bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multiplex qPCR approach for detection of pfhrp2 and pfhrp3 gene deletions in multiple strain infections of Plasmodium falciparum
Authors: Schindler Tobias , Deal Anna C. , Fink Martina , Guirou Etienne , Moser Kara A. , Mwakasungula Solomon M. , Mihayo Michael G. , Jongo Said A. , Chaki Prosper P. , Abdulla Salim , Valverde Paulo C. Manrique , Torres Katherine , Bijeri Jose R. , Silva Joana C. , Hoffman Stephen L. , Gamboa Dionicia , Tanner Marcel , Daubenberger Claudia 
Published: September 2019

AbstractThe rapid and accurate diagnosis of Plasmodium falciparum malaria infection is an essential factor in malaria control. Currently, malaria diagnosis in the field depends heavily on using rapid diagnostic tests (RDTs) many of which detect circulating parasite-derived histidine-rich protein 2 antigen (PfHRP2) in capillary blood. P. falciparum strains lacking PfHRP2, due to pfhrp2 gene deletions, are an emerging threat to malaria control programs. The novel assay described here, named qHRP2/3-del, is well suited for high-throughput screening of P. falciparum isolates to identify these gene deletions. The qHRP2/3-del assay identified pfhrp2 and pfhrp3 deletion status correctly in 93.4% of samples with parasitemia levels higher than 5 parasites/µL when compared to nested PCR. The qHRP2/3-del assay can correctly identify pfhrp2 and pfhrp3 gene deletions in multiple strain co-infections, particularly prevalent in Sub-Saharan countries. Deployment of this qHRP2/3-del assay will provide rapid insight into the prevalence and potential spread of P. falciparum isolates that escape surveillance by RDTs.
The earliest evidence of Acheulian occupation in Northwest Europe and the rediscovery of the Moulin Quignon site, Somme valley, France
Authors: Antoine Pierre , Moncel Marie-Hélène , Voinchet Pierre , Locht Jean-Luc , Amselem Daniel , Hérisson David , Hurel Arnaud , Bahain Jean-Jacques 
Published: September 2019

AbstractThe dispersal of hominin groups with an Acheulian technology and associated bifacial tools into northern latitudes is central to the debate over the timing of the oldest human occupation of Europe. New evidence resulting from the rediscovery and the dating of the historic site of Moulin Quignon demonstrates that the first Acheulian occupation north of 50°N occurred around 670–650 ka ago. The new archaeological assemblage was discovered in a sequence of fluvial sands and gravels overlying the chalk bedrock at a relative height of 40 m above the present-day maximal incision of the Somme River and dated by ESR on quartz to early MIS 16. More than 260 flint artefacts were recovered, including large flakes, cores and five bifaces. This discovery pushes back the age of the oldest Acheulian occupation of north-western Europe by more than 100 ka and bridges the gap between the archaeological records of northern France and England. It also challenges hominin dispersal models in Europe showing that hominins using bifacial technology, such as Homo heidelbergensis, were probably able to overcome cold climate conditions as early as 670–650 ka ago and reasserts the importance of the Somme valley, where Prehistory was born at the end of the 19th century.
Exome Sequencing Reveals Immune Genes as Susceptibility Modifiers in Individuals with α1-Antitrypsin Deficiency
Authors: Rigobello Chiara , Baraldo Simonetta , Tinè Mariaenrica , Ferrarotti Ilaria , Corsico Angelo Guido , Bazzan Erica , Turato Graziella , Balestro Elisabetta , Biondini Davide , Valle Giorgio , Saetta Marina , Cosio Manuel G. 
Published: September 2019

AbstractAlpha-1 antitrypsin deficiency (AATD) is a genetic disorder associated to early onset emphysema, mainly imputable to Pi*ZZ genotype. In spite of the serious potential effects, many AATD individuals do not develop emphysema. To identify genes/variants potentially involved in emphysema development we studied 4 AATD families. Each family had at least one affected sibling with emphysema and one non-affected. Whole Exome Sequencing (WES) was performed on genomic DNA isolated from 9 individuals with AATD (4 affected/5 non-affected). Genetic variants confirmed at least in three families were prioritized using QueryOR and network analysis was used to verify enriched pathways. In affected subjects: 14 genes (57% immune-related) segregated in a recessive model and 21 (29% immune-related) in a dominant model. In non-affected subjects: 21 genes (43% immune-related) segregated in a recessive model and 50 (24% immune-related) in a dominant model. In affected siblings immune genes had an activating function, while where immune-suppressing in non-affected siblings involving antigen processing, MHC-I presentation, TCR and PD-1 signalling. This study describes possible genetic susceptibility factors for emphysema development in AATD, and suggests that gene variants involved in regulation of immune homeostasis and maintenance of self-tolerance contribute to the development or suppression of the disease.
Human decision-making biases in the moral dilemmas of autonomous vehicles
Authors: Frank Darius-Aurel , Chrysochou Polymeros , Mitkidis Panagiotis , Ariely Dan 
Published: September 2019

AbstractThe development of artificial intelligence has led researchers to study the ethical principles that should guide machine behavior. The challenge in building machine morality based on people’s moral decisions, however, is accounting for the biases in human moral decision-making. In seven studies, this paper investigates how people’s personal perspectives and decision-making modes affect their decisions in the moral dilemmas faced by autonomous vehicles. Moreover, it determines the variations in people’s moral decisions that can be attributed to the situational factors of the dilemmas. The reported studies demonstrate that people’s moral decisions, regardless of the presented dilemma, are biased by their decision-making mode and personal perspective. Under intuitive moral decisions, participants shift more towards a deontological doctrine by sacrificing the passenger instead of the pedestrian. In addition, once the personal perspective is made salient participants preserve the lives of that perspective, i.e. the passenger shifts towards sacrificing the pedestrian, and vice versa. These biases in people’s moral decisions underline the social challenge in the design of a universal moral code for autonomous vehicles. We discuss the implications of our findings and provide directions for future research.
A unique camouflaged mimarachnid planthopper from mid-Cretaceous Burmese amber
Authors: Jiang Tian , Szwedo Jacek , Wang Bo 
Published: September 2019

AbstractPredation is a major driving force for the evolution of functional forms. Avoidance of visual predators has resulted in different kinds of anti-predator defences, such as: camouflage, crypsis, disruptive coloration, and masquerade or mimesis. Camouflage is one of the forms involving shape, colouration, structure and behaviour when the visual pattern and orientation of an animal can determine whether it lives or dies. Inferring the behaviour and function of an ancient organism from its fossilised remains is a difficult task, but in many cases it closely resembles that of its descendants on uniformitarian grounds. Here we report and discuss examples of morphological and behavioural traits involving camouflage named recently as a flatoidinisation syndrome, shown by the inclusion of a planthopper in mid-Cretaceous Burmese amber. We found a new genus and species of an extinct Cretaceous planthopper family Mimarachnidae showing peculiar complex morphological adaptations to camouflage it on tree bark. Due to convergence, it resembles an unrelated tropiduchid planthopper from Eocene Baltic amber and also a modern representatives of the planthopper family Flatidae. Flattening of the body, the horizontal position of the tegmina at repose, tegmina with an undulating margin and elevated, wavy longitudinal veins, together with colouration and more sedentary behavioral traits enable these different insects to avoid predators. Our discovery reveals flatoidinisation syndrome in mid-Cretaceous Burmese amber which may provide insights into the processes of natural selection and evolution in this ancient forest.
Staphylococcal enterotoxins modulate the effector CD4+ T cell response by reshaping the gene expression profile in adults with atopic dermatitis
Authors: Orfali Raquel Leao , Yoshikawa Fabio Seiti Yamada , Oliveira Luanda Mara da Silva , Pereira Natalli Zanete , de Lima Josenilson Feitosa , Ramos Yasmim Álefe Leuzzi , Duarte Alberto José da Silva , Sato Maria Notomi , Aoki Valeria 
Published: September 2019

AbstractStaphylococcus aureuscolonizes the skin of atopic dermatitis (AD) individuals, but the impact of its enterotoxins on the chronic activation of CD4+T cells demands further analysis. We aimed to analyze the CD4+T cell anergy profile and their phenotypic and functional features through differential expression of cellular activation markers, cytokine production and response to staphylococcal enterotoxin A (SEA). A panel of 84 genes relevant to T cell anergy was assessed by PCR array in FACS-sorted CD4+T cells, and the most prominent genes were validated by RT-qPCR. We evaluated frequencies of circulating CD4+T cells secreting single or multiple (polyfunctional) cytokines (IL-17A, IL-22, TNF, IFN-γ, and MIP-1β) and expression of activation marker CD38 in response to SEA stimulation by flow cytometry. Our main findings indicated upregulation of anergy-related genes (EGR2andIL13)promoted by SEA in AD patients, associated to a compromised polyfunctional response particularly in CD4+CD38+T cells in response to antigen stimulation. The pathogenic role of staphylococcal enterotoxins in adult AD can be explained by their ability to downmodulate the activated effector T cell response, altering gene expression profile such asEGR2induction, and may contribute to negative regulation of polyfunctional CD4+T cells in these patients.
De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Authors: Dhiman Nisha , Sharma Nitesh Kumar , Thapa Pooja , Sharma Isha , Kumar Swarnkar Mohit , Chawla Amit , Shankar Ravi , Bhattacharya Amita 
Published: September 2019

AbstractThis is the first report on de novo transcriptome of Dactylorhiza hatagirea, a critically-endangered, terrestrial orchid of alpine Himalayas. The plant is acclaimed for medicinal properties but little is known about its secondary-metabolites profile or cues regulating their biosynthesis. De novo transcriptome analysis was therefore, undertaken to gain basic understanding on these aspects, while circumventing the acute limitation of plant material availability. 65,384 transcripts and finally, 37,371 unigenes were assembled de novo from a total of 236 million reads obtained from shoot, tuber and leaves of the plant. Dominance of differentially-expressing-genes (DEGs) related to cold-stress-response and plant-hormone-signal-transduction; and those involved in photosynthesis, sugar-metabolism and secondary-metabolite-synthesis provided insights into carbohydrate-partitioning in the plant during its preparation for freezing winter at natural habitat. DEGs of glucomannan, ascorbic acid, carotenoids, phylloquinone/naphthoquinones, indole alkaloids, resveratrol and stilbene biosynthesis revealed the secondary-metabolite profile of D. hatagirea. UHPLC results confirmed appreciable amounts of resveratrol and trans-stilbene in D. hatagirea tubers, for the first time. Expression analysis of 15 selected genes including those of phenylpropanoid pathway confirmed the validity of RNA-seq data. Opportunistic growth, temperature- and tissue-specific-differential-expression of secondary metabolite biosynthesis and stress tolerant genes were confirmed using clonal plants growing at 8, 15 and 25 °C.
Paramagnetic gold in a highly disordered Au-Ni-O alloy
Authors: Stamatelatos A. , Poulopoulos P. , Goschew A. , Fumagalli P. , Sarigiannidou E. , Rapenne L. , Opagiste C. , Grammatikopoulos S. , Wilhelm F. , Rogalev A. 
Published: September 2019

AbstractMagnetic materials are usually classified into a distinct category such as diamagnets, paramagnets or ferromagnets. The enormous progress in materials science allows one nowadays, however, to change the magnetic nature of an element in a material. Gold, in bulk form, is traditionally a diamagnet. But in a ferromagnetic environment, it can adopt an induced ferromagnetic moment. Moreover, the growth of gold under certain conditions may lead to a spontaneous ferromagnetic or paramagnetic response. Here, we report on paramagnetic gold in a highly disordered Au–Ni–O alloy and focus on the unusual magnetic response. Such materials are mainly considered for plasmonic applications. Thin films containing Au, Ni and NiO are fabricated by co-deposition of Ni and Au in a medium vacuum of 2 × 10−2 mbar. As a result, Au is in a fully disordered state forming in some cases isolated nanocrystallites of up to 4 nm in diameter as revealed by high resolution transmission electron microscopy. The disorder and the environment, which is rich in oxygen, lead to remarkable magnetic properties of Au: an induced ferromagnetic and a paramagnetic state. This can be proven by measuring the x-ray magnetic circular dichroism. Our experiments show a way to establish and monitor Au paramagnetism in alloys.
An Experimental Approach to Rigorously Assess Paneth Cell α-Defensin (Defa) mRNA Expression in C57BL/6 Mice
Authors: Castillo Patricia A. , Nonnecke Eric B. , Ossorio Daniel T. , Tran Michelle T. N. , Goley Stephanie M. , Lönnerdal Bo , Underwood Mark A. , Bevins Charles L. 
Published: September 2019

AbstractAbundant evidence from many laboratories supports the premise that α-defensin peptides secreted from Paneth cells are key mediators of host-microbe interactions in the small intestine that contribute to host defense and homeostasis. α-defensins are among the most highly expressed antimicrobial peptides at this mucosal surface in many mammals, including humans and mice; however, there is striking variation among species in the number and primary structure of α-defensin paralogs. Studies of these biomolecules in vivo are further complicated by striking variations between laboratory mouse strains. Herein, we report an experimental approach to determine with precision and specificity expression levels of α-defensin (Defa) mRNA in the small intestine of C57BL/6 mice through an optimized set of oligonucleotide primers for qRT-PCR assays and cloned cDNA plasmids corresponding to the Defa paralogs. This approach demonstrated marked differences in α-defensin expression in C57BL/6 mice with respect to proximal/distal anatomical location and developmental stage, which have not been described previously. These data underscore the importance of careful attention to method (primer choice, proximal vs. distal location, and developmental stage) in analysis of antimicrobial peptide expression and their impact.
Liver sinusoidal endothelial cell ICAM-1 mediated tumor/endothelial crosstalk drives the development of liver metastasis by initiating inflammatory and angiogenic responses
Authors: Benedicto Aitor , Herrero Alba , Romayor Irene , Marquez Joana , Smedsrød Bård , Olaso Elvira , Arteta Beatriz 
Published: September 2019

AbstractThe prometastatic stroma generated through tumor cells/host cells interaction is critical for metastatic growth. To elucidate the role of ICAM-1 on the crosstalk between tumor and primary liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs), implicated in tumor adhesion and angiogenesis, we performed in vitro cocultures and an in vivo model of liver metastasis of colorectal cancer (CRC). ICAM-1 blockade in the LSECs decreased the adhesion and transmigration of tumor cells through an LSEC in vitro and vivo. Cocultures of C26 cells and LSECs contained higher amounts of IL-1β, IL-6, PGE-2, TNF-α and ICAM-1 than monocultures. C26 cells incubated with sICAM-1 secreted higher amounts of PGE-2, IL-6, VEGF, and MMPs, while enhanced the migration of LSECs and HSCs. HSCs cultures activated by media from C26 cells pretreated with sICAM-1 contained the largest amounts of VEGF and MMPs. C26 cell activation with sICAM-1 enhanced their metastasizing potential in vivo, while tumor LFA-1 blockade reduced tumor burden and LSECs and HSC-derived myofibroblasts recruitment. In vivo ICAM-1 silencing produced similar results. These findings uncover LSEC ICAM-1 as a mediator of the CRC metastatic cascade in the liver and identifies it as target for the inhibition of liver colonization and metastatic progression.
Selection of reference genes for measuring the expression of aiiO in Ochrobactrum quorumnocens A44 using RT-qPCR
Authors: Krzyżanowska Dorota M. , Supernat Anna , Maciąg Tomasz , Matuszewska Marta , Jafra Sylwia 
Published: September 2019

AbstractReverse transcription quantitative PCR (RT-qPCR), a method of choice for quantification of gene expression changes, requires stably expressed reference genes for normalization of data. So far, no reference genes were established for the Alphaproteobacteria of the genus Ochrobactrum. Here, we determined reference genes for gene expression studies in O. quorumnocens A44. Strain A44 was cultured under 10 different conditions and the stability of expression of 11 candidate genes was evaluated using geNorm, NormFinder and BestKeeper. Most stably expressed genes were found to be rho, gyrB and rpoD. Our results can facilitate the choice of reference genes in the related Ochrobactrum strains. O. quorumnocens A44 is able to inactivate a broad spectrum of N-acyl homoserine lactones (AHLs) – the quorum sensing molecules of many Gram-negative bacteria. This activity is attributed to AiiO hydrolase, yet it remains unclear whether AHLs are the primary substrate of this enzyme. Using the established RT-qPCR setup, we found that the expression of the aiiO gene upon exposure to two AHLs, C6-HLS and 3OC12-HSL, does not change above the 1-fold significance threshold. The implications of this finding are discussed in the light of the role of quorum sensing-interfering enzymes in the host strains.
Percolation Phase Transition from Ionic Liquids to Ionic Liquid Crystals
Authors: Li Shen , Wang Yanting 
Published: September 2019

AbstractDue to their complex molecular structures and interactions, phase behaviors of complex fluids are quite often difficult to be identified by common phase transition analysis methods. Percolation phase transition, on the other hand, only monitors the degree of connection among particles without strict geometric requirements such as translational or orientational order, and thus suitable for pinpointing phase transitions of complex fluids. As typical complex fluids, ionic liquids (ILs) exhibit phases beyond the description of simple liquid theories. In particular, with an intermediate cationic side-chain length, ILs can form the nanoscale segregated liquid (NSL) state, which will eventually transform into the ionic liquid crystal (ILC) structure when the side chains are adequately long. However, the microscopic mechanism of this transformation is still unclear. In this work, by means of coarse-grained molecular dynamics simulation, we show that, with increasing cationic side-chain length, some local pieces of non-polar domains are gradually formed by side chains aligned in parallel inside the NSL phase, before an abrupt percolation phase transition happens when the system transforms into the ILC phase. This work not only identifies that the NSL to ILC phase transition is a critical phenomenon, but also demonstrates the importance of percolation theory to complex fluids.
Recording mobile EEG in an outdoor environment reveals cognitive-motor interference dependent on movement complexity
Authors: Reiser Julian Elias , Wascher Edmund , Arnau Stefan 
Published: September 2019

AbstractOftentimes we find ourselves in situations in which we need to perform concurrent motor and cognitive tasks like simple locomotion while being cognitively involved. In the present study, we investigated in how far cognitive and motor functioning interfere in an outdoor environment. Our participants performed an auditory oddball task while concurrently completing various motor tasks on the outside premises of our institute. Beside behavioural responses and subjective workload ratings, we also analysed electrophysiological data recorded with a 30-channel mobile EEG montage. We observed an increase of subjective workload and decrease of performance with increasing movement complexity. Accordingly, we also found a decrease in the parietal P3 amplitude as well as in frontal midline Theta power with higher motor load. These results indicate that an increased movement complexity imposes a higher workload to the cognitive system, which, in turn, effectively reduces the availability of cognitive resources for the cognitive task. Overall this experiment demonstrates the feasibility of transferring classical paradigms of cognitive research to real-world settings. The findings support the notion of shared resources for motor and cognitive functions by demonstrating distinct modulations of correlates of cognitive processes across different motor tasks.
Modeling of partial dome collapse of La Soufrière of Guadeloupe volcano: implications for hazard assessment and monitoring
Authors: Peruzzetto Marc , Komorowski Jean-Christophe , Le Friant Anne , Rosas-Carbajal Marina , Mangeney Anne , Legendre Yoann 
Published: September 2019

AbstractOver the past 9,150 years, at least 9 flank collapses have been identified in the history of La Soufrière of Guadeloupe volcano. On account of the volcano’s current unrest, the possibility of such a flank collapse should not be dismissed in assessing hazards for future eruptive magmatic as well as non-magmatic scenarios. We combine morphological and geophysical data to identify seven unstable structures (volumes ranging from 1 × 106 m3 to 100 × 106 m3), including one that has a volume compatible with the last recorded flank collapse in 1530 CE. We model their dynamics and emplacement with the SHALTOP numerical model and a simple Coulomb friction law. The best-fit friction coefficient to reproduce the 1530 CE event is tan(7°) = 0.13, suggesting the transformation of the debris avalanche into a debris flow, which is confirmed by the texture of mapped deposits. Various friction angles are tested to investigate less water-rich and less mobile avalanches. The most densely populated areas of Saint-Claude and Basse-Terre, and an area of Gourbeyre south of the Palmiste ridge, are primarily exposed in the case of the more voluminous and mobile flank collapse scenarios considered. However, topography has a prominent role in controlling flow dynamics, with barrier effects and multiple channels. Classical mobility indicators, such as the Heim’s ratio, are thus not adequate for a comprehensive hazard analysis.