bluuebunny/crossref_metadata_2025_split huggingface dataset:
A digital single-molecule nanopillar SERS platform for predicting and monitoring immune toxicities in immunotherapy
Authors: Li Junrong , Wuethrich Alain , Sina Abu A. I. , Cheng Han-Hao , Wang Yuling , Behren Andreas , Mainwaring Paul N. , Trau Matt 
Published: February 2021

AbstractThe introduction of immune checkpoint inhibitors has demonstrated significant improvements in survival for subsets of cancer patients. However, they carry significant and sometimes life-threatening toxicities. Prompt prediction and monitoring of immune toxicities have the potential to maximise the benefits of immune checkpoint therapy. Herein, we develop a digital nanopillar SERS platform that achieves real-time single cytokine counting and enables dynamic tracking of immune toxicities in cancer patients receiving immune checkpoint inhibitor treatment - broader applications are anticipated in other disease indications. By analysing four prospective cytokine biomarkers that initiate inflammatory responses, the digital nanopillar SERS assay achieves both highly specific and highly sensitive cytokine detection down to attomolar level. Significantly, we report the capability of the assay to longitudinally monitor 10 melanoma patients during immune inhibitor blockade treatment. Here, we show that elevated cytokine concentrations predict for higher risk of developing severe immune toxicities in our pilot cohort of patients.
Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework
Authors: Kirschner Philipp , Arthofer Wolfgang , Pfeifenberger Stefanie , Záveská Eliška , Schönswetter Peter ,   The STEPPE Consortium, Frajman Božo , Gamisch Alexander , Hilpold Andreas , Paun Ovidiu , Sanmartín Isabel , Trucchi Emiliano , Steiner Florian M. , Schlick-Steiner Birgit C. 
Published: February 2021

AbstractMulti-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
Safety envelope of pedestrians upon motor vehicle conflicts identified via active avoidance behaviour
Authors: Nie Bingbing , Li Quan , Gan Shun , Xing Bobin , Huang Yuan , Li Shengbo Eben 
Published: February 2021

AbstractHuman reaction plays a key role in improved protection upon emergent traffic situations with motor vehicles. Understanding the underlying behaviour mechanisms can combine active sensing system on feature caption and passive devices on injury mitigation for automated vehicles. The study aims to identify the distance-based safety boundary (“safety envelope”) of vehicle–pedestrian conflicts via pedestrian active avoidance behaviour recorded in well-controlled, immersive virtual reality-based emergent traffic scenarios. Via physiological signal measurement and kinematics reconstruction of the complete sequence, we discovered the general perception-decision-action mechanisms under given external stimulus, and the resultant certain level of natural harm-avoidance action. Using vision as the main information source, 70% pedestrians managed to avoid the collision by adapting walking speeds and directions, consuming overall less “decision” time (0.17–0.24 s vs. 0.41 s) than the collision cases, after that, pedestrians need enough “execution” time (1.52–1.84 s) to take avoidance action. Safety envelopes were generated by combining the simultaneous interactions between the pedestrian and the vehicle. The present investigation on emergent reaction dynamics clears a way for realistic modelling of biomechanical behaviour, and preliminarily demonstrates the feasibility of incorporating in vivo pedestrian behaviour into engineering design which can facilitate improved, interactive on-board devices towards global optimal safety.
Contrasting effects of male immigration and rainfall on rank-related patterns of miscarriage in female olive baboons
Authors: Bailey Andrea , Eberly Lynn E. , Packer Craig 
Published: February 2021

AbstractIn mammalian species with prolonged maternal investment in which high-ranking males gain disproportionate numbers of mating opportunities, males that quickly ascend the hierarchy may benefit from eliminating the dependent offspring of their competitors. In savanna baboons, high-ranking females are the most profitable targets of infanticide or feticide, because their offspring have higher survival rates and their daughters reach sexual maturity at a younger age. However, such patterns may be obscured by environmental stressors that are known to exacerbate fetal losses, especially in lower-ranking females. Using 30 years of data on wild olive baboons (Papio anubis) in Gombe National Park, Tanzania, we found evidence that rapidly-rising immigrant males induced miscarriages in high-ranking females outside of drought conditions. However, miscarriage rates were largely reversed during prolonged periods of low rainfall, suggesting that low-ranking females are particularly vulnerable to low food availability and social instability. Infanticide did not emerge as a recurrent male strategy in this population, likely because of the protective behavior of resident males towards vulnerable juveniles.
Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma
Authors: Jones Christine L. , Degasperi Andrea , Grandi Vieri , Amarante Tauanne D. ,   Genomics England Research Consortium, Ambrose John C. , Arumugam Prabhu , Baple Emma L. , Bleda Marta , Boardman-Pretty Freya , Boissiere Jeanne M. , Boustred Christopher R. , Brittain Helen , Caulfield Mark J. , Chan Georgia C. , Craig Clare E. H. , Daugherty Louise C. , de Burca Anna , Devereau Andrew , Elgar Greg , Foulger Rebecca E. , Fowler Tom , Furió-Tarí Pedro , Giess Adam , Hackett Joanne M. , Halai Dina , Hamblin Angela , Henderson Shirley , Holman James E. , Hubbard Tim J. P. , Ibáñez Kristina , Jackson Rob , Jones Louise J. , Kasperaviciute Dalia , Kayikci Melis , Kousathanas Athanasios , Lahnstein Lea , Lawson Kay , Leigh Sarah E. A. , Leong Ivonne U. S. , Lopez Javier F. , Maleady-Crowe Fiona , Mason Joanne , McDonagh Ellen M. , Moutsianas Loukas , Mueller Michael , Murugaesu Nirupa , Need Anna C. , O’Donovan Peter , Odhams Chris A. , Orioli Andrea , Patch Christine , Pereira Mariana Buongermino , Perez-Gil Daniel , Polychronopoulos Dimitris , Pullinger John , Rahim Tahrima , Rendon Augusto , Riesgo-Ferreiro Pablo , Rogers Tim , Ryten Mina , Savage Kevin , Sawant Kushmita , Scott Richard H. , Siddiq Afshan , Sieghart Alexander , Smedley Damian , Smith Katherine R. , Smith Samuel C. , Sosinsky Alona , Spooner William , Stevens Helen E. , Stuckey Alexander , Sultana Razvan , Tanguy Mélanie , Thomas Ellen R. A. , Thompson Simon R. , Tregidgo Carolyn , Tucci Arianna , Walsh Emma , Watters Sarah A. , Welland Matthew J. , Williams Eleanor , Witkowska Katarzyna , Wood Suzanne M. , Zarowiecki Magdalena , Mitchell Tracey J. , Nik-Zainal Serena , Whittaker Sean J. 
Published: February 2021

AbstractT-cell non-Hodgkin’s lymphomas develop following transformation of tissue resident T-cells. We performed a meta-analysis of whole exome sequencing data from 403 patients with eight subtypes of T-cell non-Hodgkin’s lymphoma to identify mutational signatures and associated recurrent gene mutations. Signature 1, indicative of age-related deamination, was prevalent across all T-cell lymphomas, reflecting the derivation of these malignancies from memory T-cells. Adult T-cell leukemia-lymphoma was specifically associated with signature 17, which was found to correlate with the IRF4 K59R mutation that is exclusive to Adult T-cell leukemia-lymphoma. Signature 7, implicating UV exposure was uniquely identified in cutaneous T-cell lymphoma (CTCL), contributing 52% of the mutational burden in mycosis fungoides and 23% in Sezary syndrome. Importantly this UV signature was observed in CD4 + T-cells isolated from the blood of Sezary syndrome patients suggesting extensive re-circulation of these T-cells through skin and blood. Analysis of non-Hodgkin’s T-cell lymphoma cases submitted to the national 100,000 WGS project confirmed that signature 7 was only identified in CTCL strongly implicating UV radiation in the pathogenesis of cutaneous T-cell lymphoma.
An analysis framework for the integration of broadband NIRS and EEG to assess neurovascular and neurometabolic coupling
Authors: Pinti P. , Siddiqui M. F. , Levy A. D. , Jones E. J. H. , Tachtsidis Ilias 
Published: February 2021

AbstractWith the rapid growth of optical-based neuroimaging to explore human brain functioning, our research group has been developing broadband Near Infrared Spectroscopy (bNIRS) instruments, a technological extension to functional Near Infrared Spectroscopy (fNIRS). bNIRS has the unique capacity of monitoring brain haemodynamics/oxygenation (measuring oxygenated and deoxygenated haemoglobin),andmetabolism (measuring the changes in the redox state of cytochrome-c-oxidase). When combined with electroencephalography (EEG), bNIRS provides a unique neuromonitoring platform to explore neurovascular coupling mechanisms. In this paper, we present a novel pipeline for the integrated analysis of bNIRS and EEG signals, and demonstrate its use on multi-channel bNIRS data recorded with concurrent EEG on healthy adults during a visual stimulation task. We introduce the use of the Finite Impulse Response functions within the General Linear Model for bNIRS and show its feasibility to statistically localize the haemodynamic and metabolic activity in the occipital cortex. Moreover, our results suggest that the fusion of haemodynamic and metabolic measures unveils additional information on brain functioning over haemodynamic imaging alone. The cross-correlation-based analysis of interrelationships between electrical (EEG) and haemodynamic/metabolic (bNIRS) activity revealed that the bNIRS metabolic signal offers a unique marker of brain activity, being more closely coupled to the neuronal EEG response.
Plasma phospholipid n-3 polyunsaturated fatty acids and major depressive disorder in Japanese elderly: the Japan Public Health Center-based Prospective Study
Authors: Hamazaki Kei , Matsuoka Yutaka J. , Yamaji Taiki , Sawada Norie , Mimura Masaru , Nozaki Shoko , Shikimoto Ryo , Tsugane Shoichiro 
Published: February 2021

AbstractThe beneficial effects of n-3 polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on depression are not definitively known. In a previous population-based prospective cohort study, we found a reverse J-shaped association of intake of fish and docosapentaenoic acid (DPA), the intermediate metabolite of EPA and DHA, with major depressive disorder (MDD). To examine the association further in a cross-sectional manner, in the present study we analyzed the level of plasma phospholipid n-3 PUFAs and the risk of MDD in 1,213 participants aged 64–86 years (mean 72.9 years) who completed questionnaires and underwent medical check-ups, a mental health examination, and blood collection. In multivariate logistic regression analysis, odds ratios and 95% confidence intervals were calculated for MDD according to plasma phospholipid n-3 PUFA quartiles. MDD was diagnosed in 103 individuals. There were no significant differences in any n-3 PUFAs (i.e., EPA, DHA, or DPA) between individuals with and without MDD. Multivariate logistic regression analysis showed no significant association between any individual n-3 PUFAs and MDD risk. Overall, based on the results of this cross-sectional study, there appears to be no association of plasma phospholipid n-3 PUFAs with MDD risk in the elderly Japanese population.
Highly stretchable large area woven, knitted and robust braided textile based interconnection for stretchable electronics
Authors: Yun Min Ju , Sim Yeon Hyang , Lee Dong Yoon , Cha Seung I. 
Published: February 2021

AbstractWith the rapid development of stretchable and wearable technologies, stretchable interconnection technology also demanded along it. Stretchable interconnections should have high stretchability and stable conductivity for use as an electrode. In addition, to develop to commercialization scale from research scale, a simple fabrication process that can be scaled up, and the stretchable interconnection should be able to be electrically connected to devices or modules directly. To date, printable conductor inks, liquid metals and stretchable structured interconnections have been reported for stretchable interconnections. These approaches have demonstrated high stretchability and conductivity, but in aspect of scale, it is appropriate to apply in micro-scale devices. For requirements of stretchability, conductivity and direct integration into meso- or centimeter-scale electronic devices or modules, here we introduce stretchable interconnections with a textile structure composed of metal fibers. The stretchable woven and knitted textiles show 67% strain and stable conductivity, and the cylindrical textile shows more than 700% strain with high strength. The stretchable textiles were fabricated using a weaving, knitting and braiding machine that can be used to produce textiles without any limit to length or area. These textiles exhibit high and stable conductivity even under deformation, and can be directly integrated into devices or modules by soldering. These high-performance stretchable textiles have great potential for commercial applications.
Impaired NEPHRIN localization in kidney organoids derived from nephrotic patient iPS cells
Authors: Ohmori Tomoko , De Shankhajit , Tanigawa Shunsuke , Miike Koichiro , Islam Mazharul , Soga Minami , Era Takumi , Shiona Shinichi , Nakanishi Koichi , Nakazato Hitoshi , Nishinakamura Ryuichi 
Published: February 2021

AbstractMutations in the NPHS1 gene, which encodes NEPHRIN, cause congenital nephrotic syndrome, resulting from impaired slit diaphragm (SD) formation in glomerular podocytes. We previously reported NEPHRIN and SD abnormalities in the podocytes of kidney organoids generated from patient-derived induced pluripotent stem cells (iPSCs) with an NPHS1 missense mutation (E725D). However, the mechanisms underlying the disease may vary depending on the mutations involved, and thus generation of iPSCs from multiple patients is warranted. Here we established iPSCs from two additional patients with different NPHS1 mutations and examined the podocyte abnormalities in kidney organoids derived from these cells. One patient had truncating mutations, and NEPHRIN was undetectable in the resulting organoids. The other patient had a missense mutation (R460Q), and the mutant NEPHRIN in the organoids failed to accumulate on the podocyte surface to form SD precursors. However, the same mutant protein behaved normally when overexpressed in heterologous cells, suggesting that NEPHRIN localization is cell context-dependent. The localization of another SD-associated protein, PODOCIN, was impaired in both types of mutant organoids in a cell domain-specific manner. Thus, the new iPSC lines and resultant kidney organoids will be useful resources for dissecting the disease mechanisms, as well as for drug development for therapies.
Exploring the edible gum (galactomannan) biosynthesis and its regulation during pod developmental stages in clusterbean using comparative transcriptomic approach
Authors: Sharma Sandhya , Tyagi Anshika , Srivastava Harsha , Ramakrishna G. , Sharma Priya , Sevanthi Amitha Mithra , Solanke Amolkumar U. , Sharma Ramavtar , Singh Nagendra Kumar , Sharma Tilak Raj , Gaikwad Kishor 
Published: February 2021

AbstractGalactomannan is a polymer of high economic importance and is extracted from the seed endosperm of clusterbean (C. tetragonoloba). In the present study, we worked to reveal the stage-specific galactomannan biosynthesis and its regulation in clusterbean. Combined electron microscopy and biochemical analysis revealed high protein and gum content in RGC-936, while high oil bodies and low gum content in M-83. A comparative transcriptome study was performed between RGC-936 (high gum) and M-83 (low gum) varieties at three developmental stages viz. 25, 39, and 50 days after flowering (DAF). Total 209,525, 375,595 and 255,401 unigenes were found at 25, 39 and 50 DAF respectively. Differentially expressed genes (DEGs) analysis indicated a total of 5147 shared unigenes between the two genotypes. Overall expression levels of transcripts at 39DAF were higher than 50DAF and 25DAF. Besides, 691 (RGC-936) and 188 (M-83) candidate unigenes that encode for enzymes involved in the biosynthesis of galactomannan were identified and analyzed, and 15 key enzyme genes were experimentally validated by quantitative Real-Time PCR. Transcription factor (TF) WRKY was observed to be co-expressed with key genes of galactomannan biosynthesis at 39DAF. We conclude that WRKY might be a potential biotechnological target (subject to functional validation) for developing high gum content varieties.
Insecticidal and oviposition deterrent effects of essential oils of Baccharis spp. and histological assessment against Drosophila suzukii (Diptera: Drosophilidae)
Authors: de Souza Michele Trombin , de Souza Mireli Trombin , Bernardi Daniel , de Melo Douglas José , Zarbin Paulo Henrique Gorgatti , Zawadneak Maria Aparecida Cassilha 
Published: February 2021

AbstractThe diverse flora of the Atlantic Forest is fertile ground for discovering new chemical structures with insecticidal activity. The presence of species belonging to the genusBaccharisis of particular interest, as these species have shown promise in pest management applications. The objective of this study is to chemically identify the constituents expressed in the leaves of seven species ofBaccharis(B. anomalaDC.,B. calvescensDC.,B. mesoneuraDC.,B. millefloraDC.,B. oblongifoliaPers.,B. trimera(Less) DC. andB. uncinellaDC.) and to evaluate the toxicological and morphological effects caused by essential oils (EOs) on the larvae and adults ofDrosophila suzukii(Diptera: Drosophilidae). Chemical analysis using gas chromatography-mass spectrometry (GC–MS) indicated that limonene was the main common constituent in allBaccharisspecies. This constituent in isolation, as well as the EOs ofB. calvescens,B. mesoneura, andB. oblongifolia, caused mortality in over 80% of adults ofD. suzukiiat a discriminatory concentration of 80 mg L−1in bioassays of ingestion and topical application. These results are similar to the effect of spinosyn-based synthetic insecticides (spinetoram 75 mg L−1) 120 h after exposure. Limonene and EOs from all species had the lowest LC50and LC90values relative to spinosyn and azadirachtin (12 g L−1) in both bioassays. However, they showed the same time toxicity over time as spinetoram when applied to adults ofD. suzukii(LT50ranging from 4.6 to 8.7 h) in a topical application bioassay. In olfactometry tests, 92% ofD. suzukiifemales showed repellent behavior when exposed to the EOs and limonene. Likewise, the EOs ofB. calvescens,B. mesoneura, andB. oblongifoliasignificantly reduced the number of eggs in artificial fruits (≅ 7.6 eggs fruit−1), differing from the control treatment with water (17.2 eggs fruit−1) and acetone (17.6 eggs fruit−1). According to histological analyses, the L3 larvae ofD. suzukiihad morphological and physiological alterations and deformations after exposure to treatments containing EOs and limonene, which resulted in high larval, pupal, and adult mortality. In view of the results,BaccharisEOs and their isolated constituent, limonene, proved to be promising alternatives for developing bioinsecticides to manage ofD. suzukii.
Antagonist effects of the leek Allium porrum as a companion plant on aphid host plant colonization
Authors: Baudry Xavier , Doury Géraldine , Couty Aude , Fourdrain Yvelise , van Havermaet Robin , Lateur Marc , Ameline Arnaud 
Published: February 2021

AbstractCombining a non-host plant (companion plant or CP) with a target cultivated plant is considered as a promising strategy to reduce pest pressure. Among the companion plants (CP) commonly used in integrated systems, those belonging to the Amaryllidaceae family (chives, garlic, onion, leek) exhibit characteristics related to certain volatile organic compounds (VOCs) with promising repellent potentialities. The aim of this work was to investigate the potential disruption of sweet pepper (host plant) colonization by the green peach aphid (Myzus persicae) when exposed to leek (Allium porrum) as a CP. Retention/dispersion, EPG and clip-cage/Petri dish laboratory experiments were thus performed to study the effect of leek VOCs on aphid settlement/migration, feeding behavior and life history traits parameters, respectively. This work revealed that leek as a CP had a negative effect on aphid feeding behavior, by disturbing the balance between phloem and xylem sap ingestion, but had no influence concerning aphid settlement. Surprisingly, leek as a CP triggered some unexpected probiotic effects on certain life history traits such as aphid survival, biomass, and fecundity, suggesting a possible hormetic effect of leek VOCs on aphid physiology. The possibility of experience-induced preference of aphids for leek VOCs was also discussed.
Role of adenomatous polyposis coli in proliferation and differentiation of colon epithelial cells in organoid culture
Authors: Yamazaki Daisuke , Hashizume Osamu , Taniguchi Shiho , Funato Yosuke , Miki Hiroaki 
Published: February 2021

AbstractAdenomatous polyposis coli (APC) is a tumor-suppressing protein whose inactivation triggers the formation of colorectal polyps. Numerous studies using cell lines or genetically engineered mice have revealed its role in suppressing Wnt/β-catenin signaling pathway and regulating cell proliferation and differentiation. Here, we performed genetic analyses of APC using a three-dimensional organoid culture of mouse colon epithelia, which enables the detailed examination of epithelial properties. Analyses of Apc-knockout colon organoids not only confirmed the importance of APC in suppressing Wnt/β-catenin signaling and regulating cell differentiation, but also revealed several novel features: a significant decrease in proliferating speed and an increase in cross-sectional area of cells. Moreover, we found a significant number of lysozyme-positive Paneth-like cells, which were never observed in wild-type colon tissues or organoids, but have been reported to emerge in colon cancers. Therefore, APC autonomously suppresses ectopic differentiation into lysozyme-positive cells, specifically in the colon epithelia. Colon organoids would be an ideal material to investigate the molecular mechanism and biological importance of the ectopic differentiation associated with cancer development.