the Losiny Ostrov National Park. Macrofossil data demonstrate that the bog development started from the stage of a spring calcetrophic fen at the very beginning of the Holocene. After 9.9 ka BP it became a meso-oligotrophic herbaceous-sphagnum bog. Pollen data manifest early spread of spruce in the Moscow region (before 10.2 ka BP). Predominance of broad-leaved temperate deciduous forests is characteristic of the Holocene thermal optimum (8.5-4.8 ka BP). The new spread of spruce forests began after 4.8 ka BP. The first signs of deforestation for agriculture date back to 1.8-1.7 ka BP (Early Iron Age). The next massive deforestation for agriculture was recorded 0.7-0.4 ka BP (Middle Age). After the 17th century, anthropogenic activity decreased, as a result of the establishment of the reserve status.
Holocene vegetation and climate changes in the North-Eastern Caucasus (pollen data from mountains and plain peatlands)
Authors: Ryabogina N E , Nasonova E D , Borisov A V , Idrisov I A 
Published: February 2020

Abstract
Dagestan (North-Eastern part of the Caucasus) is characterized by a unique historical and environment development, however, there is little, if no, data on nature changes throughout the Holocene history of the region. In contrast to the much-studied neighboring Caucasus regions, Dagestan remains mostly unexplored from the standpoint of paleoecology. In 2017, we investigated a detailed radiocarbon-dated 185 cm peat sequence from the Shotota swamp located in the mountainous zone of Dagestan. Peat and soil deposits span most of the Holocene (about 9000 years), and they let us study vegetation history of the Eastern Caucasus for the first time. The results of the study show significant discrepancies in the timing and sequence of the expansion of tree species in the Holocene in comparison with Transcaucasia and the Western Caucasus. The second key study, an examination of a 270 cm peat sequence from Arkida swamp, formed in the second half of the Holocene, also provided new paleoenvironmental data on the south of the Caspian lowland. The vegetation of the flat parts of Dagestan, adjacent to the mountainous zone, has been dry and treeless for the last four thousand years, however, humidification fluctuations and vegetation changes were distinguished.
Dynamics of soil salinization in the Nero Lake depression (Upper Volga) in connection with the latest climate change
Authors: Simonova J V , Rusakov A V , Popov A I 
Published: February 2020

Abstract
Over the last 30–40 years, climate changes have resulted in environmental changes within the Upper Volga basin. In this study, an attempt to analyze the soil record of recent climate changes was made. An example of soil evolution induced by climate change was studied on hydromorphic saline soils in the nature reserve of the Varnicy Saline Spring. In a humid climate, soil salinization occurring in discharge areas can quickly change in response to the changed hydrothermal regime because of close relationships between climatic conditions and groundwater systems. In a poorly drained depression, we could observe an increasing soil salinity and developing hydrogenic accumulation of salts, whereas the groundwater salinity was stable.
Superlubricity in phosphorene identified by means of ab initio calculations
Authors: Losi Gabriele , Restuccia Paolo , Righi M C 
Published: February 2020

Abstract
Phosphorene possesses a great potential for tribological applications due to its layered structure and for the capability of phosphorus to reduce friction and adhesion in steel–steel contacts. Here we present a comprehensive analysis of the static tribological properties of phosphorene based on first principles calculations. The most suitable exchange-correlation functional for describing the structural and electronic properties of multilayer phosphorene is carefully selected. The interlayer binding energy and shear strength are then calculated for two relative orientations of the layers. Layers stacked with the same orientation (armchair–armchair and zigzag–zigzag) are slippery as common solid lubricants, as MoS2 and graphite. While the armchair–zigzag orientation shows a remarkable superlubricity, with a reduction of one order of magnitude for the shear stress. We uncover the microscopic origin of such superlubric phase by analyzing the electronic charge at the layer interface.
Repetitive readout enhanced by machine learning
Authors: Liu Genyue , Chen Mo , Liu Yi-Xiang , Layden David , Cappellaro Paola 
Published: February 2020

Abstract
Single-shot readout is a key component for scalable quantum information processing. However, many solid-state qubits with favorable properties lack the single-shot readout capability. One solution is to use the repetitive quantum-non-demolition readout technique, where the qubit is correlated with an ancilla, which is subsequently read out. The readout fidelity is therefore limited by the back-action on the qubit from the measurement. Traditionally, a threshold method is taken, where only the total photon count is used to discriminate qubit state, discarding all the information of the back-action hidden in the time trace of repetitive readout measurement. Here we show by using machine learning (ML), one obtains higher readout fidelity by taking advantage of the time trace data. ML is able to identify when back-action happened, and correctly read out the original state. Since the information is already recorded (but usually discarded), this improvement in fidelity does not consume additional experimental time, and could be directly applied to preparation-by-measurement and quantum metrology applications involving repetitive readout.
ShinySOM: graphical SOM-based analysis of single-cell cytometry data
Authors: Kratochvíl Miroslav , Bednárek David , Sieger Tomáš , Fišer Karel , Vondrášek Jiří 
Published: February 2020

Abstract

Summary
ShinySOM offers a user-friendly interface for reproducible, high-throughput analysis of high-dimensional flow and mass cytometry data guided by self-organizing maps. The software implements a FlowSOM-style workflow, with improvements in performance, visualizations and data dissection possibilities. The outputs of the analysis include precise statistical information about the dissected samples, and R-compatible metadata useful for the batch processing of large sample volumes.

Availability and implementation
ShinySOM is free and open-source, available online at gitlab.com/exaexa/ShinySOM.

Supplementary information
Supplementary data are available at Bioinformatics online.
CPFD simulation on particle behaviour in an entrained-flow gasifier
Authors: Liang Yongshi , Guo Cliff Y , Zhao Xianglong , Qin Qiang , Cheng Yi , He Lixin 
Published: February 2020

Abstract
A computational particle fluid dynamics simulation model for entrained-flow gasification was established in this study. The simulation results agree with the experimental data. The detailed particle information and residence-time distribution were obtained by injecting particle tracers in the simulation. The results show that the particles in the gasifier can be classified into three flowing zones, i.e. a fast-flowing zone, a recirculation zone and a spreading zone. The criterion for this classification was also provided. The rapid gas expansion caused by the fast reactions plays a significant role in forming the particle stream into these three zones. It accelerates the particles in the centre of the gasifier while pushing the particles near the expansion edge into the gas recirculation. Also, the concentrated oxygen distribution in the gasifier results in the formation of high- and low-temperature regions. The particles in the fast-flowing zone flow directly through the high-temperature region and most of these particles in this zone were fully reacted with a short residence time. Since particles in the recirculation zone are in a relatively low-temperature region, most of these particles are not fully gasified, although with a long residence time. The rest of particles in the spreading zone show moderate properties between the above two zones.
Metal-Organic Framework Stationary Phases for One- and Two-Dimensional Micro-Gas Chromatographic Separations of Light Alkanes and Polar Toxic Industrial Chemicals
Authors: Read Douglas H , Sillerud Colin H , Whiting Joshua J , Achyuthan Komandoor E 
Published: February 2020

Abstract
Despite promising advances with metal-organic frameworks (MOFs) as stationary phases for chromatography, the application of MOFs for one- and two-dimensional micro-gas chromatography (μGC and μGC × μGC) applications has yet to be shown. We demonstrate for the first time, μGC columns coated with two different MOFs, HKUST-1 and ZIF-8, for the rapid separation of high volatility light alkane hydrocarbons (natural gas) and determined the partition coefficients for toxic industrial chemicals, using μGC and μGC × μGC systems. Complete separation of natural gas components, methane through pentane, was completed within 1 min, with sufficient resolution to discriminate n-butane from i-butane. Layer-by-layer controlled deposition cycles of the MOFs were accomplished to establish the optimal film thickness, which was validated using GC (sorption thermodynamics), quartz-crystal microbalance gravimetric analysis and scanning electron microscopy. Complete surface coverage was not observed until after ~17 deposition cycles. Propane retention factors with HKUST-1-coated μGC and a state-of-the-art polar, porous-layer open-tubular (PLOT) stationary phase were approximately the same at ~7.5. However, with polar methanol, retention factors with these two stationary phases were 748 and 59, respectively, yielding methanol-to-propane selectivity factors of ~100 and ~8, respectively, a 13-fold increase in polarity with HKUST-1. These studies advance the applications of MOFs as μGC stationary phase.
Pelacarsen for lowering lipoprotein(a): implications for patients with chronic kidney disease
Authors: Fernandez-Prado Raul , Perez-Gomez Maria Vanessa , Ortiz Alberto 
Published: February 2020

AbstractChronic kidney disease (CKD) patients are at an increased risk of cardiovascular disease (CVD) and statins may not be protective in advanced CKD. The reasons for the limited efficacy of statins in advanced CKD are unclear, but statins may increase plasma levels of the highly atherogenic molecule lipoprotein(a), also termed Lp(a), as well as PCSK9 (protein convertase subtilisin/kexin type 9) levels. Lp(a) has also been linked to calcific aortic stenosis, which is common in CKD. Moreover, circulating Lp(a) levels increase in nephrotic syndrome with declining renal function and are highest in patients on peritoneal dialysis. Thus, the recent publication of the Phase 2 randomized controlled trial of pelacarsen [also termed AKCEA-APO(a)-LRx and TQJ230], a hepatocyte-directed antisense oligonucleotide targeting the LPA gene messenger RNA, in persons with CVD should be good news for nephrologists. Pelacarsen safely and dose-dependently decreased Lp(a) levels by 35–80% and a Phase 3 trial [Lp(a)HORIZON, NCT04023552] is planned to run from 2020 to 2024. Unfortunately, patients with estimated glomerular filtration rate &lt;60 mL/min or urinary albumin:creatinine ratio &gt;100 mg/g were excluded from Phase 2 trials and those with ‘significant kidney disease’ will be excluded from the Phase 3 trial. Optimized exclusion criteria for Lp(a)HORIZON would provide insights into the role of Lp(a) in CVD in CKD patients.
Ecosystem consequences of multi-trait response to environmental changes in Japanese medaka, Oryzias latipes
Authors: Diaz Pauli Beatriz , Edeline Eric , Evangelista Charlotte 
Published: February 2020

AbstractIntraspecific trait variation has large effects on the ecosystem and is greatly affected by human activities. To date, most studies focused on single-trait analyses, while considering multiple traits is expected to better predict how an individual interacts with its environment. Here, we used a mesocosm experiment with fish Oryzias latipes to test whether individual growth, boldness and functional traits (feeding rate and stoichiometric traits) formed one functional pace-of-life syndrome (POLS). We then tested the effects of among-individual mean and variance of fish functional POLSs within mesocosms on invertebrate community (e.g. zoobenthos and zooplankton abundances) and ecosystem processes (e.g. ecosystem metabolism, algae stock, nutrient concentrations). Stoichiometric traits correlated with somatic growth and behaviours, forming two independent functional POLS (i.e. two major covariance axes). Mean values of the first syndrome were sex- and environment-dependent and were associated with (i) long-term (10 generations; 4 years) selection for small or large body size resulting in contrasting life histories and (ii) short-term (6 weeks) effects of experimental treatments on resource availability (through manipulation of light intensity and interspecific competition). Specifically, females and individuals from populations selected for a small body size presented fast functional POLS with faster growth rate, higher carbon body content and lower boldness. Individuals exposed to low resources (low light and high competition) displayed a slow functional POLS. Higher mesocosm mean and variance values in the second functional POLS (i.e. high feeding rate, high carbon:nitrogen body ratio, low ammonium excretion rate) were associated to decreased prey abundances, but did not affect any of the ecosystem processes. We highlighted the presence of functional multi-trait covariation in medaka, which were affected by sex, long-term selection history and short-term environmental conditions, that ultimately had cascading ecological consequences. We stressed the need for applying this approach to better predict ecosystem response to anthropogenic global changes.