bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of conspecific negative density dependence to species diversity is increasing towards low environmental limitation in Japanese forests
Authors: Fibich Pavel , Ishihara Masae I. , Suzuki Satoshi N. , Doležal Jiří , Altman Jan 
Published: September 2021

AbstractSpecies coexistence is a result of biotic interactions, environmental and historical conditions. The Janzen-Connell hypothesis assumes that conspecific negative density dependence (CNDD) is one of the local processes maintaining high species diversity by decreasing population growth rates at high densities. However, the contribution of CNDD to species richness variation across environmental gradients remains unclear. In 32 large forest plots all over the Japanese archipelago covering > 40,000 individual trees of > 300 species and based on size distributions, we analysed the strength of CNDD of individual species and its contribution to species number and diversity across altitude, mean annual temperature, mean annual precipitation and maximum snow depth gradients. The strength of CNDD was increasing towards low altitudes and high tree species number and diversity. The effect of CNDD on species number was changing across altitude, temperature and snow depth gradients and their combined effects contributed 11–18% of the overall explained variance. Our results suggest that CNDD can work as a mechanism structuring forest communities in the Japanese archipelago. Strong CNDD was observed to be connected with high species diversity under low environmental limitations where local biotic interactions are expected to be stronger than in niche-based community assemblies under high environmental filtering.
Palaeoclimate has a major effect on the diversity of endemic species in the hotspot of mountain biodiversity in Tajikistan
Authors: Raduła Małgorzata , Świerszcz Sebastian , Nobis Marcin , Nowak Sylwia , Nobis Agnieszka , Nowak Arkadiusz 
Published: September 2021

AbstractIn a period of ongoing climate changes, identifying drivers of overall and endemic species diversity is a key element in constructing new ecological patterns and determining the main goals of conservation. Such studies are especially crucial if they concern biodiversity hotspot areas. In this study, we explore patterns and drivers of plant endemism (the proportion of endemic plant species to overall plant species richness; PE) in Tajikistan. We used three groups of climatic measures featuring the contemporary and glacial climates as well as climatic changes since the Last Glacial Maximum in the Pleistocene (LGM). To explore relationships between PE and climatic groups, and the most important climatic variables, we applied the Generalised Additive Model and regression trees method respectively. Glacial climate predicted PE variation the most (74.3%), followed by climate stability (55.4%) and current climate (62.4%). The most important variables represented change in precipitation of driest quarter, glacial mean annual temperature and current annual precipitation. LGM climate and its change to date have the greatest influence on contemporary PE patterns in Tajikistan, revealing the evolutionary dependencies between limited-range plants and past climate. Accordingly, annual temperature and precipitation regimes have been the most crucial drivers of PE since the LGM until today. The study revealed the dependence of the PE on a stabilized water-energy supply. The changing temperature and precipitations regimes during the ongoing climate warming may, therefore, increases the threat to geographically isolated cryophilous plants of Tajikistan, while their escape potential to suitable cold habitats is highly topographically limited.
A novel bioluminescent herpes simplex virus 1 for in vivo monitoring of herpes simplex encephalitis
Authors: Uyar Olus , Plante Pier-Luc , Piret Jocelyne , Venable Marie-Christine , Carbonneau Julie , Corbeil Jacques , Boivin Guy 
Published: September 2021

AbstractHerpes simplex virus 1 (HSV-1) is responsible for herpes simplex virus encephalitis (HSE), associated with a 70% mortality rate in the absence of treatment. Despite intravenous treatment with acyclovir, mortality remains significant, highlighting the need for new anti-herpetic agents. Herein, we describe a novel neurovirulent recombinant HSV-1 (rHSV-1), expressing the fluorescent tdTomato and Gaussia luciferase (Gluc) enzyme, generated by the Clustered regularly interspaced short palindromic repeats (CRISPR)—CRISPR-associated protein 9 (Cas9) (CRISPR-Cas9) system. The Gluc activity measured in the cell culture supernatant was correlated (P = 0.0001) with infectious particles, allowing in vitro monitoring of viral replication kinetics. A significant correlation was also found between brain viral titers and Gluc activity in plasma (R2 = 0.8510, P < 0.0001) collected from BALB/c mice infected intranasally with rHSV-1. Furthermore, evaluation of valacyclovir (VACV) treatment of HSE could also be performed by analyzing Gluc activity in mouse plasma samples. Finally, it was also possible to study rHSV-1 dissemination and additionally to estimate brain viral titers by in vivo imaging system (IVIS). The new rHSV-1 with reporter proteins is not only as a powerful tool for in vitro and in vivo antiviral screening, but can also be used for studying different aspects of HSE pathogenesis.
Effect of density, phonon scattering and nanoporosity on the thermal conductivity of anisotropic cellulose nanocrystal foams
Authors: Apostolopoulou-Kalkavoura Varvara , Munier Pierre , Dlugozima Lukasz , Heuthe Veit-Lorenz , Bergström Lennart 
Published: September 2021

AbstractAnisotropic cellulose nanocrystal (CNC) foams with densities between 25 and 130 kg m−3 (CNC25 –CNC130) were prepared by directional ice-templating of aqueous dispersions. Estimates of the solid and gas conduction contributions to the thermal conductivity of the foams using a parallel resistor model showed that the relatively small increase of the radial thermal conductivity with increasing foam density can be attributed to interfacial phonon scattering. The foam wall nanoporosity and, to a lesser extent, the orientation of the CNC particles and alignment of the columnar macropores, also influence the insulation performance of the foams. The insight on the importance of phonon scattering for the thermal insulation properties of nanocellulose foams provides useful guidelines for tailoring nanofibrillar foams for super-insulating applications.
Relationship of low molecular weight fluorophore levels with clinical factors and fenofibrate effects in adults with type 2 diabetes
Authors: Januszewski Andrzej S. , Chen David , Scott Russell S. , O’Connell Rachel L. , Aryal Nanda R. , Sullivan David R. , Watts Gerald F. , Taskinen Marja-Riitta , Barter Philip J. , Best James D. , Simes R. John , Keech Anthony C. , Jenkins Alicia J. 
Published: September 2021

AbstractPeople with diabetes are at risk of chronic complications and novel biomarkers, such as Advanced glycation end-products (AGEs) may help stratify this risk. We assessed whether plasma low-molecular weight AGEs, also known as LMW-fluorophores (LMW-F), are associated with risk factors, predict complications, and are altered by fenofibrate in adults with type 2 diabetes. Plasma LMW-F were quantified at baseline, after six weeks fenofibrate, and one year post-randomisation to fenofibrate or placebo. LMW-F associations with existing and new composite vascular complications were determined, and effects of fenofibrate assessed. LMW-F correlated positively with age, glycated haemoglobin (HbA1c), pulse pressure, kidney dysfunction and inflammation; and negatively with urate, body mass index, oxidative stress and leptin, albeit weakly (r = 0.04–0.16, allp < 0.01). Independent determinants of LMW-F included smoking, diastolic blood pressure, prior cardiovascular disease or microvascular complications, Caucasian ethnicity, kidney function, HbA1c and diabetes duration (allp ≤ 0.01). Baseline LMW-F tertiles correlated with on-trial macrovascular and microvascular complications (trendp < 0.001) on univariate analyses only. Six weeks of fenofibrate increased LMW-F levels by 21% (p < 0.001). In conclusion, LMW-F levels correlate with many risk factors and chronic diabetes complications, and are increased with fenofibrate. LMW-F tertiles predict complications, but not independently of traditional risk factors.
An experimentally validated fading model for THz wireless systems
Authors: Papasotiriou Evangelos N. , Boulogeorgos Alexandros-Apostolos A. , Haneda Katsuyuki , de Guzman Mar Francis , Alexiou Angeliki 
Published: September 2021

AbstractAs the wireless world moves towards the sixth generation (6G) era, the demand of supporting bandwidth-hungry applications in ultra-dense deployments becomes more and more imperative. Driven by this requirement, both the research and development communities have turned their attention into the terahertz (THz) band, where more than$$20\,{\text {GHz}}$$20GHzof contiguous bandwidth can be exploited. As a result, novel wireless system and network architectures have been reported promising excellence in terms of reliability, massive connectivity, and data-rates. To assess their feasibility and efficiency, it is necessary to develop stochastic channel models that account for the small-scale fading. However, to the best of our knowledge, only initial steps have been so far performed. Motivated by this, this contribution is devoted to take a new look to fading in THz wireless systems, based on three sets of experimental measurements. In more detail, measurements, which have been conducted in a shopping mall, an airport check-in area, and an entrance hall of a university towards different time periods, are used to accurately model the fading distribution. Interestingly, our analysis shows that conventional distributions, such as Rayleigh, Rice, and Nakagami-m, lack fitting accuracy, whereas, the more general, yet tractable,$$\alpha $$α–$$\mu $$μdistribution has an almost-excellent fit. In order to quantify their fitting efficiency, we used two well-defined and widely-accepted tests, namely the Kolmogorov–Smirnov and the Kullback–Leibler tests. By accurately modeling the THz wireless channel, this work creates the fundamental tools of developing the theoretical and optimization frameworks for such systems and networks.
Achieving broad absorption band and high incident angles by stochastically-distributed oblique-flat-sheet metamaterial perfect absorbers
Authors: Lu Cheng-Yu , Chung Chin-Chien , Yen Ta-Jen , Huang Tsung-Yu 
Published: September 2021

AbstractIn this work, we integrated a periodic seed layer and oblique deposition method to fabricate a stochastically-distributed oblique-flat-sheet metamaterial perfect absorber (MPA). Such design could increase its absorption bandwidth and tolerance to high angle-incidence due to the fact that various oblique flat sheets offer different resonance conditions while even a single oblique flat sheet could provide different optical paths for resonance. On the other hand, a seed layer could reduce uncertainty regarding to direct oblique deposition and provide abilities to manipulate the bandwidth of the MPA. We also setup a simulation model in the aids of Visual Basic Application and examined the absorption behavior of the MPA under TM and TE oblique incidence that could achieve high absorbance under 80° and 60° incidence, respectively. Finally, in measurement, the fabricated sample owns 65% absorbance within 80–250 THz and over 90% absorbance within 250–320 THz at x-polarization normal incidence; as for the y-polarization normal incidence, we could achieve overall 70% absorbance within 80–300 THz. The measured results reveal similar tendency compared to the simulated ones.
Thermal growth in solar water pump using Prandtl–Eyring hybrid nanofluid: a solar energy application
Authors: Jamshed Wasim , Nasir Nor Ain Azeany Mohd , Isa Siti Suzilliana Putri Mohamed , Safdar Rabia , Shahzad Faisal , Nisar Kottakkaran Sooppy , Eid Mohamed R. , Abdel-Aty Abdel-Haleem , Yahia I. S. 
Published: September 2021

AbstractNowadays, with the advantages of nanotechnology and solar radiation, the research of Solar Water Pump (SWP) production has become a trend. In this article, Prandtl–Eyring hybrid nanofluid (P-EHNF) is chosen as a working fluid in the SWP model for the production of SWP in a parabolic trough surface collector (PTSC) is investigated for the case of numerous viscous dissipation, heat radiations, heat source, and the entropy generation analysis. By using a well-established numerical scheme the group of equations in terms of energy and momentum have been handled that is called the Keller-box method. The velocity, temperature, and shear stress are briefly explained and displayed in tables and figures. Nusselt number and surface drag coefficient are also being taken into reflection for illustrating the numerical results. The first finding is the improvement in SWP production is generated by amplification in thermal radiation and thermal conductivity variables. A single nanofluid and hybrid nanofluid is very crucial to provide us the efficient heat energy sources. Further, the thermal efficiency of MoS2–Cu/EO than Cu–EO is between 3.3 and 4.4% The second finding is the addition of entropy is due to the increasing level of radiative flow, nanoparticles size, and Prandtl–Eyring variable.
Identification of candidate regulators of mandibular bone loss in FcγRIIB-/- Mice
Authors: Sakunrangsit Nithidol , Pholtaisong Jatuphol , Sucharitakul Jeerus , Wanna-udom Sasithorn , Prombutara Pinidphon , Pisitkun Prapaporn , Leelahavanichkul Asada , Aporntewan Chatchawit , Greenblatt Matthew B. , Lotinun Sutada 
Published: September 2021

AbstractPatients with systemic lupus erythematosus (SLE) have increased inflammatory cytokines, leading to periodontitis and alveolar bone loss. However, the mechanisms driving this phenomenon are still unknown. Here, we have identified novel therapeutic targets for and mediators of lupus-mediated bone loss using RNA-sequencing (RNA-seq) in a FcγRIIB-/- mouse model of lupus associated osteopenia. A total of 2,710 upregulated and 3,252 downregulated DEGs were identified. The GO and KEGG annotations revealed that osteoclast differentiation, bone mineralization, ossification, and myeloid cell development were downregulated. WikiPathways indicated that Hedgehog, TNFα NF-κB and Notch signaling pathway were also decreased. We identified downregulated targets, Sufu and Serpina12, that have important roles in bone homeostasis. Sufu and Serpina12 were related to Hedgehog signaling proteins, including Gli1, Gli2, Gli3, Ptch1, and Ptch2. Gene knockdown analysis demonstrated that Sufu, and Serpina12 contributed to osteoclastogenesis and osteoblastogenesis, respectively. Osteoclast and osteoblast marker genes were significantly decreased in Sufu-deficient and Serpina12-deficient cells, respectively. Our results suggest that alterations in Hedgehog signaling play an important role in the pathogenesis of osteopenia in FcγRIIB-/- mice. The novel DEGs and pathways identified in this study provide new insight into the underlying mechanisms of mandibular bone loss during lupus development.
Topological heterogeneity and evaporation dynamics of irregular water droplets
Authors: Kim Yeseul , Gonçalves Marta , Kim Deok-Ho , Weon Byung Mook 
Published: September 2021

AbstractWater droplets sitting between wires are ubiquitous in nature and industry, often showing irregular (non-spherical) droplet shapes. To understand their topological singularity and evaporation mechanism, measuring volume changes of irregular water droplets is essential but highly challenging for small-volume water droplets. Here we experimentally explore topological heterogeneity and evaporation dynamics for irregular water droplets between wires with four-dimensional X-ray microtomography that directly provides images in three spatial dimensions as a function of time, enabling us to get three-dimensional structural and geometric information changes with time. We find that the topological heterogeneity of an irregular droplet is due to the local contact lines and the evaporation dynamics of an irregular droplet is governed by the effective contact radius. This study may offer an opportunity to understand how the topological heterogeneity contributes to the evaporation dynamics of irregular water droplets.
HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis
Authors: Bedre Renesh , Avila Carlos , Mandadi Kranthi 
Published: September 2021

AbstractUse of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSQualC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSQualC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSQualC for conducting batch analysis of HTS datasets with 322 samples with an average ~ 1 M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in ~ 3 h in distributed mode and ~ 31 h in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSQualC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.
Analysis of atmospheric temperature data by 4D spatial–temporal statistical model
Authors: Xu Ke , Wang Yaqiong 
Published: September 2021

AbstractThe meteorological data such as temperature of the upper atmosphere is ssential for accurate weather forecasting. The Universal Rawinsonde Observation Program (RAOB) establishes an extensive radiosonde network worldwide to observe atmospheric meteorological data from the surface to the low stratosphere. The RAOB data data has very high accuracy but can offer a very limited spatial coverage. Meanwhile, ERA-Interim reanalysis data is widely available but with low-quality. We propose a 4D spatiotemporal statistical model which can make effective inferences from ERA-Interim reanalysis data to RAOB data. Finally, we can obtain a huge amount of RAOB data with high-quality and can offer a very wide spatial coverage. In empirical research, we collected data from 200 launch sites around the world in January 2015. The 4D spatiotemporal statistical model successfully analyzed the observation gaps at different pressure levels.
Synthesis of a novel ternary ZIF-8/GO/MgFe2O4 nanocomposite and its application in drug delivery
Authors: Sanaei-Rad Saleheh , Ghasemzadeh Mohammad Ali , Razavian Seyyed Mohammad Hossein 
Published: September 2021

AbstractIn recent year, metal–organic frameworks (MOFs) have been displayed to be a category of promising drug delivery systems because of their crystalline structure, the potential of further functionality, and high porosity. In this research, graphene oxide was synthesized from pure graphite via hummer method and then MgFe2O4 nanoparticles was incorporated into the synthesized ZIF-8 metal–organic frameworks which followed with loading on the surfaces of graphene oxide. In continue, tetracycline as an antibiotic drug was loaded on the surfaces and the cavities of the prepared nanocomposite. The outcomes of this research revealed that 90% of the tetracycline was loaded on the synthesized ZIF-8/GO/MgFe2O4 nanostructure. Next, drug release was done at pH: 5 and pH: 7.4 within 3 days, resulting about 88% and 92% release of the tetracycline, respectively. With using different spectroscopic methods like X-ray crystallography (XRD), scanning electron microscope (SEM), energy-dispersive X-ray spectroscopy (EDX/Mapping), Fourier transform infrared (FTIR), thermalgravimetric analysis (TGA), and Brunauer–Emmett–Teller (BET), the structure of synthesized materials was confirmed. Furthermore, the antibiotic activity of tetracycline trapped into the ZIF-8/GO/MgFe2O4 was evaluated by agar-well diffusion method on both gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria, which showed good antibacterial results.
Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase
Authors: Pan Jolyn , Lian Kjersti , Sarre Aili , Leiros Hanna-Kirsti S. , Williamson Adele 
Published: September 2021

AbstractDNA ligases, the enzymes responsible for joining breaks in the phosphodiester backbone of DNA during replication and repair, vary considerably in size and structure. The smallest members of this enzyme class carry out their functions with pared-down protein scaffolds comprising only the core catalytic domains. Here we use sequence similarity network analysis of minimal DNA ligases from all biological super kingdoms, to investigate their evolutionary origins, with a particular focus on bacterial variants. This revealed that bacterial Lig C sequences cluster more closely with Eukaryote and Archaeal ligases, while bacterial Lig E sequences cluster most closely with viral sequences. Further refinement of the latter group delineates a cohesive cluster of canonical Lig E sequences that possess a leader peptide, an exclusively bacteriophage group of T7 DNA ligase homologs and a group with high similarity to the Chlorella virus DNA ligase which includes both bacterial and viral enzymes. The structure and function of the bacterially-encoded Chlorella virus homologs were further investigated by recombinantly producing and characterizing, the ATP-dependent DNA ligase from Burkholderia pseudomallei as well as determining its crystal structure in complex with DNA. This revealed that the enzyme has similar activity characteristics to other ATP-dependent DNA ligases, and significant structural similarity to the eukaryotic virus Chlorella virus including the positioning and DNA contacts of the binding latch region. Analysis of the genomic context of the B. pseudomallei ATP-dependent DNA ligase indicates it is part of a lysogenic bacteriophage present in the B. pseudomallei chromosome representing one likely entry point for the horizontal acquisition of ATP-dependent DNA ligases by bacteria.