bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple environmental factors regulate the large-scale patterns of plant water use efficiency and nitrogen availability across China’s forests
Authors: Tang Songbo , Lai Yuan , Tang Xuli , Phillips Oliver L. , Liu Jianfeng , Chen Dexiang , Wen Dazhi , Wang Silong , Chen Longchi , Tian Xingjun , Kuang Yuanwen 
Published: February 2021

Abstract
Global changes, e.g. global warming, elevated nitrogen deposition, and shifts of precipitation regime, exert a major influence on forests via affecting plant water use efficiency (WUE) and plant nitrogen (N) availability. Large-scale ecological sampling can help us to better understand variation across regions and provide opportunities to investigate the potential impacts of multiple aspects of global change on forest ecosystem responses. Here, we determine the geographical patterns of key isotopic measures of ecosystem function—plant WUE (calculated from foliar δ
13C values) and plant N availability (assessed by foliar δ
15N values)—across China’s forests covering ∼21 latitude (∼22–43°N) and ∼28 longitude (∼93–121°E) degree, and investigate how a suite of soil, plant, and atmospheric factors regulate them. We found that plant WUE increased but N availability decreased with latitude, while plant WUE and N availability did not vary with longitudinal gradient. Different factors regulate the large-scale patterns in WUE and N availability. The mean annual temperature, atmospheric N deposition, and soil water content exhibit considerable effects on plant WUE over both the north-to-south and east-to-west transects, while the mean annual precipitation, soil potassium content, foliar N, and precipitation seasonality considerably affect the latitudinal patterns of plant N availability. In addition, the east-to-west spatial pattern in plant N availability is associated with the variation in solar radiation. Our results suggest that key forest ecological functions respond to an array of environmental factors, and imply that changes in many different environmental attributes need to be considered in order to successfully assess plant WUE and N availability responses to global changes this century.
Poincaré crystal on the one-dimensional lattice
Authors: Wang Pei 
Published: February 2021

Abstract
In this paper, we develop the quantum theory that has discrete Poincaré symmetry on the one-dimensional Bravais lattice. We review the recently discovered discrete Lorentz symmetry which coexists with the discrete space translational symmetry on a Bravais lattice. The discrete Lorentz transformations and spacetime translations form the discrete Poincaré group, which are represented by unitary operators in a quantum theory. We find the conditions for the existence of representation, which are expressed as the congruence relation between quasi-momentum and quasi-energy. We then build the Lorentz-invariant many-body theory of indistinguishable particles by expressing both the unitary operators and Floquet Hamiltonians in terms of the field operators. Some typical Hamiltonians include the long-range hopping which fluctuates as the distance between sites increases. We calculate the Green’s function of the theory. The spacetime points where the Green’s function is nonzero display a lattice structure. During the propagation, the particle stays localized on a single or a few sites to preserve the Lorentz symmetry.
An assessment of some physical properties of different brands of cement in Nigeria
Authors: Ogbodo Munachiso C. , Akpabot Akpabot Ifiok 
Published: February 2021

Abstract
The durability of infrastructures has become a significant issue starring the face of professionals in the building industry as most recently constructed structures are deficient in this regard. This study was carried out to assess the physical properties of five different brands of Portland cement commonly used in Nigeria. The specific surface method was adopted in obtaining the fineness, and the specific gravity bottle was used to determine the specific gravity of the different cement brands. The result shows that sample A had the highest fineness value of 360m2/kg and the only sample that met the ASTM standard value of 280 m2/kg. This implies that Sample A has a greater surface area for hydration which should lead to faster development of early strength and a higher rate of heat evolution. Sample E had the least fineness value of 168 m2/kg. This means that Sample E has the least surface area for hydration and should be slow in early strength gain. Sample B had the highest specific gravity value of 3.266 and the highest value of bulk density of 1462.085kg/m3. The implication is that Sample B has more moisture because it has the highest specific gravity value. The quantity of sample B that will be required in the concrete making will be less relative to other samples as it had the highest bulk density.
Seismic Performance Assessment of a Typical Peruvian Public-School Building
Authors: Cardenas O , Farfan A , Huaco G , Stavridis A 
Published: February 2021

Abstract
Several Peruvian public school buildings have not performed well during earthquakes, with the level of damage varying from cracks in structural elements to the complete collapse of the building. The reasons for the unsatisfactory seismic performance of the buildings include the design codes followed at the time these schools were built, and the lack of professional engineering supervision during the design and construction phases of these schools. This study focuses on a typical school building, selected after performing a survey to public schools in the district of San Juan de Miraflores in the city of Lima, in Peru. The seismic response of the selected building to various ground motions is analysed with nonlinear static and time history analyses. The results indicate that the building does not meet the minimum seismic performance level required by the current Peruvian seismic design provisions.
Effective medium approximation based interpretation for Mueller matrix spectra of polydimethylsiloxane gratings
Authors: Wang Meng , Liu Fang , Jiang Hao , Liu Shiyuan 
Published: February 2021

Abstract
Dielectric corrugated gratings are of considerable interest due to their applications in acousto-optics, quantum electronics, integrated optics, spectroscopy, and holography integrated optics. Rigorous coupled-wave analysis has been widely used for the analysis of dielectric gratings. However, this approach is not only time-consuming and computer intensive but it also does not really promote the physical understanding of the origin of the observed optical behavior. Here, we use Mueller matrix (MM) spectroscopic ellipsometry to systematically study the sinusoidal polydimethylsiloxane grating. We correlate the observed polarization mixing in the Mueller matrix to the underlying physical origin using the physics-based approach. The calculated MM contour plots obtained from a biaxial Bruggemann effective medium approximation model are completed by the presence of Rayleigh-Woods anomalies. The roles of optical interference, geometric anisotropy, and diffraction orders are respectively identified by their different dispersion behavior, with their interactions and couplings highlighted. Such a straightforward procedure provides a new method for analyzing dielectric gratings, which requires considerably less computer power and is directly linked to the physical interpretations.
Strong localization effects in the photoluminescence of transition metal dichalcogenide heterobilayers
Authors: Rodriguez A , Kalbáč M , Frank O 
Published: February 2021

Abstract
The emergence of various exciton-related effects in transition metal dichalcogenides (TMDC) and their heterostructures has inspired a significant number of studies and brought forth several possible applications. Often, standard photoluminescence (PL) with microscale lateral resolution is utilized to identify and characterize these excitonic phenomena, including interlayer excitons (IEXs). We studied the local PL signatures of van der Waals heterobilayers composed of exfoliated monolayers of the (Mo, W)(S, Se)2 TMDC family with high spatial resolution (down to 30 nm) using tip-enhanced photoluminescence (TEPL) with different orders (top/bottom) and on different substrates. We evidence that in MoS2–WSe2 heterobilayers, other PL signals may appear near the reported energy of the IEX transitions, possibly interfering in the interpretation of the results. The extra signals are only observed locally in small areas where the topography looks distorted. We assign those signals to the PL of the individual monolayers, in which the exciton energy is altered by the local strains caused by the formation of blisters and nanobubbles, and the PL is extremely enhanced due to the decoupling of the layers. We prove that even a single nanobubble as small as 60 nm—hence not optically visible—can induce such a suspicious PL feature in the micro-PL spectrum of an otherwise flat heterobilayer. In contrast, a PL peak, which could be assigned to the interlayer exciton in MoS2–WSe2, is observed at ≈1.0 eV.
Understanding the beneficial microalloying elements in Fe-based bulk metallic glasses via clusters
Authors: Yu DeChuan , Zhang YuanXiang , Li Xue , Yuan Guo 
Published: February 2021

Abstract
Glass forming ability (GFA) is one of the key factors hindering the application of bulk metallic glasses (BMGs). Microalloying has shown beneficial effects on GFA. However, the mechanism is still unclear. A new guidance via clusters was applied to understand and quickly choose beneficial microalloying elements for enhancing GFA which might help build a foundation for further quantitative analysis of minor alloying via clusters. Under the guidance, a series of beneficial microalloying elements could be quickly discovered, verified and understood. The results show that the beneficial microalloying elements for enhancing GFA should be chosen under the condition of bringing in new types of topologically efficiently packed clusters.
Experimental investigations on fatigue life enhancement of composite (e-glass/epoxy) single lap joint with graphene oxide modified adhesive
Authors: Ghadge Rohit R , Prakash S , Ganorkar Shaunak A 
Published: February 2021

Abstract
With the increased use of composites in various sectors as a lightweight material exhibits high strength to weight ratio with tailor made properties. It becomes necessary to focus on various joining methods and different types of composite joints and their strength. The present study aims to improve the mechanical strength of single lap joint of composite material comprises of E-glass fibers and nano modified adhesive. Epoxy adhesive has been modified by dispersing Graphene Oxide (GO) to investigate the possibility of enhancement in the fatigue strength and fracture resistance of the single lap joint. Modified Hummer’s method has been used for synthesis of Graphene Oxide. Experimental investigations have been carried out for comparison of tensile and fatigue strength which shows significant improvement in the number of failure cycles for 0.25 wt.% and 0.75 wt.% GO concentrations respectively as compared to neat adhesive. Tension test results showed a significant increase in the fracture toughness of the joint due to addition of GO nanoparticles. There has been 33% and 19% increase in fracture toughness in 0.25 wt.% and 0.75 wt.% GO samples respectively as compared to neat adhesive. Improvement in fracture toughness, among all other nano-reinforcements has been obtained using GO, mainly because of its better capability of deviating the crack growth path to the longer path causing the final failure to retard and consequently improving mechanical properties of the adhesive for the tensile and fatigue strength parameters.
Examining the impact of inter-provincial migration on environmental health in China
Authors: Yang Yu-Ou , Hou Juan-Juan , Chen Xin-Yu , Yu Shi-Wei , Zhang Jiu-Tian , Liu Lan-Cui 
Published: February 2021

Abstract
China has a large volume of inter-provincial migrants, accounting for more than 11% of the total population. The economic benefits of inter-provincial migration have been well studied, whereas the health impacts related to environmental factors are generally ignored. In this study, the exposure-response function was used to estimate the health effects and the corresponding economic value was calculated by the adjusted-human-capital and cost-of-illness methods. Considering a scenario without personal protection, inter-provincial migration resulted in a reduction of 6114 premature deaths, 233.4 thousand hospitalization cases, and 1.5 million asthma attacks due to the PM2.5 population-weighted exposure decreasing by 3.94 μg m−3 in 2015. The avoided economic value of these health benefits was 0.02% of the national GDP in 2015. However, two-fifths of inter-provincial migrants whose destinations are areas with heavier pollution suffered greater health losses at the regional level. Additionally, personal protection does not significantly reduce the health loss. Thus, national pollution control measures are required to curb air pollution.
Revving up 13C NMR shielding predictions across chemical space: benchmarks for atoms-in-molecules kernel machine learning with new data for 134 kilo molecules
Authors: Gupta Amit , Chakraborty Sabyasachi , Ramakrishnan Raghunathan 
Published: February 2021

Abstract
The requirement for accelerated and quantitatively accurate screening of nuclear magnetic resonance spectra across the small molecules chemical compound space is two-fold: (1) a robust ‘local’ machine learning (ML) strategy capturing the effect of the neighborhood on an atom’s ‘near-sighted’ property—chemical shielding; (2) an accurate reference dataset generated with a state-of-the-art first-principles method for training. Herein we report the QM9-NMR dataset comprising isotropic shielding of over 0.8 million C atoms in 134k molecules of the QM9 dataset in gas and five common solvent phases. Using these data for training, we present benchmark results for the prediction transferability of kernel-ridge regression models with popular local descriptors. Our best model, trained on 100k samples, accurately predicts isotropic shielding of 50k ‘hold-out’ atoms with a mean error of less than 1.9 ppm. For the rapid prediction of new query molecules, the models were trained on geometries from an inexpensive theory. Furthermore, by using a Δ-ML strategy, we quench the error below 1.4 ppm. Finally, we test the transferability on non-trivial benchmark sets that include benchmark molecules comprising 10–17 heavy atoms and drugs.
Biases in Evaluating the Safety and Effectiveness of Drugs for the Treatment of COVID-19: Designing Real-World Evidence Studies
Authors: Renoux Christel , Azoulay Laurent , Suissa Samy 
Published: February 2021

Abstract
The coronavirus disease 2019 pandemic, which was caused by the severe acute respiratory syndrome coronavirus 2, has led to an unprecedented effort to generate real-world evidence on the safety and effectiveness of various treatments. A growing number of observational studies in which the effects of certain drugs were evaluated have been conducted, including several in which researchers assessed whether hydroxychloroquine improved outcomes in infected individuals and whether renin-angiotensin-aldosterone system inhibitors have detrimental effects. In the present article, we review and illustrate how immortal time bias and selection bias were present in several of these studies. Understanding these biases and how they can be avoided may prove important for future observational studies assessing the effectiveness and safety of potentially promising drugs during the coronavirus 19 pandemic.
General-term rigidity is meaning constancy
Authors: Haraldsen Fredrik 
Published: February 2021

Abstract
It is often thought that some general terms or kind terms, in particular natural kind terms, are rigid designators, and that a properly extended notion of singular-term rigidity can help explain the behaviour of such general terms. In this article, I argue that the only legitimate notion of general-term rigidity is a trivial one and identify some crucial asymmetries between a posteriori necessary truths involving names and a posteriori necessary truths involving general terms. If we pay attention to these asymmetries, it becomes clear that attempts to draw a non-trivial rigid/non-rigid distinction for general terms are bound to fail to offer the explanations we expected. As opposed to singular terms, what is interesting about the behaviour of natural kind terms, even in modal contexts, cannot be accounted for by modal distinctions like rigidity/non-rigidity but must rather track non-modal features.
Changes in plant collection practices from the 16th to 21st centuries: implications for the use of herbarium specimens in global change research
Authors: Kozlov Mikhail V , Sokolova Irina V , Zverev Vitali , Zvereva Elena L 
Published: February 2021

Abstract

Background and Aims
Herbaria were recently advertised as reliable sources of information regarding historical changes in plant traits and biotic interactions. To justify the use of herbaria in global change research, we asked whether the characteristics of herbarium specimens have changed during the past centuries and whether these changes were due to shifts in plant collection practices.

Methods
We measured nine characteristics from 515 herbarium specimens of common European trees and large shrubs collected from 1558 to 2016. We asked botanists to rank these specimens by their scientific quality, and asked artists to rank these specimens by their beauty.

Key Results
Eight of 11 assessed characteristics of herbarium specimens changed significantly during the study period. The average number of leaves in plant specimens increased 3-fold, whereas the quality of specimen preparation decreased. Leaf size negatively correlated with leaf number in specimens in both among-species and within-species analyses. The proportion of herbarium sheets containing plant reproductive structures peaked in the 1850s. The scientific value of herbarium specimens increased until the 1700s, but then did not change, whereas their aesthetic value showed no systematic trends.

Conclusions
Our findings strongly support the hypothesis that many characteristics of herbarium specimens have changed systematically and substantially from the 16th to 21st centuries due to changes in plant collection and preservation practices. These changes may both create patterns which could be erroneously attributed to environmental changes and obscure historical trends in plant traits. The utmost care ought to be taken to guard against the possibility of misinterpretation of data obtained from herbarium specimens. We recommend that directional changes in characters of herbarium specimens which occurred during the past 150‒200 years, primarily in specimen size and in the presence of reproductive structures, are accounted for when searching for the effects of past environmental changes on plant traits.
A novel method for data fusion over entity-relation graphs and its application to protein–protein interaction prediction
Authors: Raimondi Daniele , Simm Jaak , Arany Adam , Moreau Yves 
Published: February 2021

Abstract

Motivation
Modern bioinformatics is facing increasingly complex problems to solve, and we are indeed rapidly approaching an era in which the ability to seamlessly integrate heterogeneous sources of information will be crucial for the scientific progress. Here, we present a novel non-linear data fusion framework that generalizes the conventional matrix factorization paradigm allowing inference over arbitrary entity-relation graphs, and we applied it to the prediction of protein–protein interactions (PPIs). Improving our knowledge of PPI networks at the proteome scale is indeed crucial to understand protein function, physiological and disease states and cell life in general.

Results
We devised three data fusion-based models for the proteome-level prediction of PPIs, and we show that our method outperforms state of the art approaches on common benchmarks. Moreover, we investigate its predictions on newly published PPIs, showing that this new data has a clear shift in its underlying distributions and we thus train and test our models on this extended dataset.

Supplementary information
Supplementary data are available at Bioinformatics online.
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
Authors: Steenwyk Jacob L , Buida Thomas J , Labella Abigail L , Li Yuanning , Shen Xing-Xing , Rokas Antonis 
Published: February 2021

Abstract

Motivation
Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.

Results
To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.

Availability and implementation
PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).

Supplementary information
Supplementary data are available at Bioinformatics online.
Single well, single-common primer pair, dual probe, duplex qPCR assay for the quantification of mRNA splicing variants
Authors: Wang Janice , Wong Winifred P , Link Emma O , Olivares Shantel , Adelman Cade T , Henkel Anne S , El Muayed Malek 
Published: February 2021

Abstract
Quantifying the ratio of alternatively spliced mRNA variants of genes with known alternative splicing variants is highly relevant for many applications. Herein, we describe the validation of a quantitative PCR design for the simplified quantification of known mRNA splice variants. The assay uses a single-common primer pair, dual probe design for the determination of splicing variants in a single well configuration. We used murine XBP-1 splicing variants, XBP-1S and XBP-1U, to validate and demonstrate the performance characteristics of this approach. Using synthetic XBP-1S and XBP-1U cDNA as well as cDNA synthesized from mouse beta-cell line MIN6, we established the performance parameters and dynamic range of the assay. Reliable quantification of both variants at varying concentration gradients was shown. No cross detection of XBP-1U by the XBP-1S probe was detected and only marginal XBP-1S cross detection by the XBP-1U probe was detected at high concentration gradients that are unlikely to be relevant. We demonstrated that the assay accurately detected changes of XBP-1 splice variants in mouse liver subjected to pharmacologically induced ER stress without the need for normalization to a reference gene.