bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study on incipient shear stress of consolidated cohesive sediment
Authors: Shu Caiwen , Tan Guangming , Chen Peng , Wang Jun , Lv Ping
Published: September 2020

This paper analyzes the incipient motion mechanism of consolidated cohesive sediment. An experimental device based on previous studies was designed to investigate the influencing factors of the incipient shear stress, including the consolidation time, the density of dry bulk, cohesive particles content, and the composition of sediment mixtures. The experimental results indicated that the incipient shear stress of cohesive sediment increased with the increase of consolidation time, dry bulk density, and content of cohesive particles. The incipient motion mechanism of cohesive particles was further investigated using experimental data and theoretical analysis. A formula of the incipient shear stress for cohesive sediment was proposed herein, which is related to both the content of cohesive particles and the relative dry bulk density. The proposed formula was validated by the experimental data, and the calculated values of incipient shear stress using the formula were in good agreement with the experimental results.
MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples
Authors: Miya Masaki , Gotoh Ryo O. , Sado Tetsuya
Published: September 2020

We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.
Gravity of Dharwar Craton, Southern Indian Shield
Authors: Rao J. V. Rama , Kumar B. Ravi , Kumar Manish , Singh R. B. , Veeraiah B.
Published: September 2020

Dharwar craton (DC), by far the largest geological domain in South Indian Shield, occupying about 0.5 million sq. km area, is well-studied terrain both for regional geoscientific aspects and as part of mineral exploration over several important blocks such as the greenstone belts, ultramafic complexes, granite-gneissic terrain and the Proterozoic sediments of Cuddapah basin. The re-look into regional gravity data offers several insights into nature of crust, sub-divisions within the craton, bedrock geology in the covered areas and mineral potentiality of this ancient and stable crust. The regional gravity profiles drawn across the south Indian region mainly suggest that the area can be divided into five domains as Western Dharwar craton (WDC), Central Dharwar craton (CDC), Eastern Dharwar craton (EDC 1), transitory zone of EDC (EDC 2) and Eastern Ghats mobile belt (EGMB) areas. The Bouguer gravity anomaly pattern also questions some of the earlier divisions like eastern margin of Chitradurga schist belt between the WDC and EDC and the boundary of DC with southern granulite terrain (SGT) as they do not restrict at these main boundaries.

In this study, mainly four issues are addressed by qualitative and quantitative analysis of regional gravity data and those revealed significant inferences. (1) A distinct gravity character in central part of south Indian shield area occupying about 60, 000 sq. km, suggests that the transitory crustal block, faulted on both sides and uplifted. This area designated as central Dharwar craton (CDC) is characterized with schist belts having characters of both parts of western and eastern Dharwar craton. This inference also opens up the debate about the boundary between western and eastern parts of the craton. Another significant inference is the extension of major schist belts beneath both Deccan volcanic province (DVP) in northwestern part and Cuddapah basin (CB) in southeastern part. (2) Eastern Dharwar craton is reflected as two distinct domains of different gravity characters; one populated with number of circular gravity lows and a few linear gravity high closures indicative of plutonic and volcanic activity and another domain devoid of these intrusive younger granites or schist belts. (3) Large wave length gravity highs occupying thousands of sq.km area and those not relatable to surface geology in eastern Dharwar craton that may have significance for mineral exploration. (4) Gravity data was subjected to further processing like two dimensional modeling which have yielded insights into crustal architecture beneath the Dharwar craton, crustal scale lineaments, craton-mobile belt contact zone and younger intrusives.
Role of Energy Dispersive XRF (ED-XRF) in Development of Rare Earth Element-2, International Certified Standard Reference Material: Ambiguities and Constraints
Authors: Raju P. V. Sunder
Published: September 2020

The REE-2 is a carbonatite sample with rare earth elements provided from a Canadian mining company and distributed by Canadian Certified Reference Materials (CCRM), Canada. The reference material was provided to participate in the testing process (round-robin) and CSIR-NGRI, Hyderabad, state of the art analytical technique Energy Dispersive X-ray fluorescence (EDXRF) also contributed to the development of this (REE −2) reference material. In this paper, the efficacy of analytical protocol developed and comparing the results with twenty one industrial, commercial and government laboratories across globe in an inter-laboratory measurement program are presented. The CSIR-NGRI, EDXRF analytical facility contribution and steps to overcome during REE-2 development are briefly discussed. This contribution is to highlight the international analytical standards and protocols maintained at EDXRF laboratory vis-à-vis international laboratories.
Rock Mass Characterization for the Underground Surge Pool Cavern – A Case Study, India
Authors: Naithani A. K. , Jain Prasnna , Rawat D. S. , Singh L. G.
Published: September 2020

Underground surge pool cavern for the storage and lifting of water is being constructed in the part of Telangana State of India. For better rock mass characterization and support design, 3D engineering geological mapping was carried for the heading portion of the surge pool. 3D geologic mapping of heading portion is very important for large underground cavern to know about the cavern behavior during benching down. The direction of the longest axis of the cavern was finalized based on the in-situ hydrofracturing testing inside the deep borehole. The assessment of tunnel quality index ‘Q’ for the exposed granitic rock mass was done based on the information available of the rock joints and their nature, 3D geological mapping and in-situ stress measurement. Roof support and wall support pressure was estimatedbased on Q-values, and in this case applicable for the non-squeezing ground condition. For structural stability of crown and walls, rock support arrangement was recommended based on NMT technology and geological conditions of site, which includes steel fibre reinforced shotcrete, grouting, rock bolt and drainage hole provisions. The capacity of support system is determined to evaluate the efficacy of the proposed support system.
Evaluation of Groundwater Vulnerability to Pollution using GIS Based DRASTIC Method in Koradi, India - A Case Study
Authors: Janipella Ramesh , Quamar Rafat , Sanam Ramya , Jangam Chandrakanth , Balwant Pandurang , Jyothi Veligeti , Padmakar C. , Pujari Paras R.
Published: September 2020

Groundwater (GW) contamination due to urbanization, industrialization and agriculture is a major environmental problem in India. The present case study aims to estimate the vulnerability of the aquifer with the help of GIS based DRASTIC method. A micro watershed, characterized by Granites and Gondwana Formation in the vicinity of Koradi, 15 km from Nagpur in Central India has been considered. The DRASTIC method accounts for hydrogeological parameters like depth to water, net recharge, aquifer media, soil media, impact of vadose zone and hydraulic conductivity. The DRASTIC index (DI) for GW vulnerability to pollution is calculated as the sum of the product of ratings and weights assigned to each of the parameter on the scale of 1 to 10 and 1 to 5 respectively. A Groundwater vulnerability map has been prepared using the Arc GIS software (Version 10.1) and it delineates the total study area into two vulnerable zones with vulnerability score ranging from 107 to 142 and indicates that 33% and 67% of the area lies in low and moderate vulnerability zones respectively. The vulnerability score as obtained is also verified with field data.
Don’t Go Chasing Waterfalls: Motion Aftereffects and the Dynamic Snapshot Theory of Temporal Experience
Authors: McKenna Camden Alexander
Published: September 2020

The philosophical investigation of perceptual illusions can generate fruitful insights in the study of subjective time consciousness. However, the way illusions are interpreted is often controversial. Recently, proponents of the so-called dynamic snapshot theory have appealed to the Waterfall Illusion, a kind of motion aftereffect, to support a particular view of temporal consciousness according to which experience is structured as a series of instantaneous snapshots with dynamic qualities. This dynamism is meant to account for familiar features of the phenomenology of time, such as succession, continuity, and change. Previous theories have typically appealed to a subjective present occupying an interval of time; that is, a “specious present.” I argue, through analysis of motion aftereffect illusions and the rare condition of akinetopsia, i.e. motion-blindness, that the Waterfall Illusion fails to support the dynamic snapshot theory as intended. Furthermore, I suggest that future theories of subjective time should see temporal phenomenology as the result of non-localised processes closely tied to the mechanism underlying consciousness generally.
Development of wellbore compound blockage removal technology to reduce production loss in the ultra-deep and high-sulfur Yuanba gas field
Authors: Luo Wei , Wu Qiang
Published: September 2020

Wellbore compound blockage occurs in several wells of Yuanba gas field during production, which seriously affects the stable production. The prior treatment with inorganic acid injection does not show a good effect. Therefore, it is urgent to establish an effective blockage removal technology. In this work, the composition analysis of compound blockage samples is firstly carried out. Then, two types of acid solution and barite dissolvent for different types of wellbore blockage are developed. Finally, the corresponding crafts of wellbore blockage removal for different degrees of wellbore blockage are set up. Analysis results show that the inorganic components of blockages are mainly FeS2, CaCO3, BaSO4, and SiO2. The organic components of blockages are mainly the decomposition products of macromolecular materials and the asphaltene. There are differences in the components of blockages between different wells in Yuanba gas field. Some wells are the type of organic-based blockage, while others are the type of inorganic-based blockage. The field application shows that the developed wellbore compound blockage removal technology has successfully guided the in situ removal operation of eight wells in Yuanba gas field, ensuring the smooth completion of production task of this gas field. This effective blockage removal technology can be extended to similar ultra-deep and high-sulfur gas field.
Timing van de PSMA PET/CT-scan bij biochemisch recidief na radicale prostatectomie
Authors: Luiting Henk B. , van Leeuwen Pim J. , Remmers Sebastiaan , Donswijk Maarten , Busstra Martijn B. , Bakker Ingrid L. , Brabander Tessa , Stokkel Marcel , van der Poel Henk G. , Roobol Monique J.
Published: September 2020

Samenvatting

We presenteren hier een model dat de kans op het detecteren van een prostaatkankerrecidief buiten de prostaatfossa op de prostaatspecifiek membraanantigeen (PSMA) positronemissietomografie/computertomografie (PET/CT)-scan voorspelt bij patiënten met een biochemisch recidief (BCR) na radicale prostatectomie (RP). 419 patiënten met een BCR prostaatspecifiek antigeen (PSA) < 2,0 ng/ml) na RP zonder hormoontherapie die een 68Ga-PSMA PET/CT-scan ondergingen, werden geïncludeerd. Met multivariabele logistische regressieanalyse werden voorspellers voor de detectie van prostaatkankerrecidief buiten de prostaatfossa geïdentificeerd. Bij een mediane PSA-waarde van 0,40 ng/ml (interkwartielafstand 0,30–0,70) werd met PSMA PET/CT bij 174 (42%) patiënten een prostaatkankerrecidief buiten de prostaatfossa gedetecteerd. Significante voorspellers voor het detecteren van prostaatkankerrecidief buiten de prostaatfossa waren de PSA-waarde ten tijde van de PSMA PET/CT-scan en de Gleason-score, het lymfeklierstadium en het snijrandstadium van het RP-preparaat. De PSA-waarde ten tijde van de PSMA PET/CT en de Gleason-score, het lymfeklierstadium en het snijrandstadium van het RP-preparaat waren belangrijke voorspellers voor het vinden van prostaatkankerrecidief buiten de prostaatfossa met de PSMA PET/CT. Het dashboard (https://psma.prostatecancer-riskcalculator.com/) kan gebruikt worden om het klinisch meest relevante moment voor het verrichten van een PSMA PET/CT-scan te bepalen.
Solutions with peaks for a coagulation-fragmentation equation. Part II: Aggregation in peaks
Authors: Bonacini Marco , Niethammer Barbara , Velázquez Juan J.L.
Published: September 2020

The aim of this two-part paper is to investigate the stability properties of a special class of solutions to a coagulation-fragmentation equation. We assume that the coagulation kernel is close to the diagonal kernel, and that the fragmentation kernel is diagonal. In a companion paper we constructed a two-parameter family of stationary solutions concentrated in Dirac masses, and we carefully studied the asymptotic decay of the tails of these solutions, showing that this behaviour is stable. In this paper we prove that for initial data which are sufficiently concentrated, the corresponding solutions approach one of these stationary solutions for large times.
Lynching and Local Justice
Authors: Jung Danielle F. , Cohen Dara Kay
Published: September 2020

What are the social and political consequences of poor state governance and low state legitimacy? Under what conditions does lynching – lethal, extralegal group violence to punish offenses to the community – become an acceptable practice? We argue lynching emerges when neither the state nor its challengers have a monopoly over legitimate authority. When authority is contested or ambiguous, mass punishment for transgressions can emerge that is public, brutal, and requires broad participation. Using new cross-national data, we demonstrate lynching is a persistent problem in dozens of countries over the last four decades. Drawing on original survey and interview data from Haiti and South Africa, we show how lynching emerges and becomes accepted. Specifically, support for lynching most likely occurs in one of three conditions: when states fail to provide governance, when non-state actors provide social services, or when neighbors must rely on self-help.
Global well-posedness and decay estimates of strong solutions to the nonhomogeneous Boussinesq equations for magnetohydrodynamics convection
Authors: Zhong Xin
Published: September 2020

We deal with an initial boundary value problem of nonhomogeneous Boussinesq equations for magnetohydrodynamics convection in two-dimensional domains. We prove that there is a unique global strong solution. Moreover, we show that the temperature converges exponentially to zero in H1 as time goes to infinity. In particular, the initial data can be arbitrarily large and vacuum is allowed. Our analysis relies on energy method and a lemma of Desjardins (Arch. Rational Mech. Anal. 137:135–158, 1997).
Many Ways to be Right: Cross-Pressured Voters in Western Europe
Authors: Gidron Noam
Published: September 2020

Mainstream parties in Western Europe are increasingly struggling to hold together their base of support. As a lens for exploring this changing electoral landscape, this article focuses on the growing share of the electorate that is cross-pressured between conservative and progressive attitudes on economic and cultural issues. It argues that a stable asymmetry characterizes Western European mass attitudes: while support for the left is common among voters with progressive attitudes on both issues, it is enough to be conservative on one issue to turn right. Analyzing survey data collected from 1990 to 2017, the study shows that cross-pressures are resolved in favor of the right and examines the trade-offs this poses to center-right parties. These findings contribute to debates on electoral dealignment and realignment and shed light on the electoral choices of the center-right.
Bridging kinetic plasma descriptions and single-fluid models
Authors: Crestetto A. , Deluzet F. , Doyen D.
Published: September 2020

The purpose of this paper is to bridge kinetic plasma descriptions and low-frequency single-fluid models. More specifically, the asymptotics leading to magnetohydrodynamic regimes starting from the Vlasov–Maxwell system are investigated. The analogy with the derivation, from the Vlasov–Poisson system, of a fluid representation for ions coupled to the Boltzmann relation for electrons is also outlined. The aim is to identify asymptotic parameters explaining the transitions from one microscopic description to a macroscopic low-frequency model. These investigations provide groundwork for the derivation of multi-scale numerical methods, model coupling or physics-based preconditioning.
One size does not fit all: Trajectories of body image development and their predictors in early adolescence
Authors: Lacroix Emilie , Atkinson Melissa J. , Garbett Kirsty M. , Diedrichs Phillippa C.
Published: September 2020

Background: Negative body image predicts many adverse outcomes. The current study prospectively examined patterns of body esteem development in early adolescence and identified predictors of developmental subtypes. Methods: 328 girls and 429 boys reported annually across a 4-year period (Mage at baseline = 11.14, SD = 0.35) on body esteem, appearance ideal internalization, perceived sociocultural pressures, appearance comparisons, appearance-related teasing, self-esteem, positive and negative affect, and dietary restraint. We performed latent class growth analyses to identify the most common trajectories of body esteem development and examine risk and protective factors for body image development. Results: Three developmental subgroups were identified: (a) high body esteem (39.1%); (b) moderate body esteem (46.1%); and (c) low body esteem (14.8%). Body esteem was stable within the low trajectory and there were minor fluctuations in the high and moderate trajectories. Greater appearance-related teasing, lower self-esteem, less positive affect, and higher dietary restraint predicted the low trajectory, whereas higher self-esteem and lower dietary restraint best predicted the high trajectory. Conclusions: Low body esteem appears to be largely stable from age 11 years. Prevention programming may be enhanced by incorporating components to address transdiagnostic resilience factors such as self-esteem and positive affect.
Stress–response relationships related to ageing and death of orthodox seeds: a study comparing viability and RNA integrity in soya bean (Glycine max) cv. Williams 82
Authors: Walters Christina , Fleming Margaret B. , Hill Lisa M. , Dorr Emma J. , Richards Christopher M.
Published: September 2020

Characterizing non-lethal damage within dry seeds may allow us to detect early signs of ageing and accurately predict longevity. We compared RNA degradation and viability loss in seeds exposed to stressful conditions to quantify relationships between degradation rates and stress intensity or duration. We subjected recently harvested (‘fresh’) ‘Williams 82’ soya bean seeds to moisture, temperature and oxidative stresses, and measured time to 50% viability (P50) and rate of RNA degradation, the former using standard germination assays and the latter using RNA Integrity Number (RIN). RIN values from fresh seeds were also compared with those from accessions of the same cultivar harvested in the 1980s and 1990s and stored in the refrigerator (5°C), freezer (−18°C) or in vapour above liquid nitrogen (−176°C). Rates of viability loss (P50−1) and RNA degradation (RIN⋅d−1) were highly correlated in soya bean seeds that were exposed to a broad range of temperatures [holding relative humidity (RH) constant at about 30%]. However, the correlation weakened when fresh seeds were maintained at high RH (holding temperature constant at 35°C) or exposed to oxidizing agents. Both P50−1 and RIN⋅d−1 parameters exhibited breaks in Arrhenius behaviour near 50°C, suggesting that constrained molecular mobility regulates degradation kinetics of dry systems. We conclude that the kinetics of ageing reactions at RH near 30% can be simulated by temperatures up to 50°C and that RNA degradation can indicate ageing prior to and independent of seed death.
Photon and photon–neutron experimental dosimetry in Grid therapy with 18 MV photon beams
Authors: Tajiki Sareh , Gholami Somayeh , Esfahani Mahbod , Rastjoo Ali , Hakimi Amir , Beheshti Amir K. , Meigooni Ali
Published: September 2020

Propose:

Spatially fractionated Grid radiation therapy (SFGRT) in an effective technique for bulky and radio-sensitive tumours. SFGRT using a constructed block has been used to evaluate the photon and photo-neutron (PN) dose measurement in 18-MV photon beam energy.

Methods and materials:

A mounted Grid block on to a Varian Clinac 2100c linear accelerator was used to perform photon dosimetry. The percentage depth dose, in-plane and cross-plane beam profile and output factor was measured by ionization chamber in water. The PN contamination was measured after photon dosimetry using the combination of thermoluminescence dosimetry types 600 and 700, and Polycarbonate Film dosimeters on the surface and in the maximum depth dose (dmax) of solid water™ slabs.

Results:

The valley-to-peak ration for 6 and 18 MV photon beams obtained from the beam profiles was ~35 and 72%, respectively. Fast and thermal PN equivalent dose decreased in the Grid field compared to an open field (without Grid).

Conclusion:

The Grid therapy dosimetry compared to the conventional radiotherapy (without the grid) the production of fast and thermal neutrons were reduced. Using of a Grid block in high-energy photon beams for a long period of the treatment continuously might be a new source of contamination due to the interaction of photon beam resulting the activation of the Grid block
Chronische, postoperative Schmerzen
Authors: Grolimund Johannes
Published: September 2020

Zusammenfassung. Chronische, postoperative Schmerzen sind häufig, so auch bei Patienten nach handchirurgischen Eingriffen. Bezüglich der Identifikation von Risiko- und Schutzfaktoren hinsichtlich chronischer, postoperativer Schmerzen wurden beträchtliche Fortschritte erzielt. Psychologische Aspekte – das heisst kognitive, affektive und solche auf Verhaltensebene – einschliesslich Depressivität, Angst, Schmerzkatastrophisieren und Vertrauen des Patienten in den Behandler spielen eine zentrale Rolle für die Vorhersage der Wahrscheinlichkeit, chronische, postoperative Schmerzen zu entwickeln. Diese Faktoren sind messbar und dienen als wichtige Ansatzpunkte für spezifische, psychologische Interventionen durch den Chirurgen oder ein interdisziplinäres Team. Die empirische Evaluation dieser Behandlungen zeigt, dass psychologische als auch interdisziplinäre, multimodale Interventionen von chirurgischen Patienten akzeptiert werden und in der Lage sind, postoperative Schmerzen und Beeinträchtigung zu reduzieren.
Muis Receives 2019 Natural Hazards Section Award for Graduate Research
Authors:   AGU
Published: September 2020

Sanne Muis received the 2019 Natural Hazards Section Award for Graduate Research at AGU’s Fall Meeting 2019, held 9–13 December in San Francisco, Calif. The award recognizes “outstanding contributions to natural hazards research and is judged based on impact or potential impact to the field.”
Single-cell sequencing techniques from individual to multiomics analyses
Authors: Kashima Yukie , Sakamoto Yoshitaka , Kaneko Keiya , Seki Masahide , Suzuki Yutaka , Suzuki Ayako
Published: September 2020

Here, we review single-cell sequencing techniques for individual and multiomics profiling in single cells. We mainly describe single-cell genomic, epigenomic, and transcriptomic methods, and examples of their applications. For the integration of multilayered data sets, such as the transcriptome data derived from single-cell RNA sequencing and chromatin accessibility data derived from single-cell ATAC-seq, there are several computational integration methods. We also describe single-cell experimental methods for the simultaneous measurement of two or more omics layers. We can achieve a detailed understanding of the basic molecular profiles and those associated with disease in each cell by utilizing a large number of single-cell sequencing techniques and the accumulated data sets.
Single-cell multiomics: technologies and data analysis methods
Authors: Lee Jeongwoo , Hyeon Do Young , Hwang Daehee
Published: September 2020

Advances in single-cell isolation and barcoding technologies offer unprecedented opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk multiomics analyses, such as multidimensional genomic and proteogenomic analyses, have proven beneficial for obtaining a comprehensive understanding of cellular events. This benefit has facilitated the development of single-cell multiomics analysis, which enables cell type-specific gene regulation to be examined. The cardinal features of single-cell multiomics analysis include (1) technologies for single-cell isolation, barcoding, and sequencing to measure multiple types of molecules from individual cells and (2) the integrative analysis of molecules to characterize cell types and their functions regarding pathophysiological processes based on molecular signatures. Here, we summarize the technologies for single-cell multiomics analyses (mRNA-genome, mRNA-DNA methylation, mRNA-chromatin accessibility, and mRNA-protein) as well as the methods for the integrative analysis of single-cell multiomics data.
Human Cell Atlas and cell-type authentication for regenerative medicine
Authors: Panina Yulia , Karagiannis Peter , Kurtz Andreas , Stacey Glyn N. , Fujibuchi Wataru
Published: September 2020

In modern biology, the correct identification of cell types is required for the developmental study of tissues and organs and the production of functional cells for cell therapies and disease modeling. For decades, cell types have been defined on the basis of morphological and physiological markers and, more recently, immunological markers and molecular properties. Recent advances in single-cell RNA sequencing have opened new doors for the characterization of cells at the individual and spatiotemporal levels on the basis of their RNA profiles, vastly transforming our understanding of cell types. The objective of this review is to survey the current progress in the field of cell-type identification, starting with the Human Cell Atlas project, which aims to sequence every cell in the human body, to molecular marker databases for individual cell types and other sources that address cell-type identification for regenerative medicine based on cell data guidelines.
Prognostic value of tertiary lymphoid structure and tumour infiltrating lymphocytes in oral squamous cell carcinoma
Authors: Li Qunxing , Liu Xiangqi , Wang Dikan , Wang Yanqiong , Lu Huanzi , Wen Shuqiong , Fang Juan , Cheng Bin , Wang Zhi
Published: September 2020

Tertiary lymphoid structures (TLS) are ectopic lymphoid structures in cancers that are largely associated with favourable prognosis. However, the prognostic value of TLSs in oral squamous cell carcinoma (OSCC) is largely unknown, and the association between tumour infiltrating lymphocytes (TILs) and TLSs has been rarely explored in OSCC. In this study, associated markers of TLS, including peripheral node address (PNAd) in high endothelial venules, CD20 in B cells and CD3 in T cells, were examined in 168 OSCC patients, and survival analysis was performed between TLS-positive and TLS-negative cohorts. We detected the presence of TILs by staining CD8+ cytotoxic T cells and CD57+ NK cells as well. TLSs appeared as highly organized structures in 45 (26.8%) cases. TLS-positive patients had a better 5-year overall survival (OS) rate (88.9% vs. 56.1%, P < 0.001) and relapse-free survival (RFS) rate (88.9% vs. 63.4%, P = 0.002). Moreover, the presence of TLS was an independent prognostic factor for both the 5-year OS rate (hazard ratio [HR] = 3.784; 95% confidence interval [CI], 1.498–9.562) and RFS rate (HR = 3.296; 95% CI, 1.279–8.490) in multivariate analysis. Furthermore, a higher density of CD8+ T cells and CD57+ NK cells was found in TLS-positive sections than in TLS-negative counterparts (P < 0.001), and their combination provided a higher predictive accuracy (AUC = 0.730; 95% CI, 0.654–0.805). In conclusion, our results suggest that TLS is an independent positive prognostic factor for OSCC patients. These findings provide a theoretical basis for the future diagnostic and therapeutic value of TLSs in OSCC treatment.
Cytotoxic CD8+ T cells in cancer and cancer immunotherapy
Authors: Raskov Hans , Orhan Adile , Christensen Jan Pravsgaard , Gögenur Ismail
Published: September 2020

The functions of, and interactions between, the innate and adaptive immune systems are vital for anticancer immunity. Cytotoxic T cells expressing cell-surface CD8 are the most powerful effectors in the anticancer immune response and form the backbone of current successful cancer immunotherapies. Immune-checkpoint inhibitors are designed to target immune-inhibitory receptors that function to regulate the immune response, whereas adoptive cell-transfer therapies use CD8+ T cells with genetically modified receptors—chimaeric antigen receptors—to specify and enhance CD8+ T-cell functionality. New generations of cytotoxic T cells with genetically modified or synthetic receptors are being developed and evaluated in clinical trials. Furthermore, combinatory regimens might optimise treatment effects and reduce adverse events. This review summarises advances in research on the most prominent immune effectors in cancer and cancer immunotherapy, cytotoxic T cells, and discusses possible implications for future cancer treatment.
TET2 directs mammary luminal cell differentiation and endocrine response
Authors: Kim Mi Ran , Wu Meng-Ju , Zhang Yingsheng , Yang Jer-Yen , Chang Chun Ju
Published: September 2020

Epigenetic regulation plays an important role in governing stem cell fate and tumorigenesis. Lost expression of a key DNA demethylation enzyme TET2 is associated with human cancers and has been linked to stem cell traits in vitro; however, whether and how TET2 regulates mammary stem cell fate and mammary tumorigenesis in vivo remains to be determined. Here, using our recently established mammary specific Tet2 deletion mouse model, the data reveals that TET2 plays a pivotal role in mammary gland development and luminal lineage commitment. We show that TET2 and FOXP1 form a chromatin complex that mediates demethylation of ESR1, GATA3, and FOXA1, three key genes that are known to coordinately orchestrate mammary luminal lineage specification and endocrine response, and also are often silenced by DNA methylation in aggressive breast cancers. Furthermore, Tet2 deletion-PyMT breast cancer mouse model exhibits enhanced mammary tumor development with deficient ERα expression that confers tamoxifen resistance in vivo. As a result, this study elucidates a role for TET2 in governing luminal cell differentiation and endocrine response that underlies breast cancer resistance to anti-estrogen treatments.
Environmental variability supports chimpanzee behavioural diversity
Authors: Kalan Ammie K. , Kulik Lars , Arandjelovic Mimi , Boesch Christophe , Haas Fabian , Dieguez Paula , Barratt Christopher D. , Abwe Ekwoge E. , Agbor Anthony , Angedakin Samuel , Aubert Floris , Ayimisin Emmanuel Ayuk , Bailey Emma , Bessone Mattia , Brazzola Gregory , Buh Valentine Ebua , Chancellor Rebecca , Cohen Heather , Coupland Charlotte , Curran Bryan , Danquah Emmanuel , Deschner Tobias , Dowd Dervla , Eno-Nku Manasseh , Michael Fay J. , Goedmakers Annemarie , Granjon Anne-Céline , Head Josephine , Hedwig Daniela , Hermans Veerle , Jeffery Kathryn J. , Jones Sorrel , Junker Jessica , Kadam Parag , Kambi Mohamed , Kienast Ivonne , Kujirakwinja Deo , Langergraber Kevin E. , Lapuente Juan , Larson Bradley , Lee Kevin C. , Leinert Vera , Llana Manuel , Marrocoli Sergio , Meier Amelia C. , Morgan Bethan , Morgan David , Neil Emily , Nicholl Sonia , Normand Emmanuelle , Ormsby Lucy Jayne , Pacheco Liliana , Piel Alex , Preece Jodie , Robbins Martha M. , Rundus Aaron , Sanz Crickette , Sommer Volker , Stewart Fiona , Tagg Nikki , Tennie Claudio , Vergnes Virginie , Welsh Adam , Wessling Erin G. , Willie Jacob , Wittig Roman M. , Yuh Yisa Ginath , Zuberbühler Klaus , Kühl Hjalmar S.
Published: September 2020

Large brains and behavioural innovation are positively correlated, species-specific traits, associated with the behavioural flexibility animals need for adapting to seasonal and unpredictable habitats. Similar ecological challenges would have been important drivers throughout human evolution. However, studies examining the influence of environmental variability on within-species behavioural diversity are lacking despite the critical assumption that population diversification precedes genetic divergence and speciation. Here, using a dataset of 144 wild chimpanzee (Pan troglodytes) communities, we show that chimpanzees exhibit greater behavioural diversity in environments with more variability — in both recent and historical timescales. Notably, distance from Pleistocene forest refugia is associated with the presence of a larger number of behavioural traits, including both tool and non-tool use behaviours. Since more than half of the behaviours investigated are also likely to be cultural, we suggest that environmental variability was a critical evolutionary force promoting the behavioural, as well as cultural diversification of great apes.
Characterization and mitigation of gene expression burden in mammalian cells
Authors: Frei Timothy , Cella Federica , Tedeschi Fabiana , Gutiérrez Joaquín , Stan Guy-Bart , Khammash Mustafa , Siciliano Velia
Published: September 2020

Despite recent advances in circuit engineering, the design of genetic networks in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here, we demonstrate that transiently expressed genes in mammalian cells compete for limited transcriptional and translational resources. This competition results in the coupling of otherwise independent exogenous and endogenous genes, creating a divergence between intended and actual function. Guided by a resource-aware mathematical model, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the use of endogenous miRNAs as elementary components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.
High-efficiency electroporation of chytrid
fungi
Authors: Swafford Andrew J. M. , Hussey Shane P. , Fritz-Laylin Lillian K.
Published: September 2020

Two species of parasitic fungi from the phylum Chytridiomycota (chytrids)
are annihilating global amphibian populations. These chytrid species—Batrachochytrium dendrobatidis and B. salamandrivorans—have high rates of mortality and transmission. Upon
establishing infection in amphibians, chytrids rapidly multiply within the skin and
disrupt their hosts’ vital homeostasis mechanisms. Current disease models suggest that
chytrid fungi locate and infect their hosts during a motile, unicellular ‘zoospore’ life
stage. Moreover, other chytrid species parasitize organisms from across the tree of
life, making future epidemics in new hosts a likely possibility. Efforts to mitigate the
damage and spread of chytrid disease have been stymied by the lack of knowledge about
basic chytrid biology and tools with which to test molecular hypotheses about disease
mechanisms. To overcome this bottleneck, we have developed high-efficiency delivery of
molecular payloads into chytrid zoospores using electroporation. Our electroporation
protocols result in payload delivery to between 75 and 97% of living cells of three
species: B. dendrobatidis, B. salamandrivorans, and a
non-pathogenic relative, Spizellomyces punctatus.
This method lays the foundation for molecular genetic tools needed to establish
ecological mitigation strategies and answer broader questions in evolutionary and cell
biology.
Fine scale spatial investigation of multiple insecticide resistance and underlying target-site and metabolic mechanisms in Anopheles gambiae in central Côte d’Ivoire
Authors: Oumbouke Welbeck A. , Pignatelli Patricia , Barreaux Antoine M. G. , Tia Innocent Z. , Koffi Alphonsine A. , Ahoua Alou Ludovic P. , Sternberg Eleanore D. , Thomas Matthew B. , Weetman David , N’Guessan Raphael
Published: September 2020

Routine monitoring of occurrence, levels and mechanisms of insecticide resistance informs effective management strategies, and should be used to assess the effect of new tools on resistance. As part of a cluster randomised controlled trial evaluating a novel insecticide-based intervention in central Côte d’Ivoire, we assessed resistance and its underlying mechanisms in Anopheles gambiae populations from a subset of trial villages. Resistance to multiple insecticides in An. gambiae s.s. and An. coluzzii was detected across villages, with dose–response assays demonstrating extremely high resistance intensity to the pyrethroid deltamethrin (> 1,500-fold), and mortality following exposure to pyrethroid-treated bednets was low (< 30% mortality in cone bioassays). The 1014F kdr mutation was almost fixed (≥ 90%) in all villages but the 1575Y kdr-amplifying mutation was relatively rare (< 15%). The carbamate and organophosphate resistance-associated Ace-1 G119S mutation was also detected at moderate frequencies (22–43%). Transcriptome analysis identified overexpression of P450 genes known to confer pyrethroid resistance (Cyp9K1, Cyp6P3, and Cyp6M2), and also a carboxylesterase (COEAE1F) as major candidates. Cyp6P3 expression was high but variable (up to 33-fold) and correlated positively with deltamethrin resistance intensity across villages (r2 = 0.78, P = 0.02). Tools and strategies to mitigate the extreme and multiple resistance provided by these mechanisms are required in this area to avoid future control failures.
Magnon magic angles and tunable Hall conductivity in 2D twisted ferromagnetic bilayers
Authors: Ghader Doried
Published: September 2020

Twistronics is currently one of the most active research fields in condensed matter physics, following the discovery of correlated insulating and superconducting phases in twisted bilayer graphene (tBLG). Here, we present a magnonic analogue of tBLG. We study magnons in twisted ferromagnetic bilayers (tFBL) with collinear magnetic order, including exchange and weak Dzyaloshinskii-Moriya interactions (DMI). For negligible DMI, tFBL presents discrete magnon magic angles and flat moiré minibands analogous to tBLG. The DMI, however, changes the picture and renders the system much more exotic. The DMI in tFBL induces a rich topological magnon band structure for any twist angle. The twist angle turns to a control knob for the magnon valley Hall and Nernst conductivities. Gapped flat bands appear in a continuum of magic angles in tFBL with DMI. In the lower limit of the continuum, the band structure reconstructs to form several topological flat bands. The luxury of twist-angle control over band gaps, topological properties, number of flat bands, and valley Hall and Nernst conductivities renders tFBL a novel device from fundamental and applied perspectives.
Heat stress as an innovative approach to enhance the antioxidant production in Pseudooceanicola and Bacillus isolates
Authors: Hassan Abdelrahim H. A. , Hozzein Wael N. , Mousa Ahmed S. M. , Rabie Walaa , Alkhalifah Dalal Hussien M. , Selim Samy , AbdElgawad Hamada
Published: September 2020

It is well known that the quality and quantity of bioactive metabolites in plants and microorganisms are affected by environmental factors. We applied heat stress as a promising approach to stimulate the production of antioxidants in four heat-tolerant bacterial strains (HT1 to HT4) isolated from Aushazia Lake, Qassim Region, Saudi Arabia. The phylogenetic analysis of the 16S rRNA sequences indicated that HT1, HT3 and HT4 belong to genusBacillus. While HT2 is closely related toPseudooceanicola marinuswith 96.78% similarity. Heat stress differentially induced oxidative damage i.e., high lipid peroxidation, lipoxygenase and xanthine oxidase levels in HT strains. Subsequently, heat stress induced the levels of flavonoids and polyphenols in all strains and glutathione (GSH) in HT2. Heat stress also improved the antioxidant enzyme activities, namely, CAT, SOD and POX in all strains and thioredoxin activity in HT3 and HT4. While GSH cycle (GSH level and GPX, GR, Grx and GST activities) was only detectable and enhanced by heat stress in HT2. The hierarchical cluster analysis of the antioxidants also supported the strain-specific responses. In conclusion, heat stress is a promising approach to enhance antioxidant production in bacteria with potential applications in food quality improvement and health promotion.
Experimental study and parameters optimization of microalgae based heavy metals removal process using a hybrid response surface methodology-crow search algorithm
Authors: Sultana N. , Hossain S. M. Zakir , Mohammed M. Ezzudin , Irfan M. F. , Haq B. , Faruque M. O. , Razzak S. A. , Hossain M. M.
Published: September 2020

This study investigates the use of microalgae as a biosorbent to eliminate heavy metals ions from wastewater. TheChlorella kesslerimicroalgae species was employed to biosorb heavy metals from synthetic wastewater specimens. FTIR, and SEM/XRD analyses were utilized to characterize the microalgal biomass (the adsorbent). The experiments were conducted with several process parameters, including initial solution pH, temperature, and microalgae biomass dose. In order to secure the best experimental conditions, the optimum parameters were estimated using an integrated response surface methodology (RSM), desirability function (DF), and crow search algorithm (CSA) modeling approach. A maximum lead(II) removal efficiency of 99.54% was identified by the RSM–DF platform with the following optimal set of parameters: pH of 6.34, temperature of 27.71 °C, and biomass dosage of 1.5 g L−1. The hybrid RSM–CSA approach provided a globally optimal solution that was similar to the results obtained by the RSM–DF approach. The consistency of the model-predicted optimum conditions was confirmed by conducting experiments under those conditions. It was found that the experimental removal efficiency (97.1%) under optimum conditions was very close (less than a 5% error) to the model-predicted value. The lead(II) biosorption process was better demonstrated by the pseudo-second order kinetic model. Finally, simultaneous removal of metals from wastewater samples containing a mixture of multiple heavy metals was investigated. The removal efficiency of each heavy metal was found to be in the following order: Pb(II) > Co(II) > Cu(II) > Cd(II) > Cr(II).
Graphene: Preparation and Applications
Authors: Song Man , Cai Changwei , Li Xuexiong , Chen Zhihong , Cai Xingke
Published: September 2020

In this chapter, the synthesis and applications of graphene are discussed. Synthesis methods have been organized based on the synthesis route used, i.e. top–down and bottom–up strategies. The advantages and disadvantages of each method are discussed based on their scalability, cost, performance, etc., which would be beneficial for finding suitable applications for each type of graphene. Then, the properties of graphene are introduced, including their excellent electrical/thermal conductivity, high specific surface area, tunable band gap, and unique optical properties. The applications and roles of graphene in energy conversion/storage and optoelectronic devices are also discussed based on their unique properties. Application examples, such as lithium batteries, supercapacitors, solar cells, stretchable transparent electrodes, and stretchable transparent electronics, have also been summarized.
Non-volatile Bipolar Transistor Memory
Authors: Li Mengyao , Zhang Yating
Published: September 2020

In the past few years, due to the limitations of silicon-based materials, the miniaturization of devices has gradually slowed down, even reaching its limit. Finding new breakthroughs for the miniaturization of memory is an important direction for development of the electronics industry. Among many types of memories, ambipolar floating gate memory is a non-volatile memory with excellent performance. It realizes the large storage window at low programming/erasing voltage by ambipolar carrier storage, which is of great significance for low power operation. This chapter reviews the basic principles of ambipolar floating gate memory for data storage, and summarizes the application of novel micro–nano functional materials, such as nanoparticles, quantum dots, polymers, and binary materials, to the channel layer and storage layer, which play an important role in storage. The effects of material properties, device structure, and other possible factors on device performance are discussed. The consistent efforts of researchers have developed novel ambipolar floating gate storages with non-volatile, high-density storage, high switching speed, and multilevel memory. This is a good choice for the next generation of low-cost, wearable miniaturization, high-density non-volatile memory.
Cocrystals of Li+ encapsulated fullerenes and Tb(iii) double-decker single molecule magnet in a quasi-kagome lattice
Authors: Iwami Hikaru , Xing Junfei , Nakanishi Ryo , Horii Yoji , Katoh Keiichi , Breedlove Brian K. , Kawachi Kazuhiko , Kasama Yasuhiko , Kwon Eunsang , Yamashita Masahiro
Published: September 2020

Cocrystallization of a lithium ion encapsulated fullerene with a terbium(iii) phthalocyaninato porphyrinato double-decker single-molecule magnet results in a quasi-kagome lattice packing showing ferromagnetic spin arrangement.
Copper arylnitrene intermediates: formation, structure and reactivity
Authors: de Kler Noël R. M. , Roithová Jana
Published: September 2020

The mechanism of oxidation of arylamines by copper enzymes is not clarified yet. A possible pathway involves copper(ii)oxyl intermediates transforming arylamines to copper aryl nitrenes. We investigate details of this pathway in a gas phase reaction.