bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of piwi-interacting RNA pathway genes role in idiopathic non-obstructive azoospermia
Authors: Kamaliyan Zeeba , Pouriamanesh Sara , Soosanabadi Mohsen , Gholami Milad , Mirfakhraie Reza 
Published: January 2018

AbstractGenes involved in piwi-interacting RNAs (piRNAs) pathway have an essential role in spermatogenesis. HIWI and TDRD proteins are critical for piRNA biogenesis and function. Therefore, Mutations and polymorphisms in HIWI and TDRD genes may play role in male infertility. The aim of the present study was to investigate the role of HIWI2 rs508485 (T>C) and HIWI3 rs11703684 (C>T) polymorphisms and mutational analysis of TDRD5 gene in idiopathic non-obstructive azoospermia in a case-control study including 226 non-obstructive azoospermia patients and 200 fertile males. Genotyping for both polymorphisms was performed using Tetra-Primer ARMS PCR. Mutation analysis of TDRD5 gene was done using multi-temperature single strand conformation polymorphism technique (MSSCP). The frequency of rs508485TC genotype was significantly different in the studied groups (P = 0.0032; OR = 2.12; 95% CI, 1.29–3.48). In addition, the genotype frequencies showed a significant difference under dominant model (P = 0.005; OR = 2.79; 95% CI, 1.22–3.13). No mutation was detected in the Tudor domain of the TDRD5 in the studied patients. In conclusion, we provide evidence for association between genetic variation in the HIWI2 gene and idiopathic non-obstructive azoospermia in Iranian patients. Therefore, piRNA pathway genes variants can be considered as risk factors for male infertility.
Utility of brGDGTs as temperature and precipitation proxies in subtropical China
Authors: Wang Mengyuan , Zong Yongqiang , Zheng Zhuo , Man Meiling , Hu Jianfang , Tian Liping 
Published: January 2018

AbstractBacterial branched glycerol dialkyl glycerol tetraethers (brGDGTs) have been successfully used as quantitative climate proxies for reconstructing annual mean air temperature (MAT) and soil pH from sediments. However, reconstructions derived from brGDGTs in regions with diverse hydrological and atmospheric conditions require further refinement. In this study, we investigated the suitability of brGDGTs as temperature and precipitation proxies from surface soils on opposite slopes of Mount Fanjing in subtropical China. The results show a clear altitudinal lapse rate of MBT′5ME-derived MAT and between-slope differences in MAT at given altitude. Moreover, the MBT′5ME-derived MAT values are more strongly related to the MAT from March to November than that of the whole year. A turning point is also observed from the measured pH and CBT′-derived pH gradients at altitude of 1400 m~1500 m, in accordance with the fog horizon, where precipitation reaches the maximum value. The findings prove that brGDGTs from soil transects can be used as indicators for reconstructions of climate parameters from subtropical regions of China.
Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally
Authors: Phelan Jody , de Sessions Paola Florez , Tientcheu Leopold , Perdigao Joao , Machado Diana , Hasan Rumina , Hasan Zahra , Bergval Indra L. , Anthony Richard , McNerney Ruth , Antonio Martin , Portugal Isabel , Viveiros Miguel , Campino Susana , Hibberd Martin L. , Clark Taane G. 
Published: January 2018

AbstractDNA methylation is an epigenetic modification of the genome involved in regulating crucial cellular processes, including transcription and chromosome stability. Advances in PacBio sequencing technologies can be used to robustly reveal methylation sites. The methylome of the Mycobacterium tuberculosis complex is poorly understood but may be involved in virulence, hypoxic survival and the emergence of drug resistance. In the most extensive study to date, we characterise the methylome across the 4 major lineages of M. tuberculosis and 2 lineages of M. africanum, the leading causes of tuberculosis disease in humans. We reveal lineage-specific methylated motifs and strain-specific mutations that are abundant globally and likely to explain loss of function in the respective methyltransferases. Our work provides a set of sixteen new complete reference genomes for the Mycobacterium tuberculosis complex, including complete lineage 5 genomes. Insights into lineage-specific methylomes will further elucidate underlying biological mechanisms and other important phenotypes of the epi-genome.
Uncovering the inertia of dislocation motion and negative mechanical response in crystals
Authors: Tang Yizhe 
Published: January 2018

AbstractDislocations are linear defects in crystals and their motion controls crystals’ mechanical behavior. The dissipative nature of dislocation propagation is generally accepted although the specific mechanisms are still not fully understood. The inertia, which is undoubtedly the nature of motion for particles with mass, seems much less convincing for configuration propagation. We utilize atomistic simulations in conditions that minimize dissipative effects to enable uncovering of the hidden nature of dislocation motion, in three typical model metals Mg, Cu and Ta. We find that, with less/no dissipation, dislocation motion is under-damped and explicitly inertial at both low and high velocities. The inertia of dislocation motion is intrinsic, and more fundamental than the dissipative nature. The inertia originates from the kinetic energy imparted from strain energy and stored in the moving core. Peculiar negative mechanical response associated with the inertia is also discovered. These findings shed light on the fundamental nature of dislocation motion, reveal the underlying physics, and provide a new physical explanation for phenomena relevant to high-velocity dislocations.
Realization of multiple orbital angular momentum modes simultaneously through four-dimensional antenna arrays
Authors: Sun Chao , Yang Shiwen , Chen Yikai , Guo Jixin , Qu Shiwei 
Published: January 2018

AbstractElectromagnetic waves carrying orbital angular momentum (OAM) in radio frequency range have drawn great attention owing to its potential applications in increasing communication capacity. In this paper, both single-pole single-throw (SPST) switches and single-pole double-throw (SPDT) switches are designed and implemented. Optimal time sequence allows four-dimensional (4-D) circular antenna array to generate multiple OAM-carrying waves as well as enhance the field intensity of each OAM-carrying wave. A novel experimental platform is developed to measure the phase distribution when the transmitting antenna and the receiving antenna operate at different frequencies. The good agreement between the measurement and simulation results demonstrate that 4-D circular antenna array is able to generate multiple OAM modes simultaneously. Furthermore, the superiority of the 4-D circular antenna array in receiving and demodulating multiple OAM-carrying signals is validated through the filter and bit error rate (BER) simulations.
Spred2 Deficiency Exacerbates D-Galactosamine/Lipopolysaccharide -induced Acute Liver Injury in Mice via Increased Production of TNFα
Authors: Yang Xu , Fujisawa Masayoshi , Yoshimura Teizo , Ohara Toshiaki , Sato Miwa , Mino Megumi , San Thar Htet , Gao Tong , Kunkel Steven L. , Matsukawa Akihiro 
Published: January 2018

AbstractAcute liver injury (ALI) is characterized by hepatocyte damage and inflammation. In the present study, we examined whether the absence of Sprouty-related EVH1-domain-containing protein 2 (Spred2), a negative regulator of the Ras/Raf/ERK/MAPK pathway, influences ALI induced by D-galactosamine (D-GalN) and lipopolysaccharide (LPS). Compared to wild-type mice, Spred2−/−mice developed exacerbated liver injury represented by enhanced hepatocyte damage and inflammation. Enhanced ERK activation was observed in Spred2−/−-livers, and the MEK/ERK inhibitor U0126 ameliorated ALI. Hepatic tumour necrosis factor α (TNFα) and interleukin (IL)-1β levels were increased in Spred-2−/−-livers, and the neutralization of TNFα dramatically ameliorated ALI, which was associated with decreased levels of endogenous TNFα and IL-1β. When mice were challenged with D-GalN and TNFα, much severer ALI was observed in Spred2−/−mice with significant increases in endogenous TNFα and IL-1β in the livers. Immunohistochemically, Kupffer cells were found to produce TNFα, and isolated Kupffer cells from Spred2−/−mice produced significantly higher levels of TNFα than those from wild-type mice after LPS stimulation, which was significantly decreased by U0126. These results suggest that Spred2 negatively regulates D-GalN/LPS-induced ALI under the control of TNFα in Kupffer cells. Spred2 may present a therapeutic target for the treatment of ALI.
Quasi-asymmetric response of the Indian summer monsoon rainfall to opposite phases of the IOD
Authors: Behera Swadhin K. , Ratnam J. V. 
Published: January 2018

AbstractThe El Niño/Southern Oscillation has been traditionally linked to the extremes in the Indian summer monsoon rainfall (ISMR) affecting more than a billion people in the region. This trans-oceanic influence is seen to be moderated by the Indian Ocean Dipole (IOD) phenomenon in recent decades. In the presence of a positive IOD (pIOD), the otherwise subdued ISMR in an El Niño year remains close to normal even in the face of record breaking El Niños. While this general influence of pIOD on ISMR is understood, the influence of negative IOD (nIOD) on ISMR is not yet recognized. In this study, it is revealed that those opposite phases of IOD are associated with distinct regional asymmetries in rainfall anomalies. The pIOD is associated with a tripolar pattern in rainfall anomalies with above normal rainfall in central parts of India and below normal rainfall to north and south of it. Conversely, the nIOD is associated with a zonal dipole having above (below) normal rainfall on the western (eastern) half of the country. This spatial quasi-asymmetry arises from the differences in the atmospheric responses and the associated differences in moisture transports to the region during contrasting phases of the IOD.
Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages
Authors: Dai Wei , Zou Ming , Yang Liandong , Du Kang , Chen Weitao , Shen Yanjun , Mayden Richard L. , He Shunping 
Published: January 2018

AbstractThe phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes. Based on a selection of 125 nuclear genes screened from single-gene maximum likelihood (ML) analyses and sequence bias testing, well-established relationships among Otocephala were reconstructed. We suggested that Gymnotiformes are more closely related to Characiformes than to Siluriformes and Characiformes are possibly paraphyletic. We also estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major otocephalan lineages.
Clinical characteristics of stress cardiomyopathy in patients with acute poisoning
Authors: Jeon Ung , Park Samel , Park SangHo , Lee Eun-young , Gil Hyo-Wook 
Published: January 2018

AbstractPatients who attempt intentional suicide suffer from physical or emotional stress. This situation might be an important factor that causes takotsubo cardiomyopathy. We retrospectively investigated the clinical features of Takotsubo cardiomyopathy in patients with acute poisoning. This study included patients who were admitted from January 2010 to December 2015 because of intentional poisoning by ingestion. Among these patients, we selectively collected data of patients who underwent an echocardiogram. We divided the patients into three groups according to the echocardiogram; the non-cardiomyopathy group, the global hypokinesia group, and the takotsubo cardiomyopathy group. One hundred forty-seven patients were analyzed in this study. One hundred thirty-one patients had normal cardiac function without regional wall motion abnormality. Global hypokinesia was observed in five patients. The overall incidence of takotsubo cardiomyopathy was 7.5% (11/147). Levels of cardiac enzymes including CK-MB, Troponin T, a marker of cardiac muscle ischemia, were higher in the global hypokinesia group and the takotsubo cardiomyopathy group compared with the non-cardiomyopathy group. The most commonly consumed poison was organophosphate in the takotsubo cardiomyopathy group. In conclusion, takotsubo cardiomyopathy may be one of the cardiac complications in patients who attempt suicide by consuming a poison.
Silica nanoparticle stability in biological media revisited
Authors: Yang Seon-Ah , Choi Sungmoon , Jeon Seon Mi , Yu Junhua 
Published: January 2018

AbstractThe stability of silica nanostructure in the core-silica shell nanomaterials is critical to understanding the activity of these nanomaterials since the exposure of core materials due to the poor stability of silica may cause misinterpretation of experiments, but unfortunately reports on the stability of silica have been inconsistent. Here, we show that luminescent silver nanodots (AgNDs) can be used to monitor the stability of silica nanostructures. Though relatively stable in water and phosphate buffered saline, silica nanoparticles are eroded by biological media, leading to the exposure of AgNDs from AgND@SiO2 nanoparticles and the quenching of nanodot luminescence. Our results reveal that a synergistic effect of organic compounds, particularly the amino groups, accelerates the erosion. Our work indicates that silica nanostructures are vulnerable to cellular medium and it may be possible to tune the release of drug molecules from silica-based drug delivery vehicles through controlled erosion.
Increased Susceptibility to Plasmodium falciparum in Infants is associated with Low, not High, Placental Malaria Parasitemia
Authors: Tassi Yunga Samuel , Fouda Genevieve G. , Sama Grace , Ngu Julia B. , Leke Rose G. F. , Taylor Diane W. 
Published: January 2018

AbstractRisk of malaria in infants can be influenced by prenatal factors. In this study, the potential for placental parasitemia at delivery in predicting susceptibility of infants to Plasmodium falciparum (Pf) infections was evaluated. Seventy-two newborns of mothers who were placental malaria negative (PM−) and of mothers who were PM+ with below (PM+ Lo) and above (PM + Hi) median placental parasitemia, were actively monitored during their first year of life. Median time to first PCR-detected Pf infection was shorter in PM + Lo infants (2.8 months) than in both PM− infants (4.0 months, p = 0.002) and PM + Hi infants (4.1 months, p = 0.01). Total number of new infections was also highest in the PM + Lo group. Only 24% of infants experienced clinical malaria episodes but these episodes occurred earlier in PM + Lo infants than in PM + Hi infants (p = 0.05). The adjusted hazard ratio (95% CI) of having Pf infection was 3.9 (1.8–8.4) and 1.5 (0.7–3.4) for infants in the PM + Lo and PM + Hi groups, respectively. Collectively, low placental parasitemia was associated with increased susceptibility to malaria during infancy. Therefore, malaria in pregnancy preventive regimens, such as sulfadoxine-pyremethamine, that reduce but do not eliminate placental Pf in areas of drug resistance may increase the risk of malaria in infants.
Shape dependent physical mutilation and lethal effects of silver nanoparticles on bacteria
Authors: Acharya Debashish , Singha K. Malabika , Pandey Piyush , Mohanta Bidhan , Rajkumari Jina , Singha L. Paikhomba 
Published: January 2018

AbstractIn this report, spherical silver nanoparticle (AgNP-sp) and rod-shaped silver nanoparticle (AgNR) were prepared by chemical reduction method and their antibacterial activity against various Gram-positive and Gram-negative bacteria had been evaluated for their efficiency. Minimal inhibitory concentration (MIC) tests were conducted to study the antibacterial properties, and substantiated with killing kinetics of silver nanoparticles (AgNPs). The study revealed that both AgNP-sp and AgNRs are good antibacterial candidates. Bacterial sensitivity to nanoparticles (NPs) was found to vary depending on microbial species. Disc diffusion studies revealed the greater effectiveness of AgNP-sp and AgNR against Klebsiella pneumoniae AWD5 at the doses of 249 and 392 µg. The dose dependent activities of prepared NPs were also observed on the batch studies of disc diffusion and MIC with various strains. The optical and morphological structures of NPs were analyzed by UV-visible, XRD, FE-SEM and TEM. Further, FESEM of bacterial culture treated with AgNPs confirmed antibacterial activity of NPs by showing rupture of bacterial cell wall. Also, the genome of test organism was found to have CusCFBA and CusRS operons. The killing kinetics confirmed that the death rate of K. pneumoniae was higher against AgNP-sp as compared to AgNR.
Coupling Modern Portfolio Theory and Marxan enhances the efficiency of Lesser White-fronted Goose’s (Anser erythropus) habitat conservation
Authors: Liang Jie , Gao Xiang , Zeng Guangming , Hua Shanshan , Zhong Minzhou , Li Xiaodong , Li Xin 
Published: January 2018

AbstractClimate change and human activities cause uncertain changes to species biodiversity by altering their habitat. The uncertainty of climate change requires planners to balance the benefit and cost of making conservation plan. Here optimal protection approach for Lesser White-fronted Goose (LWfG) by coupling Modern Portfolio Theory (MPT) and Marxan selection were proposed. MPT was used to provide suggested weights of investment for protected area (PA) and reduce the influence of climatic uncertainty, while Marxan was utilized to choose a series of specific locations for PA. We argued that through combining these two commonly used techniques with the conservation plan, including assets allocation and PA chosing, the efficiency of rare bird’s protection would be enhanced. In MPT analyses, the uncertainty of conservation-outcome can be reduced while conservation effort was allocated in Hunan, Jiangxi and Yangtze River delta. In Marxan model, the optimal location for habitat restorations based on existing nature reserve was identified. Clear priorities for the location and allocation of assets could be provided based on this research, and it could help decision makers to build conservation strategy for LWfG.
Large-scale sill emplacement in Brazil as a trigger for the end-Triassic crisis
Authors: Heimdal Thea H. , Svensen Henrik. H. , Ramezani Jahandar , Iyer Karthik , Pereira Egberto , Rodrigues René , Jones Morgan T. , Callegaro Sara 
Published: January 2018

AbstractThe end-Triassic is characterized by one of the largest mass extinctions in the Phanerozoic, coinciding with major carbon cycle perturbations and global warming. It has been suggested that the environmental crisis is linked to widespread sill intrusions during magmatism associated with the Central Atlantic Magmatic Province (CAMP). Sub-volcanic sills are abundant in two of the largest onshore sedimentary basins in Brazil, the Amazonas and Solimões basins, where they comprise up to 20% of the stratigraphy. These basins contain extensive deposits of carbonate and evaporite, in addition to organic-rich shales and major hydrocarbon reservoirs. Here we show that large scale volatile generation followed sill emplacement in these lithologies. Thermal modeling demonstrates that contact metamorphism in the two basins could have generated 88,000 Gt CO2. In order to constrain the timing of gas generation, zircon from two sills has been dated by the U-Pb CA-ID-TIMS method, resulting in 206Pb/238U dates of 201.477 ± 0.062 Ma and 201.470 ± 0.089 Ma. Our findings demonstrate synchronicity between the intrusive phase and the end-Triassic mass extinction, and provide a quantified degassing scenario for one of the most dramatic time periods in the history of Earth.
Epstein-Barr virus-encoded RNAs (EBERs) complement the loss of Herpesvirus telomerase RNA (vTR) in virus-induced tumor formation
Authors: Kheimar Ahmed , Kaufer Benedikt B. 
Published: January 2018

AbstractMarek’s disease virus (MDV) is an alphaherpesvirus that causes fatal lymphomas in chickens and is used as a natural virus-host model for herpesvirus-induced tumorigenesis. MDV encodes a telomerase RNA subunit (vTR) that is crucial for efficient MDV-induced lymphoma formation; however, the mechanism is not completely understood. Similarly, Epstein Barr-virus (EBV) encodes two RNAs (EBER-1 and EBER-2) that are highly expressed in EBV-induced tumor cells, however their role in tumorigenesis remains unclear. Intriguingly, vTR and EBER-1 have interaction partners in common that are highly conserved in humans and chickens. Therefore, we investigated if EBER-1 and/or EBER-2 can complement the loss of vTR in MDV-induced tumor formation. We first deleted vTR (v∆vTR) and replaced it by either EBER-1 or EBER-2 in the very virulent RB-1B strain. Insertion of either EBER-1 or EBER-2 did not affect MDV replication and their expression levels were comparable to vTR in wild type virus. Intriguingly, EBER-2 restored tumor formation of MDV that lacks vTR. EBER-1 partially restored MDV oncogenicity, while tumor formation was severely impaired in chickens infected with v∆vTR. Our data provides the first evidence that EBERs possess tumor-promoting properties in vivo using this natural model for herpesvirus-tumorigenesis.
In vivo STED microscopy visualizes PSD95 sub-structures and morphological changes over several hours in the mouse visual cortex
Authors: Wegner Waja , Mott Alexander C. , Grant Seth G. N. , Steffens Heinz , Willig Katrin I. 
Published: January 2018

AbstractThe post-synaptic density (PSD) is an electron dense region consisting of ~1000 proteins, found at the postsynaptic membrane of excitatory synapses, which varies in size depending upon synaptic strength. PSD95 is an abundant scaffolding protein in the PSD and assembles a family of supercomplexes comprised of neurotransmitter receptors, ion channels, as well as signalling and structural proteins. We use superresolution STED (STimulated Emission Depletion) nanoscopy to determine the size and shape of PSD95 in the anaesthetised mouse visual cortex. Adult knock-in mice expressing eGFP fused to the endogenous PSD95 protein were imaged at time points from 1 min to 6 h. Superresolved large assemblies of PSD95 show different sub-structures; most large assemblies were ring-like, some horse-shoe or figure-8 shaped, and shapes were continuous or made up of nanoclusters. The sub-structure appeared stable during the shorter (minute) time points, but after 1 h, more than 50% of the large assemblies showed a change in sub-structure. Overall, these data showed a sub-morphology of large PSD95 assemblies which undergo changes within the 6 hours of observation in the anaesthetised mouse.