bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of Continental Shallow Cumulus Populations Using an Observation‐Constrained Cloud‐System Resolving Model
Authors: Tai Sheng‐Lun , Fast Jerome D. , Gustafson William I. , Chand Duli , Gaudet Brian , Feng Zhe , Newsom Rob 
Published: August 2020

AbstractContinental shallow cumulus (ShCu) clouds observed on 30 August 2016 during the Holistic Interactions of Shallow Clouds, Aerosols, and Land‐Ecosystems (HI‐SCALE) field campaign are simulated by using an observation‐constrained cloud‐system resolving model. On this day, ShCu forms over Oklahoma and southern Kansas and some of these clouds transition to deeper, precipitating convection during the afternoon. We apply a four‐dimensional ensemble‐variational (4DEnVar) hybrid technique in the Community Gridpoint Statistical Interpolation (GSI) system to assimilate operational data sets and unique boundary layer measurements including a Raman lidar, radar wind profilers, radiosondes, and surface stations collected by the U.S. Department of Energy's (DOE) Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) atmospheric observatory into the Weather Research and Forecasting (WRF) model to ascertain how improved environmental conditions can influence forecasts of ShCu populations and the transition to deeper convection. Independent observations from aircraft, satellite, as well as ARM's remote sensors are used to evaluate model performance in different aspects. Several model experiments are conducted to identify the impact of data assimilation (DA) on the prediction of clouds evolution. The analyses indicate that ShCu populations are more accurately reproduced after DA in terms of cloud initiation time and cloud base height, which can be attributed to an improved representation of the ambient meteorological conditions and the convective boundary layer. Extending the assimilation to 18 UTC (local noon) also improved the simulation of shallow‐to‐deep transitions of convective clouds.
Dynamic full-field optical coherence tomography: 3D live-imaging of retinal organoids
Authors: Scholler Jules , Groux Kassandra , Goureau Olivier , Sahel José-Alain , Fink Mathias , Reichman Sacha , Boccara Claude , Grieve Kate 
Published: August 2020

AbstractOptical coherence tomography offers astounding opportunities to image the complex structure of living tissue but lacks functional information. We present dynamic full-field optical coherence tomography as a technique to noninvasively image living human induced pluripotent stem cell-derived retinal organoids. Coloured images with an endogenous contrast linked to organelle motility are generated, with submicrometre spatial resolution and millisecond temporal resolution, creating a way to identify specific cell types in living tissue via their function.
Consequences of NMDA receptor deficiency can be rescued in the adult brain
Authors: Mielnik Catharine A. , Binko Mary A. , Chen Yuxiao , Funk Adam J. , Johansson Emily M. , Intson Katheron , Sivananthan Nirun , Islam Rehnuma , Milenkovic Marija , Horsfall Wendy , Ross Ruth A. , Groc Laurent , Salahpour Ali , McCullumsmith Robert E. , Tripathy Shreejoy , Lambe Evelyn K. , Ramsey Amy J. 
Published: August 2020

AbstractN-methyl-D-aspartate receptors (NMDARs) are required to shape activity-dependent connections in the developing and adult brain. Impaired NMDAR signalling through genetic or environmental insults causes a constellation of neurodevelopmental disorders that manifest as intellectual disability, epilepsy, autism, or schizophrenia. It is not clear whether the developmental impacts of NMDAR dysfunction can be overcome by interventions in adulthood. This question is paramount for neurodevelopmental disorders arising from mutations that occur in the GRIN genes, which encode NMDAR subunits, and the broader set of mutations that disrupt NMDAR function. We developed a mouse model where a congenital loss-of-function allele of Grin1 can be restored to wild type by gene editing with Cre recombinase. Rescue of NMDARs in adult mice yields surprisingly robust improvements in cognitive functions, including those that are refractory to treatment with current medications. These results suggest that neurodevelopmental disorders arising from NMDAR deficiency can be effectively treated in adults.
Clustering by phenotype and genome-wide association study in autism
Authors: Narita Akira , Nagai Masato , Mizuno Satoshi , Ogishima Soichi , Tamiya Gen , Ueki Masao , Sakurai Rieko , Makino Satoshi , Obara Taku , Ishikuro Mami , Yamanaka Chizuru , Matsubara Hiroko , Kuniyoshi Yasutaka , Murakami Keiko , Ueno Fumihiko , Noda Aoi , Kobayashi Tomoko , Kobayashi Mika , Usuzaki Takuma , Ohseto Hisashi , Hozawa Atsushi , Kikuya Masahiro , Metoki Hirohito , Kure Shigeo , Kuriyama Shinichi 
Published: August 2020

AbstractAutism spectrum disorder (ASD) has phenotypically and genetically heterogeneous characteristics. A simulation study demonstrated that attempts to categorize patients with a complex disease into more homogeneous subgroups could have more power to elucidate hidden heritability. We conducted cluster analyses using the k-means algorithm with a cluster number of 15 based on phenotypic variables from the Simons Simplex Collection (SSC). As a preliminary study, we conducted a conventional genome-wide association study (GWAS) with a data set of 597 ASD cases and 370 controls. In the second step, we divided cases based on the clustering results and conducted GWAS in each of the subgroups vs controls (cluster-based GWAS). We also conducted cluster-based GWAS on another SSC data set of 712 probands and 354 controls in the replication stage. In the preliminary study, which was conducted in conventional GWAS design, we observed no significant associations. In the second step of cluster-based GWASs, we identified 65 chromosomal loci, which included 30 intragenic loci located in 21 genes and 35 intergenic loci that satisfied the threshold of P < 5.0 × 10−8. Some of these loci were located within or near previously reported candidate genes for ASD: CDH5, CNTN5, CNTNAP5, DNAH17, DPP10, DSCAM, FOXK1, GABBR2, GRIN2A5, ITPR1, NTM, SDK1, SNCA, and SRRM4. Of these 65 significant chromosomal loci, rs11064685 located within the SRRM4 gene had a significantly different distribution in the cases vs controls in the replication cohort. These findings suggest that clustering may successfully identify subgroups with relatively homogeneous disease etiologies. Further cluster validation and replication studies are warranted in larger cohorts.
Farnesoid X receptor antagonizes Wnt/β-catenin signaling in colorectal tumorigenesis
Authors: Yu Junhui , Li Shan , Guo Jing , Xu Zhengshui , Zheng Jianbao , Sun Xuejun 
Published: August 2020

AbstractFarnesoid X receptor (FXR, encoded by NR1H4), a critical regulator of bile acid homeostasis, is widely implicated in human tumorigenesis. However, the functional role of FXR in colorectal cancer (CRC) and the precise molecular mechanism remain unclear. In this study, we demonstrated that FXR expression was downregulated in colon cancer tissues and decreased expression of FXR predicted a poor prognosis. Knockdown of FXR promoted colon cancer cell growth and invasion in vitro, and facilitated xenograft tumor formation and distant metastasis in vivo, whereas ectopic expression of FXR had the reserved change. Mechanistic studies indicated that FXR exerted its tumor suppressor functions by antagonizing Wnt/β-catenin signaling. Furthermore, we identified an FXR/β-catenin interaction in colon cancer cells. The FXR/β-catenin interaction impaired β-catenin/TCF4 complex formation. In addition, our study suggested a reciprocal relationship between FXR and β-catenin, since loss of β-catenin increased the transcriptional activation of SHP by FXR. Altogether, these data indicated that FXR functions a tumor-suppressor role in CRC by antagonizing Wnt/β-catenin signaling.
Exciton-driven change of phonon modes causes strong temperature dependent bandgap shift in nanoclusters
Authors: Muckel Franziska , Lorenz Severin , Yang Jiwoong , Nugraha Taufik Adi , Scalise Emilio , Hyeon Taeghwan , Wippermann Stefan , Bacher Gerd 
Published: August 2020

AbstractThe fundamental bandgap Eg of a semiconductor—often determined by means of optical spectroscopy—represents its characteristic fingerprint and changes distinctively with temperature. Here, we demonstrate that in magic sized II-VI clusters containing only 26 atoms, a pronounced weakening of the bonds occurs upon optical excitation, which results in a strong exciton-driven shift of the phonon spectrum. As a consequence, a drastic increase of dEg/dT (up to a factor of 2) with respect to bulk material or nanocrystals of typical size is found. We are able to describe our experimental data with excellent quantitative agreement from first principles deriving the bandgap shift with temperature as the vibrational entropy contribution to the free energy difference between the ground and optically excited states. Our work demonstrates how in small nanoparticles, photons as the probe medium affect the bandgap—a fundamental semiconductor property.
Photothermogenetic inhibition of cancer stemness by near-infrared-light-activatable nanocomplexes
Authors: Yu Yue , Yang Xi , Reghu Sheethal , Kaul Sunil C. , Wadhwa Renu , Miyako Eijiro 
Published: August 2020

AbstractStrategies for eradicating cancer stem cells (CSCs) are urgently required because CSCs are resistant to anticancer drugs and cause treatment failure, relapse and metastasis. Here, we show that photoactive functional nanocarbon complexes exhibit unique characteristics, such as homogeneous particle morphology, high water dispersibility, powerful photothermal conversion, rapid photoresponsivity and excellent photothermal stability. In addition, the present biologically permeable second near-infrared (NIR-II) light-induced nanocomplexes photo-thermally trigger calcium influx into target cells overexpressing the transient receptor potential vanilloid family type 2 (TRPV2). This combination of nanomaterial design and genetic engineering effectively eliminates cancer cells and suppresses stemness of cancer cells in vitro and in vivo. Finally, in molecular analyses of mechanisms, we show that inhibition of cancer stemness involves calcium-mediated dysregulation of the Wnt/β-catenin signalling pathway. The present technological concept may lead to innovative therapies to address the global issue of refractory cancers.
Dynamic evolution and reversibility of single-atom Ni(II) active site in 1T-MoS2 electrocatalysts for hydrogen evolution
Authors: Pattengale Brian , Huang Yichao , Yan Xingxu , Yang Sizhuo , Younan Sabrina , Hu Wenhui , Li Zhida , Lee Sungsik , Pan Xiaoqing , Gu Jing , Huang Jier 
Published: August 2020

Abstract1T-MoS2 and single-atom modified analogues represent a highly promising class of low-cost catalysts for hydrogen evolution reaction (HER). However, the role of single atoms, either as active species or promoters, remains vague despite its essentiality toward more efficient HER. In this work, we report the unambiguous identification of Ni single atom as key active sites in the basal plane of 1T-MoS2 (Ni@1T-MoS2) that result in efficient HER performance. The intermediate structure of this Ni active site under catalytic conditions was captured by in situ X-ray absorption spectroscopy, where a reversible metallic Ni species (Ni0) is observed in alkaline conditions whereas Ni remains in its local structure under acidic conditions. These insights provide crucial mechanistic understanding of Ni@1T-MoS2 HER electrocatalysts and suggest that the understanding gained from such in situ studies is necessary toward the development of highly efficient single-atom decorated 1T-MoS2 electrocatalysts.
Human NMD ensues independently of stable ribosome stalling
Authors: Karousis Evangelos D. , Gurzeler Lukas-Adrian , Annibaldis Giuditta , Dreos René , Mühlemann Oliver 
Published: August 2020

AbstractNonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway that is important for the elimination of faulty, and the regulation of normal, mRNAs. The molecular details of the early steps in NMD are not fully understood but previous work suggests that NMD activation occurs as a consequence of ribosome stalling at the termination codon (TC). To test this hypothesis, we established an in vitro translation-coupled toeprinting assay based on lysates from human cells that allows monitoring of ribosome occupancy at the TC of reporter mRNAs. In contrast to the prevailing NMD model, our in vitro system reveals similar ribosomal occupancy at the stop codons of NMD-sensitive and NMD-insensitive reporter mRNAs. Moreover, ribosome profiling reveals a similar density of ribosomes at the TC of endogenous NMD-sensitive and NMD-insensitive mRNAs in vivo. Together, these data show that NMD activation is not accompanied by stable stalling of ribosomes at TCs.
Synthetic photoplethysmogram generation using two Gaussian functions
Authors: Tang Qunfeng , Chen Zhencheng , Ward Rabab , Elgendi Mohamed 
Published: August 2020

AbstractEvaluating the performance of photoplethysmogram (PPG) event detection algorithms requires a large number of PPG signals with different noise levels and sampling frequencies. As publicly available PPG databases provide few options, artificially constructed PPG signals can also be used to facilitate this evaluation. Here, we propose a dynamic model to synthesize PPG over specified time durations and sampling frequencies. In this model, a single pulse was simulated by two Gaussian functions. Additionally, the beat-to-beat intervals were simulated using a normal distribution with a specific mean value and a specific standard deviation value. To add periodicity and to generate a complete signal, the circular motion principle was used. We synthesized three classes of pulses by emulating three different templates: excellent (systolic and diastolic waves are salient), acceptable (systolic and diastolic waves are not salient), and unfit (systolic and diastolic waves are noisy). The optimized model fitting of the Gaussian functions to the templates yielded 0.99, 0.98, and 0.85 correlations between the template and synthetic pulses for the excellent, acceptable, and unfit classes, respectively, with mean square errors of 0.001, 0.003, and 0.017, respectively. By comparing the heart rate variability of real PPG and randomly synthesized PPG for 5 min in 116 records from the MIMIC III database, strong correlations were found in SDNN, RMSSD, LF, HF, SD1, and SD2 (0.99, 0.89, 0.84, 0.89, 0.90 and 0.95, respectively).
Characterization of native plant growth promoting rhizobacteria and their anti-oomycete potential against Phytophthora capsici affecting chilli pepper (Capsicum annum L.)
Authors: Hyder Sajjad , Gondal Amjad Shahzad , Rizvi Zarrin Fatima , Ahmad Raees , Alam Muhammad Mohsin , Hannan Abdul , Ahmed Waqas , Fatima Nida , Inam-ul-Haq M. 
Published: August 2020

AbstractPhytophthora capsici is a notorious fungus which infects many crop plants at their early and late growth stages. In the present study, twelve P. capsici isolates were morphologically characterized, and based on pathogenicity assays; two highly virulent isolates causing post-emergence damping-off on locally cultivated chilli pepper were screened. Two P. capsici isolates, HydPak1 (MF322868) and HydPk2 (MF322869) were identified based on internal transcribed spacer (ITS) sequence homology. Plant growth promoting rhizobacteria (PGPR) play a significant role in disease suppression and plant growth promotion in various crops. Out of fifteen bacterial strains recovered from chilli rhizosphere, eight were found potential antagonists to P. capsici in vitro. Bacterial strains with strong antifungal potential were subjected to biochemical and molecular analysis. All tested bacterial strains, were positive for hydrogen cyanide (HCN), catalase production and indole-3-acetic acid (IAA) production (ranging from 6.10 to 56.23 µg ml−1), while siderophore production varied between 12.5 and 33.5%. The 16S rRNA sequence analysis of tested bacterial strains showed 98–100% identity with Pseudomonas putida, P. libanensis, P. aeruginosa, Bacillus subtilis, B. megaterium, and B. cereus sequences available in the National Center for Biotechnology Information (NCBI) GenBank nucleotide database. All sequences of identified bacteria were submitted to GenBank for accessions numbers (MH796347-50, MH796355-56, MH801129 and MH801071). Greenhouse studies concluded that all tested bacterial strains significantly suppressed the P. capsici infections (52.3–63%) and enhanced the plant growth characters in chilli pepper. Efficacy of many of these tested rhizobacteria is being first time reported against P. capsici from Pakistan. Plant growth promoting rhizobacteria (PGPR) exhibiting multiple traits may be used in the development of new, eco-friendly, and effective bioformulations as an alternative to synthetic fungicides.
Actinobacteria from Antarctica as a source for anticancer discovery
Authors: Silva Leonardo Jose , Crevelin Eduardo José , Souza Danilo Tosta , Lacerda-Júnior Gileno Vieira , de Oliveira Valeria Maia , Ruiz Ana Lucia Tasca Gois , Rosa Luiz Henrique , Moraes Luiz Alberto Beraldo , Melo Itamar Soares 
Published: August 2020

AbstractAlthough many advances have been achieved to treat aggressive tumours, cancer remains a leading cause of death and a public health problem worldwide. Among the main approaches for the discovery of new bioactive agents, the prospect of microbial secondary metabolites represents an effective source for the development of drug leads. In this study, we investigated the actinobacterial diversity associated with an endemic Antarctic species, Deschampsia antarctica, by integrated culture-dependent and culture-independent methods and acknowledged this niche as a reservoir of bioactive strains for the production of antitumour compounds. The 16S rRNA-based analysis showed the predominance of the Actinomycetales order, a well-known group of bioactive metabolite producers belonging to the Actinobacteria phylum. Cultivation techniques were applied, and 72 psychrotolerant Actinobacteria strains belonging to the genera Actinoplanes, Arthrobacter, Kribbella, Mycobacterium, Nocardia, Pilimelia, Pseudarthrobacter, Rhodococcus, Streptacidiphilus, Streptomyces and Tsukamurella were identified. The secondary metabolites were screened, and 17 isolates were identified as promising antitumour compound producers. However, the bio-guided assay showed a pronounced antiproliferative activity for the crude extracts of Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653. The TGI and LC50 values revealed the potential of these natural products to control the proliferation of breast (MCF-7), glioblastoma (U251), lung/non-small (NCI-H460) and kidney (786-0) human cancer cell lines. Cinerubin B and actinomycin V were the predominant compounds identified in Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653, respectively. Our results suggest that the rhizosphere of D. antarctica represents a prominent reservoir of bioactive actinobacteria strains and reveals it as an important environment for potential antitumour agents.
A comparison of the metabolic effects of sustained strenuous activity in polar environments on men and women
Authors: Hattersley John , Wilson Adrian J. , Gifford Rob , Facer-Childs Jamie , Stoten Oliver , Cobb Rinn , Thake C. Doug , Reynolds Rebecca M. , Woods David , Imray Chris 
Published: August 2020

AbstractThis study investigates differences in pre- to post-expedition energy expenditure, substrate utilisation and body composition, between the all-male Spear17 (SP-17) and all-female Ice Maiden (IM) transantarctic expeditions (IM: N = 6, 61 days, 1700 km; SP-17: N = 5, 67 days, 1750 km). Energy expenditure and substrate utilisation were measured by a standardised 36 h calorimetry protocol; body composition was determined using air displacement plethysmography. Energy balance calculation were used to assess the physical challenge. There was difference in the daily energy expenditure (IM: 4,939 kcal day−1; SP-17: 6,461 kcal day−1, p = 0.004); differences related to physical activity were small, but statistically significant (IM = 2,282 kcal day−1; SP-17 = 3,174 kcal day−1; p = 0.004). Bodyweight loss was modest (IM = 7.8%, SP-17 = 6.5%; p > 0.05) as was fat loss (IM = 30.4%, SP-17 = 40.4%; p > 0.05). Lean tissue weight change was statistically significant (IM = − 2.5%, SP-17 = + 1.0%; p = 0.05). No difference was found in resting or sleeping energy expenditure, normalised to lean tissue weight (p > 0.05); nor in energy expenditure when exercising at 80, 100 and 120 steps min−1, normalised to body weight (p > 0.05). Similarly, no difference was found in the change in normalised substrate utilisation for any of the activities (p > 0.05). Analysis suggested that higher daily energy expenditures for the men in Spear-17 was the result of higher physical demands resulting in a reduced demand for energy to thermoregulate compared to the women in Ice Maiden. The lack of differences between men and women in the change in energy expenditure and substrate utilisation, suggests no sex difference in response to exposure to extreme environments.
A common partitivirus infection in United States and Czech Republic isolates of bat white-nose syndrome fungal pathogen Pseudogymnoascus destructans
Authors: Ren Ping , Rajkumar Sunanda S. , Zhang Tao , Sui Haixin , Masters Paul S. , Martinkova Natalia , Kubátová Alena , Pikula Jiri , Chaturvedi Sudha , Chaturvedi Vishnu 
Published: August 2020

AbstractThe psychrophilic (cold-loving) fungus Pseudogymnoascus destructans was discovered more than a decade ago to be the pathogen responsible for white-nose syndrome, an emerging disease of North American bats causing unprecedented population declines. The same species of fungus is found in Europe but without associated mortality in bats. We found P. destructans was infected with a mycovirus [named Pseudogymnoascus destructans partitivirus 1 (PdPV-1)]. The virus is bipartite, containing two double-stranded RNA (dsRNA) segments designated as dsRNA1 and dsRNA2. The cDNA sequences revealed that dsRNA1 dsRNA is 1,683 bp in length with an open reading frame (ORF) that encodes 539 amino acids (molecular mass of 62.7 kDa); dsRNA2 dsRNA is 1,524 bp in length with an ORF that encodes 434 amino acids (molecular mass of 46.9 kDa). The dsRNA1 ORF contains motifs representative of RNA-dependent RNA polymerase (RdRp), whereas the dsRNA2 ORF sequence showed homology with the putative capsid proteins (CPs) of mycoviruses. Phylogenetic analyses with PdPV-1 RdRp and CP sequences indicated that both segments constitute the genome of a novel virus in the family Partitiviridae. The purified virions were isometric with an estimated diameter of 33 nm. Reverse transcription PCR (RT-PCR) and sequencing revealed that all US isolates and a subset of Czech Republic isolates of P. destructans were infected with PdPV-1. However, PdPV-1 appears to be not widely dispersed in the fungal genus Pseudogymnoascus, as non-pathogenic fungi P. appendiculatus (1 isolate) and P. roseus (6 isolates) tested negative. P. destructans PdPV-1 could be a valuable tool to investigate fungal biogeography and the host–pathogen interactions in bat WNS.