bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal True Time Delay Filter With Application to FPGA Firmware‐Based Phased Array Radar Signal Processing
Authors: Lehtinen Markku , Damtie Baylie , Orispää Mikko 
Published: August 2019

AbstractThe European Incoherent Scatter‐3D phased array radar system will be largely based on field‐programmable gate array (FPGA) firmware electronics that carry out the signal processing by using different digital filters. In this paper we have presented a method of designing an optimal true time delay finite impulse response filter with applications to an FPGA firmware‐based multichannel signal processing system. The method provides an optimal true time delay finite impulse response filter with the desired responses at both band pass and stopband. This is possible by finding a mathematical minimization solution for the total power of all filter coefficients longer than a prespecified half‐length. The analysis is based on freely choosing the responses in the transition band until user‐specified desired responses are achieved. We have investigated the performance of these optimal digital filters in terms of the required digital signal processing (DSP) resources in GMACs (giga multiply accumulates per second) by considering both all‐in‐one stage filtering and cascaded solutions for ion and plasma line incoherent scatter radar measurements. We have shown that the cascaded solution provides more efficient utilization of DSP resources and hence represents the optimal choice for processing the proposed European Incoherent Scatter‐3D phased array radar signals. An example is demonstrated in which 906.88 GMACs are required to process 208 ion line beams with 2×4‐bit resolution in all‐in‐one stage processing, as compared to the 79.16 GMACs needed for a similar task in a cascaded solution.
Cavity-control of interlayer excitons in van der Waals heterostructures
Authors: Förg Michael , Colombier Léo , Patel Robin K. , Lindlau Jessica , Mohite Aditya D. , Yamaguchi Hisato , Glazov Mikhail M. , Hunger David , Högele Alexander 
Published: August 2019

AbstractMonolayer transition metal dichalcogenides integrated in optical microcavities host exciton-polaritons as a hallmark of the strong light-matter coupling regime. Analogous concepts for hybrid light-matter systems employing spatially indirect excitons with a permanent electric dipole moment in heterobilayer crystals promise realizations of exciton-polariton gases and condensates with inherent dipolar interactions. Here, we implement cavity-control of interlayer excitons in vertical MoSe2-WSe2 heterostructures. Our experiments demonstrate the Purcell effect for heterobilayer emission in cavity-modified photonic environments, and quantify the light-matter coupling strength of interlayer excitons. The results will facilitate further developments of dipolar exciton-polariton gases and condensates in hybrid cavity – van der Waals heterostructure systems.
Electrical pulse-induced electrochemical biosensor for hepatitis E virus detection
Authors: Chowdhury Ankan Dutta , Takemura Kenshin , Li Tian-Cheng , Suzuki Tetsuro , Park Enoch Y. 
Published: August 2019

AbstractHepatitis E virus (HEV) is one of the leading causes of acute viral hepatitis worldwide. In this work, a pulse-triggered ultrasensitive electrochemical sensor was fabricated using graphene quantum dots and gold-embedded polyaniline nanowires, prepared via an interfacial polymerization and then self-assembly approach. Introducing an external electrical pulse during the virus accumulation step increases the sensitivity towards HEV due to the expanded surface of the virus particle as well as the antibody-conjugated polyaniline chain length, compared to other conventional electrochemical sensors. The sensor was applied to various HEV genotypes, including G1, G3, G7 and ferret HEV obtained from cell culture supernatant and in a series of fecal specimen samples collected from G7 HEV-infected monkey. The sensitivity is similar to that detected by real-time quantitative reverse transcription-polymerase chain (RT-qPCR). These results suggests that the proposed sensor can pave the way for the development of robust, high-performance sensing methodologies for HEV detection.
IP3 receptor isoforms differently regulate ER-mitochondrial contacts and local calcium transfer
Authors: Bartok Adam , Weaver David , Golenár Tünde , Nichtova Zuzana , Katona Máté , Bánsághi Száva , Alzayady Kamil J. , Thomas V. Kaye , Ando Hideaki , Mikoshiba Katsuhiko , Joseph Suresh K. , Yule David I. , Csordás György , Hajnóczky György 
Published: August 2019

AbstractContact sites of endoplasmic reticulum (ER) and mitochondria locally convey calcium signals between the IP3 receptors (IP3R) and the mitochondrial calcium uniporter, and are central to cell survival. It remains unclear whether IP3Rs also have a structural role in contact formation and whether the different IP3R isoforms have redundant functions. Using an IP3R-deficient cell model rescued with each of the three IP3R isoforms and an array of super-resolution and ultrastructural approaches we demonstrate that IP3Rs are required for maintaining ER-mitochondrial contacts. This role is independent of calcium fluxes. We also show that, while each isoform can support contacts, type 2 IP3R is the most effective in delivering calcium to the mitochondria. Thus, these studies reveal a non-canonical, structural role for the IP3Rs and direct attention towards the type 2 IP3R that was previously neglected in the context of ER-mitochondrial calcium signaling.
Periodicity of molecular clusters based on symmetry-adapted orbital model
Authors: Tsukamoto Takamasa , Haruta Naoki , Kambe Tetsuya , Kuzume Akiyoshi , Yamamoto Kimihisa 
Published: August 2019

AbstractThe periodic table has always contributed to the discovery of a number of elements. Is there no such principle for larger-scale substances than atoms? Many stable substances such as clusters have been predicted based on the jellium model, which usually assumes that their structures are approximately spherical. The jellium model is effective to explain subglobular clusters such as icosahedral clusters. To broaden the scope of this model, we propose the symmetry-adapted orbital model, which explicitly takes into account the level splittings of the electronic orbitals due to lower structural symmetries. This refinement indicates the possibility of an abundance of stable clusters with various shapes that obey a certain periodicity. Many existing substances are also governed by the same rule. Consequently, all substances with the same symmetry can be unified into a periodic framework in analogy to the periodic table of elements, which will act as a useful compass to find missing substances.
Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes
Authors: Wang Hong , Diaz Alexander K. , Shaw Timothy I. , Li Yuxin , Niu Mingming , Cho Ji-Hoon , Paugh Barbara S. , Zhang Yang , Sifford Jeffrey , Bai Bing , Wu Zhiping , Tan Haiyan , Zhou Suiping , Hover Laura D. , Tillman Heather S. , Shirinifard Abbas , Thiagarajan Suresh , Sablauer Andras , Pagala Vishwajeeth , High Anthony A. , Wang Xusheng , Li Chunliang , Baker Suzanne J. , Peng Junmin 
Published: August 2019

AbstractHigh throughput omics approaches provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of whole proteome, phosphoproteome and transcriptome in two high-grade glioma (HGG) mouse models driven by mutated RTK oncogenes, PDGFRA and NTRK1, analyzing 13,860 proteins and 30,431 phosphosites by mass spectrometry. Systems biology approaches identify numerous master regulators, including 41 kinases and 23 transcription factors. Pathway activity computation and mouse survival indicate the NTRK1 mutation induces a higher activation of AKT downstream targets including MYC and JUN, drives a positive feedback loop to up-regulate multiple other RTKs, and confers higher oncogenic potency than the PDGFRA mutation. A mini-gRNA library CRISPR-Cas9 validation screening shows 56% of tested master regulators are important for the viability of NTRK-driven HGG cells, including TFs (Myc and Jun) and metabolic kinases (AMPKa1 and AMPKa2), confirming the validity of the multiomics integrative approaches, and providing novel tumor vulnerabilities.
Heterogeneity in respiratory electron transfer and adaptive iron utilization in a bacterial biofilm
Authors: Qin Yuxuan , He Yinghao , She Qianxuan , Larese-Casanova Philip , Li Pinglan , Chai Yunrong 
Published: August 2019

AbstractIn Bacillus subtilis, robust biofilm formation requires large quantities of ferric iron. Here we show that this process requires preferential production of a siderophore precursor, 2,3-dihydroxybenzoate, instead of the siderophore bacillibactin. A large proportion of iron is associated extracellularly with the biofilm matrix. The biofilms are conductive, with extracellular iron potentially acting as electron acceptor. A relatively small proportion of ferric iron is internalized and boosts production of iron-containing enzymes involved in respiratory electron transfer and establishing strong membrane potential, which is key to biofilm matrix production. Our study highlights metabolic diversity and versatile energy generation strategies within B. subtilis biofilms.
High-throughput screen reveals sRNAs regulating crRNA biogenesis by targeting CRISPR leader to repress Rho termination
Authors: Lin Ping , Pu Qinqin , Wu Qun , Zhou Chuanmin , Wang Biao , Schettler Jacob , Wang Zhihan , Qin Shugang , Gao Pan , Li Rongpeng , Li Guoping , Cheng Zhenyu , Lan Lefu , Jiang Jianxin , Wu Min 
Published: August 2019

AbstractDiscovery of CRISPR-Cas systems is one of paramount importance in the field of microbiology. Currently, how CRISPR-Cas systems are finely regulated remains to be defined. Here we use small regulatory RNA (sRNA) library to screen sRNAs targeting type I-F CRISPR-Cas system through proximity ligation by T4 RNA ligase and find 34 sRNAs linking to CRISPR loci. Among 34 sRNAs for potential regulators of CRISPR, sRNA pant463 and PhrS enhance CRISPR loci transcription, while pant391 represses their transcription. We identify PhrS as a regulator of CRISPR-Cas by binding CRISPR leaders to suppress Rho-dependent transcription termination. PhrS-mediated anti-termination facilitates CRISPR locus transcription to generate CRISPR RNA (crRNA) and subsequently promotes CRISPR-Cas adaptive immunity against bacteriophage invasion. Furthermore, this also exists in type I-C/-E CRISPR-Cas, suggesting general regulatory mechanisms in bacteria kingdom. Our findings identify sRNAs as important regulators of CRISPR-Cas, extending roles of sRNAs in controlling bacterial physiology by promoting CRISPR-Cas adaptation priming.
Interband resonant high-harmonic generation by valley polarized electron–hole pairs
Authors: Yoshikawa Naotaka , Nagai Kohei , Uchida Kento , Takaguchi Yuhei , Sasaki Shogo , Miyata Yasumitsu , Tanaka Koichiro 
Published: August 2019

AbstractHigh-harmonic generation in solids is a unique tool to investigate the electron dynamics in strong light fields. The systematic study in monolayer materials is required to deepen the insight into the fundamental mechanism of high-harmonic generation. Here we demonstrated nonperturbative high harmonics up to 18th order in monolayer transition metal dichalcogenides. We found the enhancement in the even-order high harmonics which is attributed to the resonance to the band nesting energy. The symmetry analysis shows that the valley polarization and anisotropic band structure lead to polarization of the high-harmonic radiation. The calculation based on the three-step model in solids revealed that the electron–hole polarization driven to the band nesting region should contribute to the high harmonic radiation, where the electrons and holes generated at neighboring lattice sites are taken into account. Our findings open the way for attosecond science with monolayer materials having widely tunable electronic structures.
Optically invariant InGaN nanowire light-emitting diodes on flexible substrates under mechanical manipulation
Authors: Asad Mohsen , Wang Renjie , Ra Yong-Ho , Gavirneni Pranav , Mi Zetian , Wong William S. 
Published: August 2019

AbstractThe integration of GaN-based light-emitting diodes (LEDs) onto flexible platforms provides opportunities for conformal lighting, wearable electronics, and bendable displays. While this technology may enhance the functionality of the light source, the development of flexible GaN LEDs suffers from performance degradation, when mechanical bending is applied during operation. A unique approach to eliminate the degradation employs dot-in-wire structures, using cylindrical light-emitting heterostructures that protrude above the flexible platform, separating the active light-emitting region from the bending substrate. Here, we demonstrate the optical enhancement of nanowire light emitters by changing the geometric orientation within a 1 × 1 mm2 array of nanowires on a flexible platform through bending of the substrate platform. The flexible structures were achieved by transferring GaN nanowire LEDs from sapphire substrates onto flexible polyethylene terephthalate (PET) using a “paste-and-cut” integration process. The I–V characteristics of the nanowire LEDs showed negligible change after integration onto the PET, with a turn-on voltage of 2.5 V and a forward current of 400 μA at 4 V. A significant advantage for the nanowire devices on PET was demonstrated by tilting the LEDs through substrate bending that increased the electroluminescence (EL) intensity, while the I–V characteristics and the EL peak position remained constant. Through finite-element analysis and three-dimensional finite-difference time-domain modeling, it was determined that tilting the protruding devices changed the effective distance between the structures, enhancing their electromagnetic coupling to increase light output without affecting the electrical properties or peak emission wavelength of the LEDs.
Electronic band tuning under pressure in MoTe2 topological semimetal
Authors: Dissanayake Sachith , Duan Chunruo , Yang Junjie , Liu Jun , Matsuda Masaaki , Yue Changming , Schneeloch John A. , Teo Jeffrey C. Y. , Louca Despina 
Published: August 2019

AbstractTopological superconductors (TSC) can host exotic quasiparticles such as Majorana fermions, poised as the fundamental qubits for quantum computers. TSC’s are predicted to form a superconducting gap in the bulk, and gapless surface/edges states which can lead to the emergence of Majorana zero energy modes. A candidate TSC is the layered dichalcogenide MoTe2, a type-II Weyl (semi)metal in the non-centrosymmetric orthorhombic (Td) phase. It becomes superconducting upon cooling below 0.25 K, while under pressure, superconductivity extends well beyond the structural boundary between the orthorhombic and monoclinic (1T′) phases. Here, we show that under pressure, coupled with the electronic band transition across the Td to 1T′ phase boundary, evidence for a new phase, we call Td* is observed and appears as the volume fraction of the Td phase decreases in the coexistence region. Td* is most likely centrosymmetric. In the region of space where Td* appears, Weyl nodes are destroyed. Td* disappears upon entering the monoclinic phase as a function of temperature or on approaching the suppression of the orthorhombic phase under pressure above 1 GPa. Our calculations in the orthorhombic phase under pressure show significant band tilting around the Weyl nodes that most likely changes the spin-orbital texture of the electron and hole pockets near the Fermi surface under pressure that may be linked to the observed suppression of magnetoresistance with pressure.
Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma
Authors: Jafarnejad Mohammad , Sové Richard J. , Danilova Ludmila , Mirando Adam C. , Zhang Yu , Yarchoan Mark , Tran Phuoc T. , Pandey Niranjan B. , Fertig Elana J. , Popel Aleksander S. 
Published: August 2019

AbstractHepatocyte growth factor (HGF) signaling through its receptor Met has been implicated in hepatocellular carcinoma tumorigenesis and progression. Met interaction with integrins is shown to modulate the downstream signaling to Akt and ERK (extracellular-regulated kinase). In this study, we developed a mechanistically detailed systems biology model of HGF/Met signaling pathway that incorporated specific interactions with integrins to investigate the efficacy of integrin-binding peptide, AXT050, as monotherapy and in combination with other therapeutics targeting this pathway. Here we report that the modeled dynamics of the response to AXT050 revealed that receptor trafficking is sufficient to explain the effect of Met–integrin interactions on HGF signaling. Furthermore, the model predicted patient-specific synergy and antagonism of efficacy and potency for combination of AXT050 with sorafenib, cabozantinib, and rilotumumab. Overall, the model provides a valuable framework for studying the efficacy of drugs targeting receptor tyrosine kinase interaction with integrins, and identification of synergistic drug combinations for the patients.
TRPM1 Mutations are the Most Common Cause of Autosomal Recessive Congenital Stationary Night Blindness (CSNB) in the Palestinian and Israeli Populations
Authors: AlTalbishi Alaa , Zelinger Lina , Zeitz Christina , Hendler Karen , Namburi Prasanthi , Audo Isabelle , Sheffer Ruth , Yahalom Claudia , Khateb Samer , Banin Eyal , Sharon Dror 
Published: August 2019

AbstractPrecise genetic and phenotypic characterization of congenital stationary night blindness (CSNB) patients is needed for future therapeutic interventions. The aim of this study was to estimate the prevalence of CSNB in our populations and to study clinical and genetic aspects of the autosomal recessive (AR) form of CSNB. This is a retrospective cohort study of Palestinian and Israeli CSNB patients harboring mutations in TRPM1 underwent comprehensive ocular examination. Genetic analysis was performed using homozygosity mapping and sequencing. 161 patients (from 76 families) were recruited for this study, leading to a prevalence of 1:6210 in the vicinity of Jerusalem, much higher than the worldwide prevalence. 61% of the families were consanguineous with AR inheritance pattern. Biallelic pathogenic TRPM1 mutations were identified in 36 families (72 patients). Two founder mutations explain the vast majority of cases: a nonsense mutation c.880A>T (p.Lys294*) identified in 22 Palestinian families and a large genomic deletion (36,445 bp) encompassing exons 2–7 of TRPM1 present in 13 Ashkenazi Jewish families. Most patients were myopic (with mean BCVA of 0.40 LogMAR) and all had absent rod responses in full field electroretinography. To the best of our knowledge, this is the largest report of a clinical and genetic analysis of patients affected with CSNB due to TRPM1 mutations.
Biochar amendment improves degraded pasturelands in Brazil: environmental and cost-benefit analysis
Authors: Latawiec Agnieszka E. , Strassburg Bernardo B. N. , Junqueira André B. , Araujo Ednaldo , D. de Moraes Luiz Fernando , Pinto Helena A. N. , Castro Ana , Rangel Marcio , Malaguti Gustavo A. , Rodrigues Aline F. , Barioni Luis Gustavo , Novotny Etelvino H. , Cornelissen Gerard , Mendes Maiara , Batista Nilcileny , Guerra Jose Guilherme , Zonta Everaldo , Jakovac Catarina , Hale Sarah E. 
Published: August 2019

AbstractMost deforested lands in Brazil are occupied by low-productivity cattle ranching. Brazil is the second biggest meat producer worldwide and is projected to increase its agricultural output more than any other country. Biochar has been shown to improve soil properties and agricultural productivity when added to degraded soils, but these effects are context-dependent. The impact of biochar, fertilizer and inoculant on the productivity of forage grasses in Brazil (Brachiaria spp. and Panicum spp.) was investigated from environmental and socio-economic perspectives. We showed a 27% average increase in Brachiaria production over two years but no significant effects of amendment on Panicum yield. Biochar addition also increased the contents of macronutrients, soil pH and CEC. Each hectare amended with biochar saved 91 tonnes of CO2eq through land sparing effect, 13 tonnes of CO2eq sequestered in the soil, equating to U$455 in carbon payments. The costs of biochar production for smallholder farmers, mostly because of labour cost, outweighed the potential benefits of its use. Biochar is 617% more expensive than common fertilizers. Biochar could improve productivity of degraded pasturelands in Brazil if investments in efficient biochar production techniques are used and biochar is subsidized by low emission incentive schemes.
The Effect of Mindfulness Meditation on Impulsivity and its Neurobiological Correlates in Healthy Adults
Authors: Korponay Cole , Dentico Daniela , Kral Tammi R. A. , Ly Martina , Kruis Ayla , Davis Kaley , Goldman Robin , Lutz Antoine , Davidson Richard J. 
Published: August 2019

AbstractInterest has grown in using mindfulness meditation to treat conditions featuring excessive impulsivity. However, while prior studies find that mindfulness practice can improve attention, it remains unclear whether it improves other cognitive faculties whose deficiency can contribute to impulsivity. Here, an eight-week mindfulness intervention did not reduce impulsivity on the go/no-go task or Barratt Impulsiveness Scale (BIS-11), nor produce changes in neural correlates of impulsivity (i.e. frontostriatal gray matter, functional connectivity, and dopamine levels) compared to active or wait-list control groups. Separately, long-term meditators (LTMs) did not perform differently than meditation-naïve participants (MNPs) on the go/no-go task. However, LTMs self-reported lower attentional impulsivity, but higher motor and non-planning impulsivity on the BIS-11 than MNPs. LTMs had less striatal gray matter, greater cortico-striatal-thalamic functional connectivity, and lower spontaneous eye-blink rate (a physiological dopamine indicator) than MNPs. LTM total lifetime practice hours (TLPH) did not significantly relate to impulsivity or neurobiological metrics. Findings suggest that neither short- nor long-term mindfulness practice may be effective for redressing impulsive behavior derived from inhibitory motor control or planning capacity deficits in healthy adults. Given the absence of TLPH relationships to impulsivity or neurobiological metrics, differences between LTMs and MNPs may be attributable to pre-existing differences.
Interaction of microtubules and actin during the post-fusion phase of exocytosis
Authors: Müller M. Tabitha , Schempp Rebekka , Lutz Anngrit , Felder Tatiana , Felder Edward , Miklavc Pika 
Published: August 2019

AbstractExocytosis is the intracellular trafficking step where a secretory vesicle fuses with the plasma membrane to release vesicle content. Actin and microtubules both play a role in exocytosis; however, their interplay is not understood. Here we study the interaction of actin and microtubules during exocytosis in lung alveolar type II (ATII) cells that secrete surfactant from large secretory vesicles. Surfactant extrusion is facilitated by an actin coat that forms on the vesicle shortly after fusion pore opening. Actin coat compression allows hydrophobic surfactant to be released from the vesicle. We show that microtubules are localized close to actin coats and stay close to the coats during their compression. Inhibition of microtubule polymerization by colchicine and nocodazole affected the kinetics of actin coat formation and the extent of actin polymerisation on fused vesicles. In addition, microtubule and actin cross-linking protein IQGAP1 localized to fused secretory vesicles and IQGAP1 silencing influenced actin polymerisation after vesicle fusion. This study demonstrates that microtubules can influence actin coat formation and actin polymerization on secretory vesicles during exocytosis.