bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of HIV transmitting CD11c+ human epidermal dendritic cells
Authors: Bertram Kirstie M. , Botting Rachel A. , Baharlou Heeva , Rhodes Jake W. , Rana Hafsa , Graham J. Dinny , Patrick Ellis , Fletcher James , Plasto Toby M. , Truong Naomi R. , Royle Caroline , Doyle Chloe M. , Tong Orion , Nasr Najla , Barnouti Laith , Kohout Mark P. , Brooks Andrew J. , Wines Michael P. , Haertsch Peter , Lim Jake , Gosselink Martijn P. , Ctercteko Grahame , Estes Jacob D. , Churchill Melissa J. , Cameron Paul U. , Hunter Eric , Haniffa Muzlifah A. , Cunningham Anthony L. , Harman Andrew N. 
Published: June 2019

AbstractLangerhans cells (LC) are thought to be the only mononuclear phagocyte population in the epidermis where they detect pathogens. Here, we show that CD11c+ dendritic cells (DCs) are also present. These cells are transcriptionally similar to dermal cDC2 but are more efficient antigen-presenting cells. Compared to LCs, epidermal CD11c+ DCs are enriched in anogenital tissues where they preferentially interact with HIV, express the higher levels of HIV entry receptor CCR5, support the higher levels of HIV uptake and replication and are more efficient at transmitting the virus to CD4 T cells. Importantly, these findings are observed using both a lab-adapted and transmitted/founder strain of HIV. We also describe a CD33low cell population, which is transcriptionally similar to LCs but does not appear to function as antigen-presenting cells or acts as HIV target cells. Our findings reveal that epidermal DCs in anogenital tissues potentially play a key role in sexual transmission of HIV.
Evidence for low density holes in Jupiter’s ionosphere
Authors: Imai Masafumi , Kolmašová Ivana , Kurth William S. , Santolík Ondřej , Hospodarsky George B. , Gurnett Donald A. , Brown Shannon T. , Bolton Scott J. , Connerney John E. P. , Levin Steven M. 
Published: June 2019

AbstractIntense electromagnetic impulses induced by Jupiter’s lightning have been recognised to produce both low-frequency dispersed whistler emissions and non-dispersed radio pulses. Here we report the discovery of electromagnetic pulses associated with Jovian lightning. Detected by the Juno Waves instrument during its polar perijove passes, the dispersed millisecond pulses called Jupiter dispersed pulses (JDPs) provide evidence of low density holes in Jupiter’s ionosphere. 445 of these JDP emissions have been observed in snapshots of electric field waveforms. Assuming that the maximum delay occurs in the vicinity of the free space ordinary mode cutoff frequency, we estimate the characteristic plasma densities (5.1 to 250 cm−3) and lengths (0.6 km to 1.3 × 105 km) of plasma irregularities along the line of propagation from lightning to Juno. These irregularities show a direct link to low plasma density holes with ≤250 cm−3 in the nightside ionosphere.
Learning cellular morphology with neural networks
Authors: Schubert Philipp J. , Dorkenwald Sven , Januszewski Michał , Jain Viren , Kornfeld Joergen 
Published: June 2019

AbstractReconstruction and annotation of volume electron microscopy data sets of brain tissue is challenging but can reveal invaluable information about neuronal circuits. Significant progress has recently been made in automated neuron reconstruction as well as automated detection of synapses. However, methods for automating the morphological analysis of nanometer-resolution reconstructions are less established, despite the diversity of possible applications. Here, we introduce cellular morphology neural networks (CMNs), based on multi-view projections sampled from automatically reconstructed cellular fragments of arbitrary size and shape. Using unsupervised training, we infer morphology embeddings (Neuron2vec) of neuron reconstructions and train CMNs to identify glia cells in a supervised classification paradigm, which are then used to resolve neuron reconstruction errors. Finally, we demonstrate that CMNs can be used to identify subcellular compartments and the cell types of neuron reconstructions.
Phononic integrated circuitry and spin–orbit interaction of phonons
Authors: Fu Wei , Shen Zhen , Xu Yuntao , Zou Chang-Ling , Cheng Risheng , Han Xu , Tang Hong X. 
Published: June 2019

AbstractHigh-index-contrast optical waveguides are crucial for the development of photonic integrated circuits with complex functionalities. Despite many similarities between optical and acoustic waves, high-acoustic-index-contrast phononic waveguides remain elusive, preventing intricate manipulation of phonons on par with its photonic counterpart. Here, we present the realization of such phononic waveguides and the formation of phononic integrated circuits through exploiting a gallium-nitride-on-sapphire platform, which provides strong confinement and control of phonons. By demonstrating key building blocks analogous to photonic circuit components, we establish the functionality and scalability of the phononic circuits. Moreover, the unidirectional excitation of propagating phononic modes allows the exploration of unconventional spin–orbit interaction of phonons in this circuit platform, which opens up the possibility of novel applications such as acoustic gyroscopic and non-reciprocal devices. Such phononic integrated circuits could provide an invaluable resource for both classical and quantum information processing.
Reliable electrochemical phase diagrams of magnetic transition metals and related compounds from high-throughput ab initio calculations
Authors: Huang Liang-Feng , Rondinelli James M. 
Published: June 2019

AbstractMagnetic transition metals (mTM = Cr, Mn, Fe, Co, and Ni) and their complex compounds (oxides, hydroxides, and oxyhydroxides) are highly important material platforms for diverse technologies, where electrochemical phase diagrams with respect to electrode potential and solution pH can be used to effectively understand their corrosion and oxidation behaviors in relevant aqueous environments. Many previous decades-old mTM–Pourbaix diagrams are inconsistent with various direct electrochemical observations, because experimental complexities associated with extracting reliable free energies of formation (ΔfG) lead to inaccuracies in the data used for modeling. Here, we develop a high-throughput simulation approach based on density-functional theory (DFT), which quickly screens structures and compounds using efficient DFT methods and calculates accurate ΔfGvalues, using high-level exchange-correlation functions to obtain ab initio Pourbaix diagrams in comprehensive and close agreement with various important electrochemical, geological, and biomagnetic observations reported over the last few decades. We also analyze the microscopic mechanisms governing the chemical trends among the ΔfGvalues and Pourbaix diagrams to further understand the electrochemical behaviors of mTM-based materials. Last, we provide probability profiles at variable electrode potential and solution pH to show quantitatively the likely coexistence of multiple-phase areas and diffuse phase boundaries.
Robust dynamical invariants in sequential neural activity
Authors: Elices Irene , Levi Rafael , Arroyo David , Rodriguez Francisco B. , Varona Pablo 
Published: June 2019

AbstractBy studying different sources of temporal variability in central pattern generator (CPG) circuits, we unveil fundamental aspects of the instantaneous balance between flexibility and robustness in sequential dynamics -a property that characterizes many systems that display neural rhythms. Our analysis of the triphasic rhythm of the pyloric CPG (Carcinus maenas) shows strong robustness of transient dynamics in keeping not only the activation sequences but also specific cycle-by-cycle temporal relationships in the form of strong linear correlations between pivotal time intervals, i.e. dynamical invariants. The level of variability and coordination was characterized using intrinsic time references and intervals in long recordings of both regular and irregular rhythms. Out of the many possible combinations of time intervals studied, only two cycle-by-cycle dynamical invariants were identified, existing even outside steady states. While executing a neural sequence, dynamical invariants reflect constraints to optimize functionality by shaping the actual intervals in which activity emerges to build the sequence. Our results indicate that such boundaries to the adaptability arise from the interaction between the rich dynamics of neurons and connections. We suggest that invariant temporal sequence relationships could be present in other networks, including those shaping sequences of functional brain rhythms, and underlie rhythm programming and functionality.
Analysis of enriched rare variants in JPH2-encoded junctophilin-2 among Greater Middle Eastern individuals reveals a novel homozygous variant associated with neonatal dilated cardiomyopathy
Authors: Jones Edward G. , Mazaheri Neda , Maroofian Reza , Zamani Mina , Seifi Tahereh , Sedaghat Alireza , Shariati Gholamreza , Jamshidi Yalda , Allen Hugh D. , Wehrens Xander H. T. , Galehdari Hamid , Landstrom Andrew P. 
Published: June 2019

AbstractJunctophilin-2 (JPH2) is a part of the junctional membrane complex that facilitates calcium-handling in the cardiomyocyte. Previously, missense variants in JPH2 have been linked to hypertrophic cardiomyopathy; however, pathogenic “loss of function” (LOF) variants have not been described. Family-based genetic analysis of GME individuals with cardiomyopathic disease identified an Iranian patient with dilated cardiomyopathy (DCM) as a carrier of a novel, homozygous single nucleotide insertion in JPH2 resulting in a stop codon (JPH2-p.E641*). A second Iranian family with consanguineous parents hosting an identical heterozygous variant had 2 children die in childhood from cardiac failure. To characterize ethnicity-dependent genetic variability in JPH2 and to identify homozygous JPH2 variants associated with cardiac disease, we identified variants in JPH2 in a worldwide control cohort (gnomAD) and 2 similar cohorts from the Greater Middle East (GME Variome, Iranome). These were compared against ethnicity-matched clinical whole exome sequencing (WES) referral tests and a case cohort of individuals with hypertrophic cardiomyopathy (HCM) based on comprehensive review of the literature. Worldwide, 1.45% of healthy individuals hosted a rare JPH2 variant with a significantly higher proportion among GME individuals (4.45%); LOF variants were rare overall (0.04%) yet were most prevalent in GME (0.21%). The increased prevalence of LOF variants in GME individuals was corroborated among region-specific, clinical WES cohorts. In conclusion, we report ethnic-specific differences in JPH2 rare variants, with GME individuals being at higher risk of hosting homozygous LOF variants. This conclusion is supported by the identification of a novel JPH2 LOF variant confirmed by segregation analysis resulting in autosomal recessive pediatric DCM due to presumptive JPH2 truncation.
Optical Coherence Tomography Angiography for Diagnosis of Choroidal Neovascularization in Chronic Central Serous Chorioretinopathy after Photodynamic Therapy
Authors: Wu Jian-Sheng , Chen San-Ni 
Published: June 2019

AbstractThe authors evaluated the proportion of choroidal neovascularization (CNV) detected by spectral-domain optical coherence tomography angiography (OCTA) in eyes with chronic central serous chorioretinopathy (CSC) (more than 3 months) with previous treatment via half-dose photodynamic therapy (PDT). All patients were followed up with at least twelve months. Macular angiograms were obtained using spectral-domain OCT (SD-OCT, RTVue XR; Optovue). CNV was defined as flow in the outer retinal slab between the outer plexiform layer and Bruch’s membrane. Clinical characteristics were compared between CNV and non-CNV groups. Seventy eyes of 61 patients (51 male and 10 female) were included. The average age was 46.2 years old. The average duration of symptom was 32.9 months. All patients were treated with half-dose PDT initially. Eleven eyes (15.7%) received more than one session of PDT. CNV was diagnosed in 32 of 70 eyes (45.7%) based on OCTA. Only 6 of the 32 eyes (18.8%) needed intravitreal anti- vascular endothelial growth factor (VEGF) therapy for the exudative activity of CNV. Older age (p = 0.059), larger PDT spot size (p = 0.024), and thinner subfoveal choroidal thickness (p = 0.008) were noted in CNV group. The authors conclude that OCTA reveals high rates of CNV associated with chronic CSC after PDT. Patients in the CNV group had older age, larger PDT spot size, and thinner subfoveal choroidal thickness. OCTA may be considered as a first step in identifying CNV in chronic CSC following PDT.
Drug repurposing in alternative medicine: herbal digestive Sochehwan exerts multifaceted effects against metabolic syndrome
Authors: Lim Dong-Woo , Kim Hyuck , Kim Young-Mi , Chin Young-Won , Park Won-Hwan , Kim Jai-Eun 
Published: June 2019

AbstractNew drug development is a challenging process that requires high-risk, huge costs and long lead times. Therefore, drug repurposing is considered a strategic and economic way towards successful drug development. Sochehwan (SCH) is a herbal formula well known as a digestive aid in traditional oriental medicine, is referred to in classic medical texts, and is available as an over-the-counter drug for indications of digestive ailments. Interestingly, another medical text written in earlier age describes different indication of SCH yet to be examined. We conducted a series of investigations using maturated adipocytes, free fatty acid (FFA) induced hepatic steatosis model in vitro and high-fat diet (HFD) mice model in vivo. Exposure to SCH regulated expression of adipogenic genes and proteins, significantly inhibiting formation of lipid droplets in 3T3-L1 cells. Similarly, SCH treatment modulated proteins related with energy metabolism decreasing lipid accumulation in FFA induced HepG2 cells. Furthermore, HFD-fed c57BL/6 J mice supplemented with SCH exhibited significant changes in serum glucose and lipid profiles. Histologic analysis of mice liver and adipose tissue showed that SCH administration attenuated hepatic steatosis and hypertrophy of adipose tissue. In overall, the results show that SCH can potentially be used to treat metabolic syndrome (MetS) by enhancing glucose metabolism and inhibiting lipogenesis through activating AMP-activated protein kinase (AMPK) and its downstream signaling. Furthermore, it seems to be a feasible drug repurposing strategy for drugs originating from alternative medicine to revise the value for buried indications of some herbal prescription in old traditional Chinese Medicine (TCM) classics.
Polymorphisms of the cryptochrome 2 and mitoguardin 2 genes are associated with the variation of lipid-related traits in Duroc pigs
Authors: Mármol-Sánchez Emilio , Quintanilla Raquel , Cardoso Taina F. , Jordana Vidal Jordi , Amills Marcel 
Published: June 2019

AbstractThe genetic factors determining the phenotypic variation of porcine fatness phenotypes are still largely unknown. We investigated whether the polymorphism of eight genes (MIGA2, CRY2, NPAS2, CIART, ARNTL2, PER1, PER2 and PCK1), which display differential expression in the skeletal muscle of fasted and fed sows, is associated with the variation of lipid and mRNA expression phenotypes in Duroc pigs. The performance of an association analysis with the GEMMA software demonstrated that the rs330779504 SNP in the MIGA2 gene is associated with LDL concentration at 190 days (LDL2, corrected P-value = 0.057). Moreover, the rs320439526 SNP of the CRY2 gene displayed a significant association with stearic acid content in the longissimus dorsi muscle (LD C18:0, corrected P-value = 0.015). Both SNPs were also associated with the mRNA levels of the corresponding genes in the gluteus medius skeletal muscle. From a biological perspective these results are meaningful because MIGA2 protein plays an essential role in mitochondrial fusion, a process tightly connected with the energy status of the cell, while CRY2 is a fundamental component of the circadian clock. However, inclusion of these two SNPs in chromosome-wide association analyses demonstrated that they are not located at the peaks of significance for the two traits under study (LDL2 for rs330779504 and LD C18:0 for rs320439526), thus implying that these two SNPs do not have causal effects.
In-plane Aligned Colloidal 2D WS2 Nanoflakes for Solution-Processable Thin Films with High Planar Conductivity
Authors: Mastria Rosanna , Scarfiello Riccardo , Altamura Davide , Giannini Cinzia , Liscio Andrea , Kovtun Alessandro , Bianco Giuseppe Valerio , Bruno Giovanni , Grillo Vincenzo , Tavabi Amir H. , Dunin-Borkowski Rafal E. , Nobile Concetta , Cola Adriano , Cozzoli P. Davide , Gambino Salvatore , Rizzo Aurora 
Published: June 2019

AbstractTwo-dimensional transition-metal dichalcolgenides (2D-TMDs) are among the most intriguing materials for next-generation electronic and optoelectronic devices. Albeit still at the embryonic stage, building thin films by manipulating and stacking preformed 2D nanosheets is now emerging as a practical and cost-effective bottom-up paradigm to obtain excellent electrical properties over large areas. Herein, we exploit the ultrathin morphology and outstanding solution stability of 2D WS2colloidal nanocrystals to make thin films of TMDs assembled on a millimetre scale by a layer-by-layer deposition approach. We found that a room-temperature surface treatment with a superacid, performed with the precise scope of removing the native insulating surfactants, promotes in-plane assembly of the colloidal WS2nanoflakes into stacks parallel to the substrate, along with healing of sulphur vacancies in the lattice that are detrimental to electrical conductivity. The as-obtained 2D WS2thin films, characterized by a smooth and compact morphology, feature a high planar conductivity of up to 1 μS, comparable to the values reported for epitaxially grown WS2monolayers, and enable photocurrent generation upon light irradiation over a wide range of visible to near-infrared frequencies.
A Simple Procedure for Creating Scalable Phenotypic Screening Assays in Human Neurons
Authors: Sridharan BanuPriya , Hubbs Christopher , Llamosas Nerea , Kilinc Murat , Singhera Fakhar U. , Willems Erik , Piper David R. , Scampavia Louis , Rumbaugh Gavin , Spicer Timothy P. 
Published: June 2019

AbstractNeurons created from human induced pluripotent stem cells (hiPSCs) provide the capability of identifying biological mechanisms that underlie brain disorders. IPSC-derived human neurons, or iNs, hold promise for advancing precision medicine through drug screening, though it remains unclear to what extent iNs can support early-stage drug discovery efforts in industrial-scale screening centers. Despite several reported approaches to generate iNs from iPSCs, each suffer from technological limitations that challenge their scalability and reproducibility, both requirements for successful screening assays. We addressed these challenges by initially removing the roadblocks related to scaling of iNs for high throughput screening (HTS)-ready assays. We accomplished this by simplifying the production and plating of iNs and adapting them to a freezer-ready format. We then tested the performance of freezer-ready iNs in an HTS-amenable phenotypic assay that measured neurite outgrowth. This assay successfully identified small molecule inhibitors of neurite outgrowth. Importantly, we provide evidence that this scalable iN-based assay was both robust and highly reproducible across different laboratories. These streamlined approaches are compatible with any iPSC line that can produce iNs. Thus, our findings indicate that current methods for producing iPSCs are appropriate for large-scale drug-discovery campaigns (i.e. >10e5compounds) that read out simple neuronal phenotypes. However, due to the inherent limitations of currently available iN differentiation protocols, technological advances are required to achieve similar scalability for screens that require more complex phenotypes related to neuronal function.
Effects of ten years organic and conventional farming on early seedling traits of evolving winter wheat composite cross populations
Authors: A.V. Vijaya Bhaskar , Baresel Jörg Peter , Weedon Odette , Finckh Maria R. 
Published: June 2019

AbstractEarly vigour traits of wheat composite cross populations (CCPs) based on high yielding (Y) or high quality (Q) or Y*Q varietal intercross evolving under organic or conventional conditions in parallel populations were studied hydroponically. To eliminate storage and year effects, frozen F6, F10, F11and F15seeds were multiplied in one field, resulting in the respective Fx.1generations. This eliminated generation and growing system effects on seed size for the F6.1F10.1and F15.1.Due to a severe winter kill affecting the F11, the generation effect persisted, leading to larger seeds and markedly different seedling traits in the F11.1compared to the F10.1and F15.1. Seedling traits were similar among parallel populations. Shoot length and weight increased in both systems until the F11.1across farming systems and remained constant thereafter. Over time,seminal root length and root weight of organic CCPs increased and total- and specific- root length decreased significantly compared to the conventional CCPs. Rooting patterns under organic conditions suggests better ability to reach deeper soil nutrients. In both systems, Q and YQ CCPs were more vigorous than Y CCPs, confirming genetic differences among populations. Overall, heterogeneous populations appear very plastic and selection pressure was stronger in organic systems.
Sources, distribution and fate of microfibres on the Great Barrier Reef, Australia
Authors: Jensen Lene H. , Motti Cherie A. , Garm Anders L. , Tonin Hemerson , Kroon Frederieke J. 
Published: June 2019

AbstractMarine microdebris, in particular microplastics (plastics <5 mm), has become an issue of international concern due to its prevalence, persistence and potential adverse impacts on marine ecosystems. Informing source reduction based on ecological effects requires an understanding of the origin, distribution and characteristics of microdebris and the interactions with marine organisms. Here we show widespread contamination of the central Great Barrier Reef environment with microdebris, with microfibres comprising 86% of all items detected. Microdebris intake by coral reef fish was non-random, with chemical composition, shape and colour differing significantly from that detected in surface waters. Furthermore, the origin of microdebris contamination in surface waters is non-random with riverine discharge a likely source for microdebris detected at inshore, but not at offshore reef locations. Our findings demonstrate the complexities associated with determining marine microdebris exposure and fate, and assist in improving future ecological assessments and prioritizing source reduction.