bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Dynamics Simulation of Homo-DNA: The Role of Crystal Packing in Duplex Conformation
Authors: Sheehan Jonathan H. , Smith Jarrod A. , Pallan Pradeep S. , Lybrand Terry P. , Egli Martin
Published: October 2019

The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not cross-pair with DNA. Molecular modeling and NMR solution studies of homo-DNA duplexes pointed to a conformation that was nearly devoid of a twist and a stacking distance in excess of 4.5 Å. By contrast, the crystal structure of the homo-DNA octamer dd(CGAATTCG) revealed a right-handed duplex with average values for helical twist and rise of ca. 15° and 3.8 Å, respectively. Other key features of the structure were strongly inclined base-pair and backbone axes in the duplex with concomitant base-pair slide and cross-strand stacking, and the formation of a dimer across a crystallographic dyad with inter-duplex base swapping. To investigate the conformational flexibility of the homo-DNA duplex and a potential influence of lattice interactions on its geometry, we used molecular dynamics (MD) simulations of the crystallographically observed dimer of duplexes and an isolated duplex in the solution state. The dimer of duplexes showed limited conformational flexibility, and key parameters such as helical rise, twist, and base-pair slide exhibited only minor fluctuations. The single duplex was clearly more flexible by comparison and underwent partial unwinding, albeit without significant lengthening. Thus, base stacking was preserved in the isolated duplex and two adenosines extruded from the stack in the dimer of duplexes were reinserted into the duplex and pair with Ts in a Hoogsteen mode. Our results confirmed that efficient stacking in homo-DNA seen in the crystal structure of a dimer of duplexes was maintained in the separate duplex. Therefore, lattice interactions did not account for the different geometries of the homo-DNA duplex in the crystal and earlier models that resembled inclined ladders with large base-pair separations that precluded efficient stacking.
Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW)
Authors: Jiang Mengchao , He Hongxing , Su Wu-Pei
Published: October 2019

A thyroid receptor alpha structure (PDB ID: 4LNW) was studied for ab initio phasing. With the diffraction intensity data, protein sequence, and ligand structure as the only input, a high-resolution structure was successfully reconstructed by using an iterative projective method based on the hybrid input–output (HIO) algorithm.
Forest Diversity and Structure in the Amazonian Mountain Ranges of Southeastern Ecuador
Authors: Quizhpe Wilson , Benítez Ángel , Cuenca Klever , Uvidia Hernán , Huamantupa Isau , Muñoz Jesús , Cabrera Omar
Published: October 2019

We analyze the structure of diameter, richness, and diversity of the forests in the upper limit of the great Amazon basin located in the Ecuadorian territory of the Cordilleras del Cóndor and Cutucú. Our hypothesis was that the forests of the eastern mountain ranges are not homogeneous, but rather present differences in their structure, richness, and floristic diversity. Our main objective was to classify the types of forests based on the characteristics of the diameter structure and the species composition of the Amazonian forests of the eastern mountain ranges in southern Ecuador, and we determined the influence of critical edaphic, environmental, and geomorphological factors, For this we installed eight permanent plots of one hectare in homogeneous and well preserved forest stands, four plots in the province of Zamora Chinchipe and four in the province of Morona Santiago. We identified and measured all trees >10 cm at chest height and for each plot, soil samples, as well as environmental and slope data were taken. We performed an non-metric multidimensional scaling analysis (NMDS) analysis to evaluate changes in climatic and geomorphological gradients, and used the CCA analysis to assess the relationship between the composition of the species at the plot level and the edapho-climatic variables. Finally, we modeled the change in diversity ad species (Fisher’s alpha) in relation to climatic, altitudinal, and geomorphological gradients using a GLM. We determined the existence of two different types of forest, the first called Terra Firme, characterized by the presence of a greater number of species and individuals per plot as compared to the second type of forest called Tepuy or Sandstone forest. Species richness was negatively correlated with the phosphorus content of the soil and the pH, annual average temperature, annual rainfall, and altitude. Terra Firme forests, settled in more stable and nutrient-rich climatic areas, were more diverse and Sandstone forests are poor in nutrients and develop in areas with greater seasonality.
Müllerian Anomalies Prevalence Diagnosed by Hysteroscopy and Laparoscopy in Mexican Infertile Women: Results from a Cohort Study
Authors: Reyes-Muñoz Enrique , Vitale Salvatore Giovanni , Alvarado-Rosales Deisi , Iyune-Cojab Esther , Vitagliano Amerigo , Lohmeyer Franziska Michaela , Guevara-Gómez Yenara Patricia , Villarreal-Barranca Alma , Romo-Yañez José , Montoya-Estrada Araceli , Morales-Hernández Fela Vanesa , Aguayo-González Patricia
Published: October 2019

Background: To evaluate the prevalence of Müllerian anomalies (MAs) in a cohort of infertile Mexican women candidates for infertility treatments (intrauterine insemination or IVF (In vitro fertilization) cycles). Methods: We performed a retrospective observational study on a cohort of consecutive women, who underwent hysteroscopy and laparoscopy as part of the basic infertility workup from 2002 to 2014, at our center. Our aim was to calculate the prevalence of MAs and each subtype. Results: A total of 4005 women were included in the study. The MA prevalence was 4.4% (95% CI; 3.8–5.1; n = 177). Among women with MAs, the prevalence of different MA types was: septate uterus 54.2% (n = 96), arcuate uterus 15.8% (n = 28), bicornuate uterus 10.7% (n = 19), unicornuate uterus 8.5% (n = 15), didelphys uterus 6.2% (n = 11) and hypoplasia/agenesis 3.4% (n = 6), unclassifiable 1.1% (n = 2). Women with MAs who achieved pregnancy were: 33.3% (n = 59). The MA associated with the highest pregnancy rate was septate uterus after hysteroscopic correction, at 38.5% (37/96). Conclusions: The prevalence of MAs among infertile Mexican women can be considered as low, but not negligible. The septate uterus is the most common MA in women with infertility.
Very Low Crosstalk Measurement of Substrate Integrated Coaxial Line (SICL)
Authors: Lu Cheng , Yang Liang , Yin Xiaoxing , Zhao Hongxin , Liu Leilei
Published: October 2019

When designing a microwave circuit involving substrate integrated coaxial lines (SICLs), it is important to know what real crosstalk between SICLs is. A measured crosstalk will be a good reference value in a practical design. In addition, it is also needed to compare and check the crosstalk from the simulation and calculation formula with measured results. However, it is very difficult to measure the crosstalk between SICLs because it is theoretically very low. In this study, for the first time, the crosstalk characteristics of a SICL are evaluated through experimental design and measurements. By adjusting the layout of the structures and implementing controlled experiments, interference caused by the presence of leaks and radiation at the interface and structural transitions is effectively suppressed. The experimental results show that for two parallel SICLs with a length of 30 mm and an interval of 5 mm, the isolation is greater than 80 dB for the measured frequency range of 1–8 GHz, significantly better than the results of the grounded coplanar waveguide (GCPW).
Data-Dense and Miniature Chipless Moisture Sensor RFID Tag for Internet of Things
Authors: Jabeen Iqra , Ejaz Asma , Rahman Muhib Ur , Naghshvarianjahromi Mahdi , Khan Muhammad Jamil , Amin Yasar , Tenhunen Hannu
Published: October 2019

A novel and miniaturized semi-elliptical 20-bit fully passive chipless RFID sensor tag is proposed in this article. The realized sensor tag is made up of semi-elliptical shaped open-end slots within the compact size of 25 mm × 17 mm. The multi-substrate analysis of the proposed tag is examined using non-flexible and flexible materials. The articulated tag configuration is capable of monitoring moisture levels when the largest resonator is covered by a heat-resistant sheet of Kapton HN (DuPontTM). The proposed tag functions in the operational frequency band of 4.1 GHz–16 GHz and possesses the overall bit density of 4.70 bit/cm2. The structure is composed of a thin passive substrate layer topped with an active layer of conductive path and is considered as a potential candidate for low-cost identification of the tagged objects. In addition to that, its moisture sensing property and flexible nature make it a reliable smart sensor for conformal applications.
Consumer Demand for Blockchain-Enabled Peer-to-Peer Electricity Trading in the United Kingdom: An Online Survey Experiment
Authors: Fell Michael J. , Schneiders Alexandra , Shipworth David
Published: October 2019

Peer-to-peer (P2P) energy trading could help address grid management challenges in a decentralizing electricity system, as well as provide other social and environmental benefits. Many existing and proposed trading schemes are enabled by blockchain, a distributed ledger technology (DLT) relying on cryptographic proof of ownership rather than human intermediaries to establish energy transactions. This study used an online survey experiment (n = 2064) to investigate how consumer demand for blockchain-enabled peer-to-peer energy trading schemes in the United Kingdom varies depending on how the consumer proposition is designed and communicated. The analysis provides some evidence of a preference for schemes offering to meet a higher proportion of participants’ energy needs and for those operating at the city/region (as compared to national or neighbourhood) level. People were more likely to say they would participate when the scheme was framed as being run by their local council, followed by an energy supplier, community energy organization, and social media company. Anonymity was the most valued DLT characteristic and mentioning blockchain’s association with Bitcoin led to a substantial decrease in intended uptake. We highlight a range of important questions and implications suggested by these findings for the introduction and operation of P2P trading schemes.
Bucket Trajectory Optimization under the Automatic Scooping of LHD
Authors: Meng Yu , Fang Huazhen , Liang Guodong , Gu Qing , Liu Li
Published: October 2019

We propose an optimal planning scheme of the bucket trajectory in the LHD (Load-Haul-Dump) automatic shoveling system to improve the effectiveness of the scooping operation. The research involves simulation of four typical shoveling methods, optimization of the scooping trajectory, establishment of a reaction force model in the scooping process and determination of optimal trajectory. Firstly, we compared the one-step, step-by-step, excavation and coordinated shoveling method by the Engineering Discrete Element Method (EDEM) simulation. The coordinated shoveling method becomes the best choice on account of its best comprehensive performance among the four methods. Based on the coordinated shoveling method, the shape of the optimized trajectory can be roughly determined. Then, we established a model of bucket force during the shoveling process by applying Coulomb’s passive earth pressure theory for the purpose of calculating energy consumption. The trajectory is finally determined through optimizing the minimum energy consumption in theory. The theoretical value is verified by the EDEM simulation.
The Effect of Hydration on Pores of Shale Oil Reservoirs in the Third Submember of the Triassic Chang 7 Member in Southern Ordos Basin
Authors: Zhao Pengfei , Fan Xiangyu , Zhang Qiangui , Wang Xiang , Zhang Mingming , Ran Jiawei , Lv Da , Liu Jinhua , Shuai Juntian , Wu Hao
Published: October 2019

Shale oil is an unconventional kind of oil and gas resource with great potential. China has huge reserves of shale oil, and shale oil resources are abundant in the third submember of the Triassic Chang 7 member in the southern Ordos Basin. At present, this area is in the initial stage of shale oil exploration and development. The reservoir pore is one of the key factors affecting oil accumulation, drilling safety, and oil production. It is also an important reservoir parameter that must be defined in the exploration stage. In general, the clay content in the shale section is high, and is prone to hydration. In order to study the effect of fluid on the pore type, structure, and distribution of shale oil reservoirs, experiments using X-ray diffraction, a porosity–permeability test, mercury porosimetry, rock casting thin section, and scanning electron microscopy were carried out. The experimental results show that the content of clay and quartz is very high in the studied formation. The pore porosity and permeability of the rock is highly heterogeneous because of the obvious stratigraphic bedding and interbeds. Microstructural observation of rocks shows that the main pore types are intergranular pores, intragranular pores, intercrystalline pores, and organic pores. Crack types are dissolution cracks, contraction cracks of organic matter, and abnormal pressure structural cracks. After hydration, the porosity of rock will increase in varying degrees, and pore size, pore content in different sizes, and pore structure will also change. The results show that the pores of tuff mainly changes at the initial stage of hydration, and the pore change of tuff is the most obvious within 6 hours of soaking in clear water. The influence of hydration on the pore of shale is greater than that of tuff, but the main change stage is later than tuff, and the pore change of shale is the most obvious within 12 to 24 hours of soaking in clear water. The soaking experiment of water-based drilling fluid (WBM-SL) shows that it can plug a certain size of holes and cracks and form a protective layer on the rock surface, thus effectively reducing hydration. In actual construction, multisized solid particles should be allocated in drilling fluid according to the formation pore’s characteristics, and the stability of the protective layer should be guaranteed. This can reduce the accident of well leakage and collapse and is conducive to the efficient and safe development of shale oil.
Study on the Effect of Turbine Inlet Temperature and Backpressure Conditions on Reduced Turbine Flow Rate Performance Characteristics and Correction Method for Automotive Turbocharger
Authors: Chung Jaewoo , Lee Siwon , Kim Namho , Lee Beumho , Kim Deokjin , Choi Seunghyun , Kim Giyong
Published: October 2019

In actual vehicle operation, the turbocharger turbine operates at various temperatures, inlet, and backpressure conditions, unlike compressors. The flow rate characteristics of the turbine are generally evaluated under certain conditions using an assembled turbocharger with a compressor and a turbine and a hot gas bench from the turbocharger manufacturer. Flow rate characteristics are also presented as the reduced mass flow rate to correct the flow rate characteristics according to the turbine inlet temperature and pressure. Therefore, the turbine mass flow rate seen in many engine development cases and studies—including the analysis of the turbine performance and characteristics, engine model configuration, and matching of the engine and turbocharger—is calculated according to the reduced turbine mass flow rate performance and turbine inlet temperature and pressure obtained through hot gas bench experiments under certain conditions. However, the performance of the reduced turbine mass flow rate is influenced by the compressor power conditions, and additional correction of the reduced turbine mass flow rate is required when the turbine inlet temperature and turbine backpressure differ from the reference test conditions, such as the hot gas bench test conditions. In this study, the effect of the turbine inlet temperature and turbine backpressure on the performance of the reduced turbine mass flow rate were examined based on the power balance relationship between the compressor and turbine of an automotive turbocharger. The principle of its correction is also presented.
Thermal Analysis of the Factors Influencing Junction Temperature of LED Panel Sources
Authors: Baran Krzysztof , Różowicz Antoni , Wachta Henryk , Różowicz Sebastian , Mazur Damian
Published: October 2019

Limiting junction temperature Tj and maintaining its low value is crucial for the lifetime and reliability of semi-conductive light sources. Obtaining the lowest possible temperature of Tj is especially important in the case of LED panels, where in a short distance there are many light sources installed, between which there occurs mutual thermal coupling. The article presents results of simulation studies connected with the influence of construction and ambient factors that influence the value of junction temperature of exemplary LED panel sources. The influence of radiator’s construction, printed circuit boards, as well as the influence of ambient factors, such as ambient temperature Ta and air flow velocity v were subjected to the analysis. Numerical calculations were done in the FloEFD software of the Mentor Graphics company, which is based on computational fluid dynamics (CFD). For construction of the LED thermal panel model the optical efficiency ηo and real thermal resistance Rthj-c were determined in a laboratory for the applied light sources.
Coupling Coefficient Measurement Method with Simple Procedures Using a Two-Port Network Analyzer for a Multi-Coil WPT System
Authors: Jeon Seon-Jae , Seo Dong-Wook
Published: October 2019

In this paper, we propose a measurement method with a simple procedure based on the definition of the impedance parameter using a two-port network analyzer. The main advantage of the proposed measurement method is that there is no limit on the number of measuring coils, and the method has a simple measurement procedure. To verify the proposed method, we measured the coupling coefficient among three coils with respect to the distance between the two farthest coils at 6.78 and 13.56 MHz, which are frequencies most common for a wireless power transfer (WPT) system in high-frequency band. As a result, the proposed method showed good agreement with results of the conventional S-parameter measurement methods.
A Novel Autonomous Current-Sharing Control Strategy for Multiple Paralleled DC–DC Converters in Islanded DC Microgrid
Authors: Zhang Qinjin , Zhuang Xuzhou , Liu Yancheng , Wang Chuan , Guo Haohao
Published: October 2019

Due to the existence of line impedances and low-bandwidth communication, the traditional peer-to-peer control method based on droop control has difficult meeting the requirements of current sharing and voltage stability in islanded DC microgrids at the same time. In this paper, a novel current-sharing control strategy based on injected small ac voltage with low frequency and low amplitude is proposed for multiple paralleled DC–DC converters. The small ac voltage is superimposed onto the output voltage of each converter. Then, the reactive circulating power is generated and used to regulate the output DC voltage of each converter. Under the droop characteristic between the injected frequency and output DC current, a feedback mechanism is generated to realize the accurate current sharing. On this basis, a reactive power-voltage limiter link and virtual negative impedance are added. Under the interaction of the two links, the bus voltage drop caused by line impedances can be almost completely eliminated. This method does not need any communication or to change the hardware structure. The controller design process is presented in detail along with a system stability analysis. Finally, the feasibility and effectiveness of the proposed control strategy are validated by the results obtained from simulations and experiments.
Load Capacity Analysis of Self-Excited Induction Generators Based on Routh Criterion
Authors: Li Jia , Wu Xinzhen , Yuan Xibo , Wang Haifeng
Published: October 2019

In this paper, the Routh criterion has been used to analyze the stability of a self-excited induction generator-based isolated system which is regarded as an autonomous system. Special focus has been given to the load capacity of the self-excited induction generator. The state matrix of self-excited induction generators with resistor-inductor load has been established based on transient equivalent circuits in the stator stationary reference-frame. The recursive Routh table of self-excited induction generators is established by the characteristic polynomial coefficients of the state matrix. According to the Routh stability criterion, the necessary and sufficient condition to predict the critical loads of self-excited induction generators is deduced, from which the critical load impedance can be calculated. A simple self-excited induction generator-based isolated power system has been built up with a 2.2 kW self-excited induction generator. The theoretical analysis and experiments were all carried out based on this platform. In the range determined by the minimum excitation capacitance (Cmin) and the maximum excitation capacitance (Cmax), the critical loads under various power factors have been calculated. The agreement of the calculated theoretical results and experimental results demonstrate the effectiveness and accuracy of the proposed analysis method. The conclusions achieved lay a foundation for further application of Routh stability criterion in self-excited induction generator-based power systems analysis.
Tree-Ring Reconstruction of Bark Beetle Disturbances in the Picea schrenkiana Fisch. et Mey. Forests of Southeast Kazakhstan
Authors: Lynch Ann M. , Mukhamadiev Nurjan S. , O’Connor Christopher D. , Panyushkina Irina P. , Ashikbaev Nursagim A. , Sagitov Abay O.
Published: October 2019

Ips hauseri Reitter is the most important bark beetle on Picea schrenkiana in southeast Kazakhstan, but its biology, ecology, and outbreak dynamics are poorly known. We dendrochronologically reconstructed a 200-year history of disturbances in the Kazakh Tien Shan P. schrenkiana forests. Only localized, low-severity bark beetle events occurred during the reconstructed period, indicating that extensive high-severity bark beetle outbreaks have not occurred historically in the Tien Shan spruce forest, unlike bark beetle outbreaks in spruce forests in North America, Europe, and Russia. Disturbance frequency doubled after about 1965, probably due to warming climate. Results, combined with the failure of an outbreak to fully develop after blowdown events associated with hurricane-force windstorms in 2011, indicate that prolonged drought may be necessary to sustain I. hauseri outbreaks, or that year-to-year variation in the Tien Shan weather prevents outbreak development. I. hauseri is probably less aggressive than I. typographus, at least on their natural hosts within their natural ranges.
Different Molecular Characterization of Soil Particulate Fractions under N Deposition in a Subtropical Forest
Authors: Geng Jing , Cheng Shulan , Fang Huajun , Pei Jie , Xu Meng , Lu Mingzhu , Yang Yan , Cao Zicheng , Li Yuna
Published: October 2019

Key Findings: Combining physical fractionation and pyrolysis–gas chromatography/mass spectrometry (py-GC/MS) technique can help better understand the dynamics of soil organic matter (SOM). Background and Objectives: SOM plays a critical role in the global carbon (C) cycle. However, its complexity remains a challenge in characterizing chemical molecular composition within SOM and under nitrogen (N) deposition. Materials and Methods: Three particulate organic matter (POM) fractions within SOM and under N treatments were studied from perspectives of distributions, C contents and chemical signatures in a subtropical forest. N addition experiment was conducted with two inorganic N forms (NH4Cl and NaNO3) applied at three rates of 0, 40, 120 kg N ha−1 yr−1. Three particle-size fractions (>250 μm, 53–250 μm and <53 μm) were separated by a wet-sieving method. Py-GC/MS technique was used to differentiate between chemical composition. Results: A progressive proportion transfer of mineral-associated organic matter (MAOM) to fine POM under N treatment was found. Only C content in fine POM was sensitive to N addition. Principal component analyses (PCA) showed that the coarse POM had the largest plant-derived markers (lignins, phenols, long-chain n-alkanes, and n-alkenes). Short-chain n-alkanes and n-alkenes, benzofurans, aromatics and polycyclic aromatic hydrocarbons mainly from black carbon prevailed in the fine POM. N compounds and polysaccharides from microbial products dominated in the MAOM. Factor analysis revealed that the degradation extent of three fractions was largely distinct. The difference in chemical structure among three particulate fractions within SOM was larger than treatments between control and N addition. In terms of N treatment impact, the MAOM fraction had fewer benzofurans compounds and was enriched in polysaccharides, indicating comparatively weaker mineralization and stronger stabilization of these substances. Conclusions: Our findings highlight the importance of chemical structure in SOM pools and help to understand the influence of N deposition on SOM transformation.
A Survey on LoRaWAN Architecture, Protocol and Technologies
Authors: Ertürk Mehmet Ali , Aydın Muhammed Ali , Büyükakkaşlar Muhammet Talha , Evirgen Hayrettin
Published: October 2019

Internet of Things (IoT) expansion led the market to find alternative communication technologies since existing protocols are insufficient in terms of coverage, energy consumption to fit IoT needs. Low Power Wide Area Networks (LPWAN) emerged as an alternative cost-effective communication technology for the IoT market. LoRaWAN is an open LPWAN standard developed by LoRa Alliance and has key features i.e., low energy consumption, long-range communication, builtin security, GPS-free positioning. In this paper, we will introduce LoRaWAN technology, the state of art studies in the literature and provide open opportunities.
Detection of Microaneurysms in Fundus Images Based on an Attention Mechanism
Authors: Zhang Lizong , Feng Shuxin , Duan Guiduo , Li Ying , Liu Guisong
Published: October 2019

Microaneurysms (MAs) are the earliest detectable diabetic retinopathy (DR) lesions. Thus, the ability to automatically detect MAs is critical for the early diagnosis of DR. However, achieving the accurate and reliable detection of MAs remains a significant challenge due to the size and complexity of retinal fundus images. Therefore, this paper presents a novel MA detection method based on a deep neural network with a multilayer attention mechanism for retinal fundus images. First, a series of equalization operations are performed to improve the quality of the fundus images. Then, based on the attention mechanism, multiple feature layers with obvious target features are fused to achieve preliminary MA detection. Finally, the spatial relationships between MAs and blood vessels are utilized to perform a secondary screening of the preliminary test results to obtain the final MA detection results. We evaluated the method on the IDRiD_VOC dataset, which was collected from the open IDRiD dataset. The results show that our method effectively improves the average accuracy and sensitivity of MA detection.
Morphological Characterization of Flower Buds Development and Related Gene Expression Profiling at Bud Break Stage in Heterodichogamous Cyclocarya paliurus (Batal.) lljinskaja
Authors: Chen Xiaoling , Mao Xia , Huang Peng , Fang Shengzuo
Published: October 2019

Cyclocarya paliurus (Batal.) Iljinskaja, a unique species growing in southern China, is a multi-function tree species with medicinal, healthcare, material, and ornamental values. So far, sexual reproduction is the main method for extensive cultivation of C. paliurus plantations, but this is limited by low seed plumpness resulted from the character of heterodichogamy. Phenological observations have revealed the asynchronism of flower development in this species. However, its molecular mechanism remains largely unknown. To reveal molecular mechanism of heterodichogamy in C. paliurus, transcriptome of female (F) and male (M) buds from two mating types (protandry, PA; protogyny, PG) at bud break stage were sequenced using Illumina Hiseq 4000 platform. The expression patterns of both 32 genes related to flowering and 58 differentially expressed transcription factors (DETFs) selected from 6 families were divided four groups (PG-F, PG-M, PA-F, and PA-M) into two categories: first flowers (PG-F and PA-M) and later flowers (PA-F and PG-M). The results indicated that genes related to plant hormones (IAA, ABA, and GA) synthesis and response, glucose metabolism, and transcription factors (especially in MIKC family) played significant roles in regulating asynchronism of male and female flowers in the same mating type. The expression of DETFs showed two patterns. One contained DETFs up-regulated in first flowers in comparison to later flowers, and the other was the reverse. Nine genes related to flowering were selected for qRT-PCR to confirm the accuracy of RNA-seq, and generally, the RPKM values of these genes were consistent with the result of qRT-PCR. The results of this work could improve our understanding in asynchronism of floral development within one mating type in C. paliurus at transcriptional level, as well as lay a foundation for further study in heterodichogamous plants.
pyjeo: A Python Package for the Analysis of Geospatial Data
Authors: Kempeneers Pieter , Pesek Ondrej , De Marchi Davide , Soille Pierre
Published: October 2019

A new Python package, pyjeo, that deals with the analysis of geospatial data has been created by the Joint Research Centre (JRC). Adopting the principles of open science, the JRC strives for transparency and reproducibility of results. In this view, it has been decided to release pyjeo as free and open software. This paper describes the design of pyjeo and how its underlying C/C++ library was ported to Python. Strengths and limitations of the design choices are discussed. In particular, the data model that allows the generation of on-the-fly data cubes is of importance. Two uses cases illustrate how pyjeo can contribute to open science. The first is an example of large-scale processing, where pyjeo was used to create a global composite of Sentinel-2 data. The second shows how pyjeo can be imported within an interactive platform for image analysis and visualization. Using an innovative mechanism that interprets Python code within a C++ library on-the-fly, users can benefit from all functions in the pyjeo package. Images are processed in deferred mode, which is ideal for prototyping new algorithms on geospatial data, and assess the suitability of the results created on the fly at any scale and location.
Identification of an Interferon-Stimulated Long Noncoding RNA (LncRNA ISR) Involved in Regulation of Influenza A Virus Replication
Authors: Pan Qidong , Zhao Zhonghui , Liao Yuan , Chiu Shih-Hsin , Wang Song , Chen Biao , Chen Na , Chen Yuhai , Chen Ji-Long
Published: October 2019

Long noncoding RNAs (lncRNAs) are involved in a diversity of biological processes. It is known that differential expression of thousands of lncRNAs occurs in host during influenza A virus (IAV) infection. However, only few of them have been well characterized. Here, we identified a lncRNA, named as interferon (IFN)-stimulated lncRNA (ISR), which can be significantly upregulated in response to IAV infection in a mouse model. A sequence alignment revealed that lncRNA ISR is present in mice and human beings, and indeed, we found that it was expressed in several human and mouse cell lines and tissues. Silencing lncRNA ISR in A549 cells resulted in a significant increase in IAV replication, whereas ectopic expression of lncRNA ISR reduced the viral replication. Interestingly, interferon-β (IFN-β) treatment was able to induce lncRNA ISR expression, and induction of lncRNA ISR by viral infection was nearly abolished in host deficient of IFNAR1, a type I IFN receptor. Furthermore, the level of IAV-induced lncRNA ISR expression was decreased either in retinoic acid-inducible gene I (RIG-I) knockout A549 cells and mice or by nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) inhibitor treatment. Together, these data elucidate that lncRNA ISR is regulated by RIG-I-dependent signaling that governs IFN-β production during IAV infection, and has an inhibitory capacity in viral replication.
Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.)
Authors: Li Yuqing , Qin Tengfei , Wei Chunyan , Sun Jialiang , Dong Tao , Zhou Ruiyang , Chen Quanjia , Wang Qinglian
Published: October 2019

Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, ‘turquoise,’ ‘blue,’ and ‘green,’ were specific for the CMS C2P5A line. The ‘turquoise’ and ‘blue’ modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The ‘green’ module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.
Glucose-Sensing Transcription Factor MondoA/ChREBP as Targets for Type 2 Diabetes: Opportunities and Challenges
Authors: Song Ziyi , Yang Hao , Zhou Lei , Yang Fajun
Published: October 2019

The worldwide increase in type 2 diabetes (T2D) is becoming a major health concern, thus searching for novel preventive and therapeutic strategies has become urgent. In last decade, the paralogous transcription factors MondoA and carbohydrate response element-binding protein (ChREBP) have been revealed to be central mediators of glucose sensing in multiple metabolic organs. Under normal nutrient conditions, MondoA/ChREBP plays vital roles in maintaining glucose homeostasis. However, under chronic nutrient overload, the dysregulation of MondoA/ChREBP contributes to metabolic disorders, such as insulin resistance (IR) and T2D. In this review, we aim to provide an overview of recent advances in the understanding of MondoA/ChREBP and its roles in T2D development. Specifically, we will briefly summarize the functional similarities and differences between MondoA and ChREBP. Then, we will update the roles of MondoA/ChREBP in four T2D-associated metabolic organs (i.e., the skeletal muscle, liver, adipose tissue, and pancreas) in physiological and pathological conditions. Finally, we will discuss the opportunities and challenges of MondoA/ChREBP as drug targets for anti-diabetes. By doing so, we highlight the potential use of therapies targeting MondoA/ChREBP to counteract T2D and its complications.
Peptidic Antifreeze Materials: Prospects and Challenges
Authors: Surís-Valls Romà , Voets Ilja K.
Published: October 2019

Necessitated by the subzero temperatures and seasonal exposure to ice, various organisms have developed a remarkably effective means to survive the harsh climate of their natural habitats. Their ice-binding (glyco)proteins keep the nucleation and growth of ice crystals in check by recognizing and binding to specific ice crystal faces, which arrests further ice growth and inhibits ice recrystallization (IRI). Inspired by the success of this adaptive strategy, various approaches have been proposed over the past decades to engineer materials that harness these cryoprotective features. In this review we discuss the prospects and challenges associated with these advances focusing in particular on peptidic antifreeze materials both identical and akin to natural ice-binding proteins (IBPs). We address the latest advances in their design, synthesis, characterization and application in preservation of biologics and foods. Particular attention is devoted to insights in structure-activity relations culminating in the synthesis of de novo peptide analogues. These are sequences that resemble but are not identical to naturally occurring IBPs. We also draw attention to impactful developments in solid-phase peptide synthesis and ‘greener’ synthesis routes, which may aid to overcome one of the major bottlenecks in the translation of this technology: unavailability of large quantities of low-cost antifreeze materials with excellent IRI activity at (sub)micromolar concentrations.
Functional Characterization of Outer Membrane Proteins (OMPs) in Xenorhabdus nematophila and Photorhabdus luminescens through Insect Immune Defense Reactions
Authors: Darsouei Reyhaneh , Karimi Javad , Dunphy Gary B.
Published: October 2019

Xenorhabdus nematophila and Photorhabdus luminescens are entomopathogenic bacterial symbionts that produce toxic proteins that can interfere with the immune system of insects. Herein, we show that outer membrane proteins (OMPs) could be involved as bacterial virulence factors. Purified totals OMPs of both bacterial species were injected into fifth instar larvae of Spodoptera exigua Hübner. Larvae were surveyed for cellular defenses fluctuations in total haemocyte counts (THC) and granulocyte percentage and for the humoral defenses protease, phospholipase A2 (PLA2), and phenoloxidase (PO) activities at specific time intervals. Changes in the expression of the three inducible antimicrobial peptides (AMPs), cecropin, attacin, and spodoptericin, were also measured. Larvae treated with OMPs of both bacterial species had more haemocytes than did the negative controls. OMPs of X. nematophila caused more haemocyte destruction than did the OMPs of P. luminescens. The OMPs of both bacterial species initially activated insect defensive enzymes post-injection, the degree of activation varying with enzyme type. The AMPs, attacin, cecropin, and spodoptericin were up-regulated by OMP injections compared with the normal larvae. The expression of these three AMPs was maximal at four hours post injection (hpi) with P. luminescens OMPs treatment. Expression of the three AMPs in X. nematophila treated insects was irregular and lower than in the P. luminescens OMPs treatment. These findings provide insights into the role of OMPs of entomopathogenic nematode bacterial symbionts in countering the physiological defenses of insects.
Electron Diagnostics for Extreme High Brightness Nano-Blade Field Emission Cathodes
Authors: Lawler Gerard , Sanwalka Kunal , Zhuang Yumeng , Yu Victor , Paschen Timo , Robles River , Williams Oliver , Sakai Yusuke , Naranjo Brian , Rosenzweig James
Published: October 2019

Electron beams are essential tools in modern science. They are ubiquitous in fields ranging from microscopy to the creation of coherent ultra-fast X-rays to lithography. To keep pace with demand, electron beam brightness must be continually increased. One of the main strategic aims of the Center for Bright Beams (CBB), a National Science Foundation Science and Technology Center, is to increase brightness from photocathodes by two orders of magnitude. Improving the state-of-the-art for photoemission-based cathodes is one possibility. Several factors have led to an alternative design becoming an increasing necessity; the nanoscale structure. Field emission sources from nano-tips would be an ideal candidate were it not for their low current and damage threshold. A 1-dimensional extended nano-fabricated blade, i.e., a projected tip, can solve the problems inherent in both designs. The novel geometry has been demonstrated to produce extremely high brightness electron beam bunches and is significantly more robust and easier to manufacture than traditional photocathodes. Theory indicates electron emission up to keV energies. We thus present a system of diagnostics capable of analyzing the cathodes and assessing their viability. The diagnostics are designed to measure the electron spectrum up to keV energies, with sub meV resolution at <100 eV, mean transverse energy (MTE), emission uniformity, and cathode lifetime. We also report preliminary data on total extracted charge and maximum detectable electron energy with a simplified retarding field spectrometer.
Validation of Identified Susceptible Gene Variants for New-Onset Diabetes in Renal Transplant Recipients
Authors: Hwang Hyeon , Hong Kyung-Won , Kim Jin , Kim Yang , Moon Ju , Jeong Kyung , Lee Sang ,   The Korean Organ Transplantation Registry Study Group
Published: October 2019

Genome-wide association studies (GWAS) and candidate gene approaches have identified single nucleotide polymorphisms (SNPs) associated with new-onset diabetes after renal transplantation (NODAT). We evaluated associations between NODAT and SNPs identified in previous studies. We genotyped 1102 renal transplant recipients from the Korean Organ Transplantation Registry (KOTRY) database; 13 SNPs were assessed for associations with NODAT (occurring in 254 patients; 23.0%), within one year after transplantation. The frequency of the T allele at KCNQ1 rs2237892 was significantly lower in patients with NODAT compared to control patients (0.30 vs. 0.39; p = 8.5 × 10−5). The T allele at rs2237892 was significantly associated with decreased risk of NODAT after adjusting for multiple variables, compared to the C allele (OR 0.63, 95% CI 0.51–0.79; p = 5.5 × 10−5). Dominant inheritance modeling showed that CT/TT genotypes were associated with a lower risk for development of NODAT (OR 0.56, 95% CI 0.42–0.76; p = 2.0 × 10−4) compared to the CC genotype. No other SNPs were associated with NODAT. Our study validated the protective effect of T allele at KCNQ1 rs2237892 on the development of NODAT in a large cohort of renal transplant recipients. Our findings on susceptibility variants might be a useful tool to predict NODAT development after renal transplantation.
Association of Nicotine with Osteochondrogenesis and Osteoarthritis Development: The State of the Art of Preclinical Research
Authors: Cai Xiaoyu , Gao Liang , Cucchiarini Magali , Madry Henning
Published: October 2019

The deleterious effects of nicotine on various health conditions have been well documented. Although many orthopedic diseases are adversely affected by nicotine, little is known about its preclinical effects on chondrogenesis or osteogenesis, cartilage formation, osteoarthritis (OA), and osteochondral repair. A systematic review was conducted examining the current scientific evidence on the effects of nicotine on chondrogenesis or osteogenesis in vitro, possible consequences of prenatal nicotine exposure (PNE) on cartilage and OA susceptibility in the offspring, and whether nicotine affects OA development and osteochondral repair in vivo, always focusing on their underlying mechanisms. The data reveal dose-dependent effects on articular chondrocytes and on the chondrogenesis and osteogenesis of medicinal signaling cells in vitro, with lower doses often resulting in positive effects and higher doses causing negative effects. PNE negatively affects articular cartilage development and induces OA in the offspring without or with nicotine exposure. In contrast, protective effects on OA development were only reported in monosodium iodoacetate-induced small animal models. Finally, nicotine repressed MSC-based osteochondral repair in vivo. Future studies need to investigate dose-dependent clinical effects of smoking on cartilage quality in offspring, OA susceptibility and progression, and osteochondral repair more in detail, thus identifying possible thresholds for its pathological effects.
Optimizing Hydroxyurea Treatment for Sickle Cell Disease Patients: The Pharmacokinetic Approach
Authors: Nazon Charlotte , Sabo Amelia-Naomi , Becker Guillaume , Lessinger Jean-Marc , Kemmel Véronique , Paillard Catherine
Published: October 2019

Background: Hydroxyurea (HU) is a FDA- and EMA-approved drug that earned an important place in the treatment of patients with severe sickle cell anemia (SCA) by showing its efficacy in many studies. This medication is still underused due to fears of physicians and families and must be optimized. Methods: We analyzed our population and identified HU pharmacokinetic (PK) parameters in order to adapt treatment in the future. Working with a pediatric population, we searched for the most indicative sampling time to reduce the number of samples needed. Results: Nine children treated by HU for severe SCA were included for this PK study. HU quantification was made using a validated gas chromatography/mass spectrometry (GC/MS) method. Biological parameters (of effectiveness and compliance) and clinical data were collected. None of the nine children reached the therapeutic target defined by Dong et al. as an area under the curve (AUC) = 115 h.mg/L; four patients were suspected to be non-compliant. Only two patients had an HbF over 20%. The 2 h sample was predictive of the medication exposure (r2 = 0.887). Conclusions: It is urgent to be more efficient in the treatment of SCA, and pharmacokinetics can be an important asset in SCA patients.
Heart Rate Variability and Perceived Stress as Measurements of Relaxation Response
Authors: Nakao Mutsuhiro
Published: October 2019

Stress is a term used to define the body’s physiological and psychological reactions to circumstances that require behavioral adjustment [...]
Exercise and Cognitive Function
Authors: Loprinzi Paul D. , Lovorn Ashley
Published: October 2019

Cognitive function is associated with longevity and is of critical importance for optimal daily functioning [...]