bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Study among the Genotype, Functional Alternations, and Phenotype of 9 SCN1A Mutations in Epilepsy Patients
Authors: Kluckova Daniela , Kolnikova Miriam , Lacinova Lubica , Jurkovicova-Tarabova Bohumila , Foltan Tomas , Demko Viktor , Kadasi Ludevit , Ficek Andrej , Soltysova Andrea 
Published: June 2020

AbstractMutations in the voltage-gated sodium channel Nav1.1 (SCN1A) are linked to various epileptic phenotypes with different severities, however, the consequences of newly identified SCN1A variants on patient phenotype is uncertain so far. The functional impact of nine SCN1A variants, including five novel variants identified in this study, was studied using whole-cell patch-clamp recordings measurement of mutant Nav1.1 channels expressed in HEK293T mammalian cells. E78X, W384X, E1587K, and R1596C channels failed to produce measurable sodium currents, indicating complete loss of channel function. E788K and M909K variants resulted in partial loss of function by exhibiting reduced current density, depolarizing shifts of the activation and hyperpolarizing shifts of the inactivation curves, and slower recovery from inactivation. Hyperpolarizing shifts of the activation and inactivation curves were observed in D249E channels along with slower recovery from inactivation. Slower recovery from inactivation was observed in E78D and T1934I with reduced current density in T1934I channels. Various functional effects were observed with the lack of sodium current being mainly associated with severe phenotypes and milder symptoms with less damaging channel alteration. In vitro functional analysis is thus fundamental for elucidation of the molecular mechanisms of epilepsy, to guide patients’ treatment, and finally indicate misdiagnosis of SCN1A related epilepsies.
Diversity hotspot and unique community structure of foraminifera in the world’s deepest marine blue hole – Sansha Yongle Blue Hole
Authors: Li Qingxia , Lei Yanli , Morard Raphaёl , Li Tiegang , Wang Baodong 
Published: June 2020

AbstractMarine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world’s deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.
Northern and southern blacklegged (deer) ticks are genetically distinct with different histories and Lyme spirochete infection rates
Authors: Xu Guang , Wielstra Ben , Rich Stephen M. 
Published: June 2020

AbstractLyme borreliosis (LB) is the archetypal emerging zoonosis and is dependent on transmission by ticks in the genusIxodes. Understanding the origin, maintenance, and spread of these ticks contributes much to our understanding of the spread of LB and other disease agents borne by these ticks. We collected 1232Ixodes scapularisticks from 17 east coast sites ranging from New Hampshire to Florida and used mtDNA, three nuclear genetic loci, and incorporated Bayesian analyses to resolve geographically distinct tick populations and compare their demographic histories. A sparse, stable, and genetically diverse population of ticks in the Southeastern US, that is rarely infected with the agent of LB is genetically distinct from an abundant, expanding, and comparatively uniform population in the Northeast, where epidemic LB now constitutes the most important vector borne disease in the United States. The contrasting geography and demography of tick populations, interpreted in the context of the geological history of the region, suggests that during the last glacial period such ticks occupied distinct refugia, with only the northern-most site of refuge giving rise to those ticks and pathogens now fueling the epidemic.
Liquid biopsy mutation panel for non-small cell lung cancer: analytical validation and clinical concordance
Authors: Schwartzberg Lee S. , Horinouchi Hidehito , Chan David , Chernilo Sara , Tsai Michaela L. , Isla Dolores , Escriu Carles , Bennett John P. , Clark-Langone Kim , Svedman Christer , Tomasini Pascale ,   Oncotype SEQ® Study Investigators and Program Team, Alexander Gregory , Baehner Frederick L. , Bauer Thomas , Bergamaschi Anna , Crown John , Davison Deborah , Eberhard David A. , Gabrail Nashat , Han James , Irvin William , Lopatin Margarita , Orsini James , Sumrall Bradley T. 
Published: June 2020

AbstractMolecular testing for genomic variants is recommended in advanced non-small cell lung cancer (NSCLC). Standard tissue biopsy is sometimes infeasible, procedurally risky, or insufficient in tumor tissue quantity. We present the analytical validation and concordance study of EGFR variants using a new 17-gene liquid biopsy assay (NCT02762877). Of 144 patients enrolled with newly diagnosed or progressive stage IV nonsquamous NSCLC, 140 (97%) had liquid assay results, and 117 (81%) had both EGFR blood and tissue results. Alterations were detected in 58% of liquid samples. Overall tissue-liquid concordance for EGFR alterations was 94.0% (95% CI 88.1%, 97.6%) with positive percent agreement of 76.7% (57.7%, 90.1%) and negative percent agreement of 100% (95.8%, 100%). Concordance for ALK structural variants was 95.7% (90.1%, 98.6%). This assay detected alterations in other therapeutically relevant genes at a rate similar to tissue analysis. These results demonstrate the analytical and clinical validity of this 17-gene assay.
SAMHD1 is a key regulator of the lineage-specific response of acute lymphoblastic leukaemias to nelarabine
Authors: Rothenburger Tamara , McLaughlin Katie-May , Herold Tobias , Schneider Constanze , Oellerich Thomas , Rothweiler Florian , Feber Andrew , Fenton Tim R. , Wass Mark N. , Keppler Oliver T. , Michaelis Martin , Cinatl Jindrich 
Published: June 2020

AbstractThe nucleoside analogue nelarabine, the prodrug of arabinosylguanine (AraG), is effective against T-cell acute lymphoblastic leukaemia (T-ALL) but not against B-cell ALL (B-ALL). The underlying mechanisms have remained elusive. Here, data from pharmacogenomics studies and a panel of ALL cell lines reveal an inverse correlation between nelarabine sensitivity and the expression ofSAMHD1, which can hydrolyse and inactivate triphosphorylated nucleoside analogues. Lower SAMHD1 abundance is detected in T-ALL than in B-ALL in cell lines and patient-derived leukaemic blasts. Mechanistically, T-ALL cells display increasedSAMHD1promoter methylation without increased global DNA methylation. SAMHD1 depletion sensitises B-ALL cells to AraG, while ectopic SAMHD1 expression in SAMHD1-null T-ALL cells induces AraG resistance. SAMHD1 has a larger impact on nelarabine/AraG than on cytarabine in ALL cells. Opposite effects are observed in acute myeloid leukaemia cells, indicating entity-specific differences. In conclusion,SAMHD1promoter methylation and, in turn,SAMHD1expression levels determine ALL cell response to nelarabine.
Biocrusts buffer against the accumulation of soil metallic nutrients induced by warming and rainfall reduction
Authors: Moreno-Jiménez Eduardo , Ochoa-Hueso Raúl , Plaza César , Aceña-Heras Sara , Flagmeier Maren , Elouali Fatima Z. , Ochoa Victoria , Gozalo Beatriz , Lázaro Roberto , Maestre Fernando T. 
Published: June 2020

AbstractThe availability of metallic nutrients in dryland soils, many of which are essential for the metabolism of soil organisms and vascular plants, may be altered due to climate change-driven increases in aridity. Biocrusts, soil surface communities dominated by lichens, bryophytes and cyanobacteria, are ecosystem engineers known to exert critical functions in dryland ecosystems. However, their role in regulating metallic nutrient availability under climate change is uncertain. Here, we evaluated whether well-developed biocrusts modulate metallic nutrient availability in response to 7 years of experimental warming and rainfall reduction in a Mediterranean dryland located in southeastern Spain. We found increases in the availability of K, Mg, Zn and Na under warming and rainfall exclusion. However, the presence of a well-developed biocrust cover buffered these effects, most likely because its constituents can uptake significant quantities of available metallic nutrients. Our findings suggest that biocrusts, a biotic community prevalent in drylands, exert an important role in preserving and protecting metallic nutrients in dryland soils from leaching and erosion. Therefore, we highlight the need to protect them to mitigate undesired effects of soil degradation driven by climate change in this globally expanding biome.
The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface
Authors: Hazzouri Khaled Michel , Sudalaimuthuasari Naganeeswaran , Kundu Biduth , Nelson David , Al-Deeb Mohammad Ali , Le Mansour Alain , Spencer Johnston J. , Desplan Claude , Amiri Khaled M. A. 
Published: June 2020

AbstractThe red palm weevil, Rhynchophorus ferrugineus, infests palm plantations, leading to large financial losses and soil erosion. Pest-host interactions are poorly understood in R. ferrugineus, but the analysis of genetic diversity and pest origins will help advance efforts to eradicate this pest. We sequenced the genome of R. ferrugineus using a combination of paired-end Illumina sequencing (150 bp), Oxford Nanopore long reads, 10X Genomics and synteny analysis to produce an assembly with a scaffold N50 of ~60 Mb. Structural variations showed duplication of detoxifying and insecticide resistance genes (e.g., glutathione S-transferase, P450, Rdl). Furthermore, the evolution of gene families identified those under positive selection including one glycosyl hydrolase (GH16) gene family, which appears to result from horizontal gene transfer. This genome will be a valuable resource to understand insect evolution and behavior and to allow the genetic modification of key genes that will help control this pest.
Ultrafast all-optical switching enabled by epsilon-near-zero-tailored absorption in metal-insulator nanocavities
Authors: Kuttruff Joel , Garoli Denis , Allerbeck Jonas , Krahne Roman , De Luca Antonio , Brida Daniele , Caligiuri Vincenzo , Maccaferri Nicolò 
Published: June 2020

AbstractUltrafast control of light−matter interactions is fundamental in view of new technological frontiers of information processing. However, conventional optical elements are either static or feature switching speeds that are extremely low with respect to the time scales at which it is possible to control light. Here, we exploit the artificial epsilon-near-zero (ENZ) modes of a metal-insulator-metal nanocavity to tailor the linear photon absorption of our system and realize a nondegenerate all-optical ultrafast modulation of the reflectance at a specific wavelength. Optical pumping of the system at its high energy ENZ mode leads to a strong redshift of the low energy mode because of the transient increase of the local dielectric function, which leads to a sub-3-ps control of the reflectance at a specific wavelength with a relative modulation depth approaching 120%.
Thermal conductance across harmonic-matched epitaxial Al-sapphire heterointerfaces
Authors: Cheng Zhe , Koh Yee Rui , Ahmad Habib , Hu Renjiu , Shi Jingjing , Liao Michael E. , Wang Yekan , Bai Tingyu , Li Ruiyang , Lee Eungkyu , Clinton Evan A. , Matthews Christopher M. , Engel Zachary , Yates Luke , Luo Tengfei , Goorsky Mark S. , Doolittle W. Alan , Tian Zhiting , Hopkins Patrick E. , Graham Samuel 
Published: June 2020

AbstractA unified fundamental understanding of interfacial thermal transport is missing due to the complicated nature of interfaces. Because of the difficulty to grow high-quality interfaces and lack of materials characterization, the experimentally measured thermal boundary conductance (TBC) in the literature are usually not the same as the ideally modelled interfaces. This work provides a systematic study of TBC across the highest-quality (atomically sharp, harmonic-matched, and ultraclean) epitaxial (111) Al||(0001) sapphire interfaces to date. The comparison of measured high TBC with theoretical models shows that elastic phonon transport dominates the interfacial thermal transport and other mechanisms play negligible roles. This is confirmed by a nearly constant transmission coefficient by scaling the TBC with the Al heat capacity and sapphire heat capacity with phonon frequency lower than 10 THz. Finally, the findings in this work will impact applications such as electronics thermal management, thermoelectric energy conversion, and battery safety.
Lithium-doped two-dimensional perovskite scintillator for wide-range radiation detection
Authors: Xie Aozhen , Hettiarachchi Chathuranga , Maddalena Francesco , Witkowski Marcin E. , Makowski Michał , Drozdowski Winicjusz , Arramel Arramel , Wee Andrew T. S. , Springham Stuart Victor , Vuong Phan Quoc , Kim Hong Joo , Dujardin Christophe , Coquet Philippe , Birowosuto Muhammad Danang , Dang Cuong 
Published: June 2020

AbstractTwo-dimensional lead halide perovskites have demonstrated their potential as high-performance scintillators for X- and gamma-ray detection, while also being low-cost. Here we adopt lithium chemical doping in two-dimensional phenethylammonium lead bromide (PEA)2PbBr4perovskite crystals to improve the properties and add functionalities with other radiation detections. Li doping is confirmed by X-ray photoemission spectroscopy and the scintillation mechanisms are explored via temperature dependent X-ray and thermoluminescence measurements. Our 1:1 Li-doped (PEA)2PbBr4demonstrates a fast decay time of 11 ns (80%), a clear photopeak with an energy resolution of 12.4%, and a scintillation yield of 11,000 photons per MeV under 662 keV gamma-ray radiation. Additionally, our Li-doped crystal shows a clear alpha particle/gamma-ray discrimination and promising thermal neutron detection through6Li enrichment. X-ray imaging pictures with (PEA)2PbBr4are also presented. All results demonstrate the potential of Li-doped (PEA)2PbBr4as a versatile scintillator covering a wide radiation energy range for various applications.
How Important Is Randomization of Swallows During Kinematic Analyses of Swallow Function?
Authors: Donohue Cara , Coyle James L. 
Published: June 2020

Purpose
In dysphagia research involving kinematic analyses on individual swallow parameters, randomization is used to ensure judges are not influenced by judgments made for other parameters within the same swallow or by judgments made for other swallows from the same participant. Yet, the necessity of randomizing swallows to avoid bias during kinematic analyses is largely assumed and untested. This study investigated whether randomization of the order of swallows presented to judges impacts analyses of temporal kinematic events from videofluoroscopic swallow studies.

Method
One hundred twenty-seven swallows were analyzed from 18 healthy adults who underwent standardized videofluoroscopic swallow studies. Swallows were first analyzed by two trained raters sequentially, analyzing all kinematic events within each swallow, and then a second time in random order, measuring one kinematic event at a time. Intrarater reliability measurements were calculated between random and sequential swallow judgments for all kinematic events using intraclass correlation coefficient and percent exact agreement within a three-frame tolerance.

Results
Intraclass correlation coefficients (1.00) and percent exact agreement (89%) were excellent for all kinematic events between analyses methods, indicating there were no significant differences in measurements performed in random or sequential order.

Conclusions
This study provides preliminary evidence that randomization may be unnecessary during temporal swallow kinematic data analyses for research, which may lead to more efficient analyses and dissemination of findings, and alignment of findings with clinical interpretations. Replication of this design with swallows from people with dysphagia would strengthen the generalizability of the results.
Deliberative democracy and historical perspectives on American Indian/Alaska native political decision-making practices
Authors: Reedy Justin , Orr Raymond , Spicer Paul , Blanchard Jessica W. , Hiratsuka Vanessa Y. , Ketchum Terry S. , Saunkeah Bobby , Wark Kyle , Woodbury R. Brian 
Published: June 2020

AbstractPublic deliberation has risen to the forefront of governance as a technique for increasing participation in policy making. Scholars and practitioners have also noted the potential for deliberation to give greater influence to historically marginalized populations, such as Indigenous peoples. However, there has been less attention paid to the potential fit between the ideals of deliberation and the governance and decision making practices of American Indian and Alaska Native (AI/AN) peoples. In this paper, we begin to address this gap by analyzing accounts of AI/AN governance from the perspective of deliberation, and note areas of overlap, synergy, and conflict. We conduct a close reading of key historical and ethnographic accounts of four historical AI/AN contexts—the Iroquois Confederation under the Great Law of Peace, 19th century accounts of the Ojibwa village, the Santa Clara Pueblo government in pre-19th century, and Yup’ik village life in the early 20th century—and a more contemporary case in the form of the Santa Clara Pueblo’s Constitution from the Indian Reorganization Act period. We then apply two sets of key criteria for deliberative democracy—from the scholars Robert Dahl and John Gastil—to these accounts and note the ways in which each system is or is not congruent with these frameworks of deliberation. We find variations between these historical tribal contexts in our analysis. Social components of deliberation, such as respectful discussion and equal opportunities to participate, were partially or fully present in many accounts of governance practices, but it was less clear whether the analytic components, such as discussion of a range of solutions, were included in some forms of tribal governance. We then explore the potential implications of our findings for public deliberation within and in AI/AN tribes. We note that deliberative scholars and practitioners should be wary of overgeneralizing about AI/AN tribes.
Stable readout of observed actions from format-dependent activity of monkey’s anterior intraparietal neurons
Authors: Lanzilotto Marco , Maranesi Monica , Livi Alessandro , Ferroni Carolina Giulia , Orban Guy A. , Bonini Luca 
Published: June 2020

Significance
The anterior intraparietal area (AIP) is a crucial hub in the observed manipulative action (OMA) network of primates. While macaques observe manipulative action videos, their AIP neuronal activity robustly encodes first the viewpoint from which the action is observed, then the actor’s body posture, and finally the observed-action identity. Despite the lack of fully invariant OMA-selective single neurons, OMA exemplars could be decoded accurately from the activity of a set of units that maintain stable OMA selectivity despite rescaling their firing rate across formats. We propose that by integrating signals multiplicatively about others’ action and their visual format, the AIP can provide a stable readout of OMA identity at the population level.
Stem cell‐derived extracellular vesicles mitigate ageing‐associated arterial stiffness and hypertension
Authors: Feng Rui , Ullah Mujib , Chen Kai , Ali Quaisar , Lin Yi , Sun Zhongjie 
Published: June 2020

ABSTRACTThe prevalence of arterial stiffness and hypertension increases with age. This study investigates the effect of induced pluripotent mesenchymal stem cell‐derived extracellular vesicles (EVs) on ageing‐associated arterial stiffness and hypertension. EVs were collected and purified from induced pluripotent stem cell‐derived mesenchymal stem cells (iPS‐MSCs). Young and old male C57BL/6 mice were used. Mice in the EVs group were injected via tail vein once a week for four weeks (18 x 106 EVs/mouse/injection). Blood pressure (BP) was measured using the tail‐cuff method and validated by direct cannulation. Pulse wave velocity (PWV) was measured using a Doppler workstation. PWV and BP were increased significantly in the old mice, indicating arterial stiffness and hypertension. Intravenous administration of EVs significantly attenuated ageing‐related arterial stiffness and hypertension, while enhancing endothelium‐dependent vascular relaxation and arterial compliance in the old EVs mice. Elastin degradation and collagen I deposition (fibrosis) were increased in aortas of the old mice, but EVs substantially improved ageing‐associated structural remodelling. Mechanistically, EVs abolished downregulation of sirtuin type 1 (SIRT1), and endothelial nitric oxide synthase (eNOS) protein expression in aortas of the older mice. In cultured human aortic endothelial cells, EVs promoted the expression of SIRT1, AMP‐activated protein kinase alpha (AMPKα), and eNOS. In conclusion, iPS‐MSC‐derived EVs attenuated ageing‐associated vascular endothelial dysfunction, arterial stiffness, and hypertension, likely via activation of the SIRT1‐AMPKα‐eNOS pathway and inhibition of MMPs and elastase. Thus, EVs mitigate arterial ageing. This finding also sheds light into the therapeutic potential of EVs for ageing‐related vascular diseases.AbbreviationsEV: Extracellular vesicles; iPS: induced pluripotent stem cell; MSC: mesenchymal stem cell; AMPKα: AMP activated protein kinase α; eNOS: endothelial nitric oxide synthase; Sirt1: sirtuin 1; JNC7: Seventh Report of the Joint National Committee; CVD: cardiovascular disease; PWV: pulse wave velocity; BP: blood pressure; SNP: sodium nitroprusside
One-pion-exchange potential with contact terms from lattice QCD simulations *
Authors: Hu Jinniu , Zhang Ying , Shen Hong , Toki Hiroshi 
Published: June 2020

Abstract
Pion-mass-dependent nucleon-nucleon (NN) potentials are obtained in terms of the one-pion exchange and contact terms from the latest lattice QCD simulations of the two-nucleon system. They assume the forms of the leading order (LO) NN potential from the chiral effective field theory and thus are referred to as the LO chiral potential in this study. We extract the coefficients of contact terms and cut-off momenta in these potentials, for the first time, by fitting the phase shifts of

and

channels obtained from the HALQCD collaboration with various pion masses from 468.6 to 1170.9 MeV. The low-energy constants in the

and

channels become weaker and approach each other for larger pion masses. These LO chiral potentials are applied to symmetric nuclear and pure neutron matter within the Brueckner-Hartree-Fock method. Presently, however, we do not yet have the information of the P-wave NN interaction to be provided by the lattice QCD simulations for a complete description of nuclear matter. Our results enhance understanding of the development of nuclear structure and nuclear matter by controlling the contribution of the pionic effect and elucidate the role of chiral symmetry of the strong interaction in complex systems.