bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and electronic properties of realistic two-dimensional amorphous topological insulators
Authors: Focassio Bruno , Schleder Gabriel R , Costa Marcio , Fazzio Adalberto , Lewenkopf Caio
Published: January 2021

We investigate the structure and electronic spectra properties of two-dimensional amorphous bismuthene structures and show that these systems are topological insulators. We employ a realistic modeling of amorphous geometries together with density functional theory for electronic structure calculations. We investigate the system topological properties throughout the amorphization process and find that the robustness of the topological phase is associated with the spin–orbit coupling strength and size of the pristine topological gap. Using recursive non-equilibrium Green’s function, we study the electronic transport properties of nanoribbons devices with lengths comparable to experimentally synthesized materials. We find a 2e
2/h conductance plateau within the topological gap and an onset of Anderson localization at the trivial insulator phase.
Concentration quenching of photoluminescence in optically transparent Lu2O3:Eu thin films deposited to be used as scintillators
Authors: Ezirmik Kadri Vefa
Published: January 2021

Photoluminescent thin films of europium doped lutetium oxide (Lu2O3:Eu) -an established material for x-ray scintillators- have been grown on glass substrates employing radio-frequency magnetron sputtering deposition technique. Optically transparent, crystalline films were obtained by only controlling the deposition process parameters. Neither any pre-treatment on glass substrate nor any post-deposition treatment on the films was applied. To our knowledge, depositing transparent but crystalline films of Lu2O3:Eu on glass substrates in such a direct way is an achievement that is reported for the first time in the literature. Using separate sputtering targets for the matrix constituent (Lu2O3) and the dopant enabled us to control the doping level of europium atoms in the films. By varying the magnetron power applied to the Eu2O3 target, we produced a series of Lu2O3:Eu thin films with different Eu concentrations. Significant quenching of luminescence by concentration was observed in the films. Detailed chemical and microstructural analyses revealed that europium atoms segregated from the matrix at high concentrations, an important contributor to concentration quenching. Some remarks have been given on finding the europium concentration that will give best scintillator performance.
CVN impact energy and fracture characteristics correlations with different oxide nanoparticles improving submerged arc welds
Authors: Jiménez-Jiménez A , Paniagua-Mercado A M , García-Bórquez A , De Ita-De la Torre A S , Mejía-García C , López-Hirata V M , Saucedo-Muñoz M L , Miguel-Díaz E
Published: January 2021

The main aim of this research is to correlate the toughness improvement with fracture features of tested Charpy V-Notch impact specimens obtained from submerged arc welds enriched by different oxide nanoparticles (TiO2, SiO2, Al2O3 and Mn2O3). Through Scanning Electron Microscopy (SEM) fractography, fracture features were determined, which are the shear fracture percent, the loading angle, as well as the diameter of dimples and the width of cleavage sheets at ductile and brittle fracture regions, respectively. It was observed an increase of the Charpy V-Notch impact energy with the decrease of loading angle and the average diameter of dimples, as well as with the increase of its shear fractures percents. Moreover, it was correlated the increase of Acicular Ferrite surface density with the decrease of width of cleavage sheets. Thus, the toughness of the submerged arc welds can be improved by adding TiO2, SiO2, Al2O3 or Mn2O3 nanoparticles.
NO gas adsorption properties of MoS2 from monolayer to trilayer: a first-principles study
Authors: Wang Zhaohua , Zhang Yanni , Ren Yanbing , Wang Miaomiao , Zhang Zhiyong , Zhao Wu , Yan Junfeng , Zhai Chunxue , Yun Jiangni
Published: January 2021

The NO gas adsorption properties of the monolayer, bilayer and trilayer MoS2 has been studied based on the first-principles calculation. The interaction between NO and MoS2 layers is weak physical adsorption, which is evidenced by the large distance (>3 Å), small adsorption energies (<0.9 eV) and deformation electron density. Moreover, the effect of the NO adsorption on the charge transfer and the electronic properties are also discussed. For all the NO adsorption cases, 0.04 e charge transfer exists by Mulliken/Hirshfeld analysis and and the charge density difference between NO molecular and MoS2 layers. The NO adsorption can obviously induces new impurity states at about 0.5 eV in the band gap that can lead to the change of the transport properties of the MoS2 layers and then it could detect the NO gas. We also performed semi-quantitatively theoretical analysis from the carrier concentration n and carrier mobility μ to obtain the effect of the NO adsorption on electrical conductivity. Our results provide a theoretical basis for the application of MoS2 layers as gas sensors for important NO polluting gases in air.
Large-scale fabrication of all-inkjet-printed resistors and WORM memories on flexible polymer films with high yield and stability
Authors: Ramon Eloi , Sowade Enrico , Martínez-Domingo Carme , Mitra Kalyan Yoti , Alcalde Ana , Baumann Reinhard R , Carrabina Jordi
Published: January 2021

We report on the development of inkjet-printed thin-film resistors using both organic and inorganic ink formulations. The passive devices were manufactured on flexible polymer substrates in ambient condition without the need for a cleanroom environment or inert atmosphere and at a maximum temperature of 150 °C. By using the same manufacturing process, the rapid electrical sintering (RES) method is demonstrated as effective for the fabrication of inkjet-printed, programmable Write-Once-Read-Many (WORM) memories. Several hundred fully inkjet-printed resistors with different parameters were fabricated and subsequently morphologically and electrically characterized with the aim of obtaining statistically significant data. From a manufacturing process viewpoint, the procedures based on inkjet printing herein described are highly attractive: they do not require high temperatures, low pressures, special atmospheric conditions, and any masks, therefore providing a versatile low-cost approach to fabricate passive electrical components and simple circuits useful for the electronic industry. Printing can be carried out at a sufficiently low temperature to avoid damage to the fabric substrate and these devices can be used in a range of applications requiring flexible and conformal devices from embedded passive filters in PCBs to wearable electronics.
A posteriori corrections to the iterative qubit coupled cluster method to minimize the use of quantum resources in large-scale calculations
Authors: Ryabinkin Ilya G , Izmaylov Artur F , Genin Scott N
Published: January 2021

The iterative qubit coupled cluster (iQCC) method is a systematic variational approach to solve the electronic structure problem on universal quantum computers. It is able to use arbitrarily shallow quantum circuits at expense of iterative canonical transformation of the Hamiltonian and rebuilding a circuit. Here we present a variety of a posteriori corrections to the iQCC energies to reduce the number of iterations to achieve the desired accuracy. Our energy corrections are based on a low-order perturbation theory series that can be efficiently evaluated on a classical computer. Moreover, capturing a part of the total energy perturbatively, allows us to formulate the qubit active-space concept, in which only a subset of all qubits is treated variationally. As a result, further reduction of quantum resource requirements is achieved. We demonstrate the utility and efficiency of our approach numerically on the examples of 10-qubit N2 molecule dissociation, the 24-qubit H2O symmetric stretch, and 56-qubit singlet-triplet gap calculations for the technologically important complex, tris-(2-phenylpyridine)iridium(III) Ir(ppy)3.
First principles calculations of magneto-crystalline anisotropy of rare-earth magnets
Authors: Hamada Tomoyuki , Okamoto Masakuni
Published: January 2021

Magneto-crystalline anisotropies, K

u
, and anisotropic magnetic fields, H

a
, of two rare-earth (RE) magnets, i.e. CeFe12, and PrFe12, are theoretically calculated by using the crystal field (CF) method based on the first principles density functional theory (DFT) and the non-collinear DFT + U (NCDFT + U) method. The CF method reproduces an experimental H

a
of PrFe12 but it failed to reproduce the H

a
of CeFe12, providing H

a
with a wrong sign. The NCDFT + U method correctly reproduces experimental H

a
of CeFe12 and PrFe12, however the optimization of effective Hubbard on-site interaction parameters, U

eff
, of the 4f electrons of the magnets is indispensable for the accurate calculation of H

a
. We have found that the CF method is valid in so far as it is used for the study of K

u
of RE magnets, which have RE atoms heavier than Pr atom. We expect that the NCDFT + U method would become a quantitative K

u
calculation method of any RE magnets if the U

eff
calculation method of 4f electrons of RE magnets is established.
Determination of the scaling characteristics of time-dependent optical properties of microalgae using electromagnetic scattering
Authors: Ma C Y
Published: January 2021

The time-dependent optical properties of microalgae are crucial for light transfer in photobioreactor (PBR) designs. In this study, the time-dependent optical properties were derived using electromagnetic scattering theory informed by the experimentally measured optical properties of Chlorella protothecoides. The temporal scaling functions (TSFs) of nearly wavelength-independent absorption and scattering cross-sections were demonstrated using electromagnetic scattering theory, leading to the first concrete expression of the TSF. The TSF establishes the relationship between the time-dependent absorption/scattering cross-sections in the stationary and growth phases of microalgal development. The concrete expression of the TSF provides a new means of calculating the time-dependent optical properties of microalgae using electromagnetic scattering theory. The TSF of microalgae has great potential in remote sensing and PBR applications.
Modulation of vegetation restoration on outdoor thermal comfort over the Loess Plateau, China from 1982 to 2015
Authors: Zhang Xuezhen , Zhang Zefan , Song Shuaifeng
Published: January 2021

This study depicts changes in the warm season (May to September) Universal Thermal Climate Index (UTCI) quantifying outdoor thermal comfort over the Loess Plateau from 1982 to 2015 and examines its relationship with large-scale climate changes and local vegetation restoration under the Grain for Green Program (GGP) after 1999. The results show that the UTCI experienced an increasing trend of 0.074/a from 1982 to 1999 and subsequently experienced a weakly decreasing trend of −0.002/a from 1999 to 2015. This trend shift in the UTCI was predominantly determined by surface air temperature changes with slopes of 0.077 °C a−1 from 1982 to 1999 and −0.005 °C a−1 from 1999 to 2015. The hiatus in the regional temperature rise after 1999 was closely related to the large-scale climate warming hiatus. Meanwhile, both measurement data analysis and climate modeling with the Weather Research and Forecasting (WRF) model suggest that the trend shift was also accelerated by vegetation restoration after 1999 through the intensification of transpiration, which increased the latent heat flux and reduced sensible heat flux. In particular, at the stations with the greatest degree of vegetation restoration, the local forcing from vegetation restoration was likely greater than that from the large-scale climate warming hiatus. This study highlights the importance of substantial vegetation restoration on local and regional thermal comfort.
Recent advances in structured illumination microscopy
Authors: Ma Ying , Wen Kai , Liu Min , Zheng Juanjuan , Chu Kaiqin , Smith Zachary J , Liu Lixin , Gao Peng
Published: January 2021

Structured illumination microscopy (SIM), is a wide-field, minimally-invasive super-resolution optical imaging approach with optical sectioning capability, and it has been extensively applied to many different fields. During the past decades, SIM has been drawing great attention for both the technique development and applications. In this review, firstly, the basic conception, instrumentation, and functionalities of SIM are introduced concisely. Secondly, recent advances in SIM which enhance SIM in different aspects are reviewed. Finally, the variants of SIM are summarized and the outlooks and perspectives of SIM are presented.
Alkali/alkaline-earth metal intercalated g-C3N4 induced charge redistribution and optimized photocatalysis: status and challenges
Authors: Cui Wen , Chen Peng , Chen Lvcun , Li Jieyuan , Zhou Ying , Dong Fan
Published: January 2021

Limited by the intrinsic graphitic sp2-hybridized array of tri-s-triazine repeating units and inert stack of layers, the insertion of intercalant between layers of graphitic carbon nitride (CN) could be an effective way to strengthen the van der Waals force between adjoining layers and induce the charge redistribution in CN for the improvement of photocatalysis. This review summarizes the latest progress related to the design and construction of alkali/alkaline-earth metal intercalated CN, including (a) single alkali/alkaline-earth metal intercalated CN, (b) alkali/alkaline-earth metal and non-metallic species co-intercalated CN, (c) alkali/alkaline-earth metal intercalated and surface modification co-functionalized CN. The promotion mechanism of each classification will be critically discussed, namely alkali/alkaline-earth metal intercalated CN-induced charge redistribution facilitates the adsorption and activation of reactants, accelerates the separation efficiency of photogenerated carriers, and optimizes the reaction pathway. Also, the influence on band structure and optical property has been discussed with the intercalation of alkali/alkaline-earth metal. Finally, this mini-review highlights crucial issues that should be addressed in future research.
Inception neural network for complete intersection Calabi–Yau 3-folds
Authors: Erbin H , Finotello R
Published: January 2021

We introduce a neural network inspired by Google’s Inception model to compute the Hodge numberh1,1of complete intersection Calabi–Yau (CICY) 3-folds. This architecture improves largely the accuracy of the predictions over existing results, giving already 97% of accuracy with just 30% of the data for training. Accuracy climbs to 99% when using 80% of the data for training. This proves that neural networks are a valuable resource to study geometric aspects in both pure mathematics and string theory.
Algebraic hyperbolicity for surfaces in toric threefolds
Authors: Haase Christian , Ilten Nathan
Published: January 2021

Adapting focal loci techniques used by Chiantini and Lopez, we provide lower bounds on the genera of curves contained in very general surfaces in Gorenstein toric threefolds. We illustrate the utility of these bounds by obtaining results on algebraic hyperbolicity of very general surfaces in toric threefolds.
Mandatory Corporate Social Responsibility? Legislative Innovation and Judicial Application in China
Authors: Lin Li-Wen
Published: January 2021

Corporate social responsibility (CSR) is often understood as voluntary corporate behavior beyond legal compliance. The recent emergence of CSR legislation is challenging this typical understanding. A number of countries including China, Indonesia, and India have expressly stated in legislation that companies shall undertake CSR. However, the CSR law is controversial. Critics of CSR see the law as an unwise effort to challenge profit maximization as the only social responsibility of the corporation. Even CSR advocates welcome the CSR law with great caution. Given the vague statutory language of CSR, the practical application of the law places high demands on the judiciary. However, as the countries that have adopted the CSR law are mainly developing countries with rather weak legal institutions, it raises a common concern that the law is simply an innovation without implementation. This Article conducts an empirical study of China, an early adopter of CSR legislation. The empirical analysis of Chinese court cases reveals what the CSR law means in judicial practice, whether CSR is in fact mandatory, and in what types of disputes CSR is relevant or outcome determinative. Among various findings, this Article shows that the CSR law is by no means as useless as commonly expected. The meaningful application of the law is attributable to the law’s compatibility with China’s legal infrastructure and sociopolitical institutions. Chinese courts have innovatively applied CSR in various contexts far beyond the traditionally Western-led focus on directors’ fiduciary duties. The Chinese experience suggests that the CSR law is more of a judicial review standard than a corporate behavior standard, which further confirms the importance of judicial capacity in implementing the vague law. This Article concludes with insights for the corporate purpose debate from a comparative perspective and with policy suggestions for adopting CSR legislation.
Addressing Measurement Error in Random Forests Using Quantitative Bias Analysis
Authors: Jiang Tammy , Gradus Jaimie L , Lash Timothy L , Fox Matthew P
Published: January 2021

Although variables are often measured with error, the impact of measurement error on machine-learning predictions is seldom quantified. The purpose of this study was to assess the impact of measurement error on the performance of random-forest models and variable importance. First, we assessed the impact of misclassification (i.e., measurement error of categorical variables) of predictors on random-forest model performance (e.g., accuracy, sensitivity) and variable importance (mean decrease in accuracy) using data from the National Comorbidity Survey Replication (2001–2003). Second, we created simulated data sets in which we knew the true model performance and variable importance measures and could verify that quantitative bias analysis was recovering the truth in misclassified versions of the data sets. Our findings showed that measurement error in the data used to construct random forests can distort model performance and variable importance measures and that bias analysis can recover the correct results. This study highlights the utility of applying quantitative bias analysis in machine learning to quantify the impact of measurement error on study results.
A natural product phillygenin suppresses osteosarcoma growth and metastasis by regulating the SHP-1/JAK2/STAT3 signaling
Authors: Ding Xiaomin , Lu Danqing , Fan Jianbo
Published: January 2021

Osteosarcoma represents one of the most devastating cancers due to its high metastatic potency and fatality. Osteosarcoma is insensitive to traditional chemotherapy. Identification of a small molecule that blocks osteosarcoma progression has been a challenge in drug development. Phillygenin, a plant-derived tetrahydrofurofuran lignin, has shown to suppress cancer cell growth and inflammatory response. However, how phillygenin plays functional roles in osteosarcoma has remained unveiled. In this study, we showed that phillygenin inhibited osteosarcoma cell growth and motility in vitro. Further mechanistic studies indicated that phillygenin blocked STAT3 signaling pathway. Phillygenin led to significant downregulation of Janus kinase 2 and upregulation of Src homology region 2 domain-containing phosphatase 1. Gene products of STAT3 regulating cell survival and invasion were also inhibited by phillygenin. Therefore, our studies provided the first evidence that phillygenin repressed osteosarcoma progression by interfering STAT3 signaling pathway. Phillygenin is a potential candidate in osteosarcoma therapy.
Application of heavy-ion-beam irradiation to breeding large rotifer
Authors: Tsuneizumi Kazuhide , Yamada Mieko , Kim Hee-Jin , Ichida Hiroyuki , Ichinose Katsunori , Sakakura Yoshitaka , Suga Koushirou , Hagiwara Atsushi , Kawata Miki , Katayama Takashi , Tezuka Nobuhiro , Kobayashi Takanori , Koiso Masahiko , Abe Tomoko
Published: January 2021

In larviculture facilities, rotifers are generally used as an initial food source, while a proper size of live feeds to connect rotifer and Artemia associated with fish larval growth is needed. The improper management of feed size and density induces mass mortality and abnormal development of fish larvae. To improve the survival and growth of target larvae, this study applied carbon and argon heavy-ion-beam irradiation in mutation breeding to select rotifer mutants with larger lorica sizes. The optimal irradiation conditions of heavy-ion beam were determined with lethality, reproductivity, mutant frequency, and morphometric characteristics. Among 56 large mutants, TYC78, TYC176, and TYA41 also showed active population growth. In conclusion, (1) heavy-ion-beam irradiation was defined as an efficient tool for mutagenesis of rotifers and (2) the aforementioned 3 lines that have larger lorica length and active population growth may be used as a countermeasure of live feed size gap during fish larviculcure.
SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments
Authors: Chen Zhanlin , Zhang Jing , Liu Jason , Zhang Zixuan , Zhu Jiangqi , Lee Donghoon , Xu Min , Gerstein Mark
Published: January 2021

scATAC-seq is a powerful approach for characterizing cell-type-specific regulatory landscapes. However, it is difficult to benchmark the performance of various scATAC-seq analysis techniques (such as clustering and deconvolution) without having a priori a known set of gold-standard cell types. To simulate scATAC-seq experiments with known cell-type labels, we introduce an efficient and scalable scATAC-seq simulation method (SCAN-ATAC-Sim) that down-samples bulk ATAC-seq data (e.g. from representative cell lines or tissues). Our protocol uses a consistent but tunable signal-to-noise ratio across cell types in a scATAC-seq simulation for integrating bulk experiments with different levels of background noise, and it independently samples twice without replacement to account for the diploid genome. Because it uses an efficient weighted reservoir sampling algorithm and is highly parallelizable with OpenMP, our implementation in C++ allows millions of cells to be simulated in less than an hour on a laptop computer.

Availability and implementation

SCAN-ATAC-Sim is available at scan-atac-sim.gersteinlab.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Divergence in life history and behaviour between hybridizing Phymata ambush bugs (Heteroptera: Reduviidae)
Authors: Punzalan David , Fang Julia T , Chen William , Rowe Locke
Published: January 2021

Life-history variation plays a central role in evolutionary and ecological processes and might be especially pertinent to divergence in closely related species. We investigated differences in life history in a pair of parapatric species of ambush bugs (Phymata) and a putative hybrid population. Despite the evidence of gene flow among these species, we found clear divergence between these parapatric populations for a suite of juvenile and adult life-history traits, including components of fitness. The higher latitude species was also less active, suggestive of potential divergence in dispersal. Increased melanism was correlated with longevity in one species, although it was unclear whether this relationship was causal. Observed differences in the life history between species were consistent with expectations of high-latitude species putting a premium on early or rapid development and increased reproductive rates. However, these results were not consistent with ‘pace-of-life syndromes’ at the species level. Individuals from the putative hybrid zone exhibited intermediate values for most traits, although they had slower development and reduced mobility, consistent with some previous work suggesting natural selection via hybrid breakdown.
Nestling, but not adult male, barn swallows emit short calls in noisy environments
Authors: Hasegawa Masaru , Arai Emi , Nakamura Masahiko
Published: January 2021

Some, but not all, animals cope with anthropogenic noise by changing the structure of their acoustic signals, possibly due to two interrelated factors: the design of the acoustic signals and the intrinsic biological state. Here, using the barn swallow (Hirundo rustica) that breed solitarily along streets, we studied male enticement calls and nestling food-begging calls in relation to ambient noise. The former calls are structurally quite similar to the latter, perhaps functioning as a sensory trap to exploit female parental care for nestlings. This provides a unique opportunity to study whether intrinsic biological state (i.e. developmental stage, here), virtually independent of acoustic design, matters in acoustic adaptation to anthropogenic noise. We found that the syllable length of nestling food-begging calls, but not of male enticement calls, decreased with increasing local noise levels within populations. The syllable lengths of the father’s enticement calls and those of the nestling’s food-begging calls were positively related, which explains why male enticement calls as well as nestling food-begging calls had shorter syllables in a noisy urban population compared to those in a quiet rural population. The current findings indicate that the intrinsic biological state of two acoustically similar sounds explains their differential relationships with ambient noise.
Left ventricular tamponade- pathophysiology determines the therapeutic approach: a case series
Authors: Kumar Barun , Kodliwadmath Ashwin , Singh Anupam , Upadhyay Amar , Darbari Anshuman , Duggal Bhanu
Published: January 2021

Background

Left ventricular (LV) tamponade is rare. LV tamponade can occur in cases of a loculated pericardial effusion overlying the LV and in cases of circumferential pericardial effusions in patients with severe pulmonary arterial hypertension (PAH). Both causes of LV tamponade share the common feature of not presenting with the classical features of cardiac tamponade. However, the therapeutic approach of the two is different.

Case summary

Here, we report two cases of LV tamponade. The first patient was a case of post-mitral valve replacement who presented with loculated posterior pericardial effusion with LV tamponade. Due to the loculated and posterior nature of the effusion, his pericardial fluid was drained from the axilla by echocardiographic and fluoroscopic guidance. The second patient presented with features of severe PAH with a circumferential pericardial effusion and LV tamponade. Due to the circumferential nature of the effusion, the pericardiocentesis was performed from the subxiphoid route.

Discussion

The pathophysiology of LV tamponade must be determined accurately before performing pericardiocentesis. Left ventricular tamponade in patients with severe PAH and non-loculated circumferential effusion can be drained from the subxiphoid route, while LV tamponade due to loculated effusion overlying LV must be drained by echocardiographic and fluoroscopic guidance from the axilla.
Functional brain isolation technique for stroke prevention in thoracic endovascular aortic repair
Authors: Tsuda Kazumasa , Washiyama Naoki , Takahashi Daisuke , Shiiya Norihiko
Published: January 2021

To prevent embolic stroke during thoracic endovascular aortic repair, we have adopted the brain isolation technique since June 2014 in 9 selected high-risk patients (9/134: 6.7%) having ulcerated or protruding atheromas within the proximal aorta. Cardiopulmonary bypass was used to prevent aortic atheromas from entering the brain. We used a heparin-coated closed-loop cardiopulmonary bypass system incorporating a soft reservoir bag with 1 mg/kg heparin to minimize the disadvantages of extracorporeal circulation. The bypass graft (right axillary-left carotid-left axillary) was used as an arterial inflow in patients undergoing zone-1 landing (n = 8), while peripheral cannulation into 3 brachiocephalic arteries was employed in the remaining patient. Initial pump flow was set at 1.3 l/min/m2, and native cardiac output was reduced by adjusting the reservoir bag volume. Aortography was performed to confirm non-visualization of the arch vessels before catheter manipulation. There was no mortality and 1 solitary left cerebellar infarction.
The association of migration with multiple tobacco product use among male adults in 15 low- and middle-income countries
Authors: Chen Daniel Tzu-Hsuan , Millett Christopher , Filippidis Filippos T
Published: January 2021

Little is known about the impact of migration on tobacco use patterns among men in low- and middle-income countries (LMICs). This study aims to explore the association between migration and tobacco use among men in LMICs. We used multilevel regression models to analyze data of 154 425 men from 15 countries from the latest wave of the Demographic and Health Survey. Results showed higher risk of single tobacco product use [relative risk ratio (RRR) = 1.22; 95% confidence interval (CI): 1.19–1.26], but importantly of dual (RR = 1.41, 95% CI: 1.36–1.49) and poly-tobacco use (RR = 1.71, 95% CI: 1.57–1.86) among migrant men compared with non-migrants.
Is COVID-19 lockdown associated with vitamin D deficiency?
Authors: Lippi Giuseppe , Ferrari Anna , Targher Giovanni
Published: January 2021

All vitamin D tests carried out for outpatients aged 18 years or older during the last 3 years at an Italian University Hospital was reviewed. The serum vitamin D concentrations measured since the Italian coronavirus diseases 2019 (COVID-19) lockdown to present did not significantly differ from the previous 2 years (78 vs. 77 nmol/l; P = 0.277), whilst the prevalence of vitamin D deficiency was found to be even marginally lower in 2020 (16.0% vs. 17.9%; P = 0.003). These results suggest that vitamin D deficiency in our province has not increased during the Italian COVID-19 outbreak or in correspondence with the nationwide lockdown.
TheTreponema denticolaDgcA protein (TDE0125) is a functional diguanylate cyclase
Authors: Patel Dhara T , O'Bier Nathaniel S , Schuler Edward J A , Marconi Richard T
Published: January 2021

Periodontal disease (PD) is a progressive inflammatory condition characterized by degradation of the gingival epithelium, periodontal ligament, and alveolar bone ultimately resulting in tooth loss. Treponema denticola is a keystone periopathogen that contributes to immune dysregulation and direct tissue destruction. As periodontal disease develops, T. denticola must adapt to environmental, immunological and physiochemical changes in the subgingival crevice. Treponema denticola produces bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP), an important regulatory nucleotide. While T. denticola encodes several putative diguanylate cyclases (DGCs), none have been studied and hence the biological role of c-di-GMP in oral treponemes remains largely unexplored. Here, we demonstrate that the T. denticola open reading frame, TDE0125, encodes a functional DGC designated as DgcA (Diguanylate cyclase A). The dgcA gene is universal among T. denticola isolates, highly conserved and is a stand-alone GGEEF protein with a GAF domain. Recombinant DgcA converts GTP to c-di-GMP using either manganese or magnesium under aerobic and anaerobic reaction conditions. Size exclusion chromatography revealed that DgcA exists as a homodimer and in larger oligomers. Site-directed mutagenesis of residues that define the putative inhibitory site of DgcA suggest that c-di-GMP production is allosterically regulated. This report is the first to characterize a DGC of an oral treponeme.
Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types
Authors: Sivakumar Smruthy , San Lucas F Anthony , Jakubek Yasminka A , Ozcan Zuhal , Fowler Jerry , Scheet Paul
Published: January 2021

Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities (“B allele” frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the “B allele” frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.
Modulation of the complex regulatory network for methionine biosynthesis in fungi
Authors: Shrivastava Manjari , Feng Jinrong , Coles Mark , Clark Benjamin , Islam Amjad , Dumeaux Vanessa , Whiteway Malcolm
Published: January 2021

The assimilation of inorganic sulfate and the synthesis of the sulfur-containing amino acids methionine and cysteine is mediated by a multibranched biosynthetic pathway. We have investigated this circuitry in the fungal pathogen Candida albicans, which is phylogenetically intermediate between the filamentous fungi and Saccharomyces cerevisiae. In S. cerevisiae, this pathway is regulated by a collection of five transcription factors (Met4, Cbf1, Met28, and Met31/Met32), while in the filamentous fungi the pathway is controlled by a single Met4-like factor. We found that in C. albicans, the Met4 ortholog is also a core regulator of methionine biosynthesis, where it functions together with Cbf1. While C. albicans encodes this Met4 protein, a Met4 paralog designated Met28 (Orf19.7046), and a Met31 protein, deletion, and activation constructs suggest that of these proteins only Met4 is actually involved in the regulation of methionine biosynthesis. Both Met28 and Met31 are linked to other functions; Met28 appears essential, and Met32 appears implicated in the regulation of genes of central metabolism. Therefore, while S. cerevisiae and C. albicans share Cbf1 and Met4 as central elements of the methionine biosynthesis control, the other proteins that make up the circuit in S. cerevisiae are not members of the C. albicans control network, and so the S. cerevisiae circuit likely represents a recently evolved arrangement.
Effects of the domestic thyroid stimulating hormone receptor (TSHR) variant on the hypothalamic-pituitary-thyroid axis and behavior in chicken
Authors: Fallahshahroudi Amir , Johnsson Martin , Sorato Enrico , Ubhayasekera S J Kumari A , Bergquist Jonas , Altimiras Jordi , Jensen Per
Published: January 2021

Domestic chickens are less fearful, have a faster sexual development, grow bigger, and lay more eggs than their primary ancestor, the red junglefowl. Several candidate genetic variants selected during domestication have been identified, but only a few studies have directly linked them with distinct phenotypic traits. Notably, a variant of the thyroid stimulating hormone receptor (TSHR) gene has been under strong positive selection over the past millennium, but it’s function and mechanisms of action are still largely unresolved. We therefore assessed the abundance of the domestic TSHR variant and possible genomic selection signatures in an extensive data set comprising multiple commercial and village chicken populations as well as wild-living extant members of the genus Gallus. Furthermore, by mean of extensive backcrossing we introgressed the wild-type TSHR variant from red junglefowl into domestic White Leghorn chickens and investigated gene expression, hormone levels, cold adaptation, and behavior in chickens possessing either the wild-type or domestic TSHR variant. While the domestic TSHR was the most common variant in all studied domestic populations and in one of two red junglefowl population, it was not detected in the other Gallus species. Functionally, the individuals with the domestic TSHR variant had a lower expression of the TSHR in the hypothalamus and marginally higher in the thyroid gland than wild-type TSHR individuals. Expression of TSHB and DIO2, two regulators of sexual maturity and reproduction in birds, was higher in the pituitary gland of the domestic-variant chickens. Furthermore, the domestic variant was associated with higher activity in the open field test. Our findings confirm that the spread of the domestic TSHR variant is limited to domesticated chickens, and to a lesser extent, their wild counterpart, the red junglefowl. Furthermore, we showed that effects of genetic variability in TSHR mirror key differences in gene expression and behavior previously described between the red junglefowl and domestic chicken.
Fall Risk-Increasing Drugs, Polypharmacy, and Falls Among Low-Income Community-Dwelling Older Adults
Authors: Ie Kenya , Chou Eric , Boyce Richard D , Albert Steven M
Published: January 2021

Background and Objectives

Medication exposure is a potential risk factor for falls and subsequent death and functional decline among older adults. However, controversy remains on the best way to assess medication exposure and which approach best predicts falls. The objective of the current study was to examine the association between different measures of medication exposure and falls risk among community-dwelling older adults.

Research Design and Methods

This retrospective cohort study was conducted using Falls Free PA program data and a linked prescription claims data from Pennsylvania’s Pharmaceutical Assistance Contract for the Elderly program. Participants were community-dwelling older adults living in Pennsylvania, United States. Three measures of medication exposure were assessed: (a) total number of regular medications (polypharmacy); (b) counts of potentially inappropriate medications derived from current prescription guidance tools (Fall Risk-Increasing Drugs [FRIDs], Beers Criteria); and (c) medication burden indices based on pharmacologic mechanisms (Anticholinergic Cognitive Burden, Drug Burden Index) all derived from claims data. The associations between the different medication risk measures and self-reported falls incidence were examined with univariate and multivariable negative binomial regression models to estimate incidence rate ratios (IRRs).

Results

Overall 343 older adults were included and there were 236 months with falls during 2,316 activity-adjusted person-months (10.2 falls per 100 activity-adjusted person-months). Of the 6 measures of medication risk assessed in multivariate models, only the use of 2 or more FRIDs (adjusted IRR 1.67 [95% CI: 1.04–2.68]) independently predicted falls risk. Among the 13 FRID drug classes, the only FRID class associated with an increased fall risk was antidepressants.

Discussion and Implications

The presence of multiple FRIDs in a prescription is an independent risk factor for falls, even in older adults with few medications. Further investigation is required to examine whether deprescribing focused on FRIDs effectively prevents falls among this population.
Heterogeneity in Husbands’ and Wives’ Physical Pain Trajectories Over Mid-Later Years: Biopsychosocial Stratification and Implications for Later-Life Well-Being
Authors: Wickrama Kandauda A S , Lee Tae Kyoung , O’Neal Catherine Walker
Published: January 2021

Background and Objectives

The present study investigated pain trajectories of husbands and wives over their mid-later years, the grouping of these trajectories, and differences in baseline biopsychosocial profiles and health and well-being outcomes in later years across the pain trajectory groups.

Research Design and Methods

Growth mixture modeling was used to identify latent classes of 244 husbands’ and wives’ physical pain trajectories over their mid-later years (1994–2015, average ages of 44–65 years). Analyses were conducted to identify how these pain trajectory classes were associated with respondents’ biopsychosocial profiles in 1994 and health and well-being in later years (2017 [>67 years]).

Results

The individual pain trajectories of husbands and wives were clustered into 3 heterogeneous groups with differing trajectory patterns. Nonnormative pain trajectory groups (with either a high pain level and/or persistent pain) were associated with adverse baseline biopsychosocial characteristics. These groups also experienced poorer health and well-being outcomes in later years (2017) compared to those with consistently low pain after controlling for lagged measures in 2015.

Discussion and Implications

The identification of pain trajectory groups and characteristics of group members provides a potentially useful prognostic tool for early preventive intervention efforts, treatment, and policy formation. Such interventions can promote and develop resiliency factors, thereby aiding in the redirection of middle-aged husbands’ and wives’ adverse pain trajectories.
Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media
Authors: Rajput Akanksha , Poudel Saugat , Tsunemoto Hannah , Meehan Michael , Szubin Richard , Olson Connor A , Seif Yara , Lamsa Anne , Dillon Nicholas , Vrbanac Alison , Sugie Joseph , Dahesh Samira , Monk Jonathan M , Dorrestein Pieter C , Knight Rob , Pogliano Joe , Nizet Victor , Feist Adam M , Palsson Bernhard O
Published: January 2021

Background

The evolving antibiotic-resistant behavior of health care–associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern. They are resistant to a broad class of antibiotics such as macrolides, aminoglycosides, fluoroquinolones, and many more.

Findings

The selection of appropriate antibiotic susceptibility examination media is very important. Thus, we use bacteriological (cation-adjusted Mueller-Hinton broth) as well as physiological (R10LB) media to determine the effect of vancomycin on USA100 strains. The study includes the profiling behavior of HA-MRSA USA100 D592 and D712 strains in the presence of vancomycin through various high-throughput assays. The US100 D592 and D712 strains were characterized at sub-inhibitory concentrations through growth curves, RNA sequencing, bacterial cytological profiling, and exo-metabolomics high throughput experiments.

Conclusions

The study reveals the vancomycin resistance behavior of HA-MRSA USA100 strains in dual media conditions using wide-ranging experiments.
Genome diversity in Ukraine
Authors: Oleksyk Taras K , Wolfsberger Walter W , Weber Alexandra M , Shchubelka Khrystyna , Oleksyk Olga T , Levchuk Olga , Patrus Alla , Lazar Nelya , Castro-Marquez Stephanie O , Hasynets Yaroslava , Boldyzhar Patricia , Neymet Mikhailo , Urbanovych Alina , Stakhovska Viktoriya , Malyar Kateryna , Chervyakova Svitlana , Podoroha Olena , Kovalchuk Natalia , Rodriguez-Flores Juan L , Zhou Weichen , Medley Sarah , Battistuzzi Fabia , Liu Ryan , Hou Yong , Chen Siru , Yang Huanming , Yeager Meredith , Dean Michael , Mills Ryan E , Smolanka Volodymyr
Published: January 2021

Background

The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage.

Results

The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population.

Conclusions

Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.
Healthy settings: supported housing for people with mental and intellectual disabilities in Denmark
Authors: Nielsen Maj Britt Dahl , Mølbak Marie-Louise , Hvass Line Raahauge , Folker Anna Paldam
Published: January 2021

Supported housing for people with mental and intellectual disabilities (IDs) is an important setting for health and may contribute positively and negatively to residents’ health. The aim of this study was to explore health promotion practices and services in supported housing in Denmark using a mixed-methods design comprising qualitative group interviews with managers and employees (n = 12) and a nationwide survey among managers (n = 276) and employees from supported housing facilities (n = 315). This study showed that employees tried to integrate health promotion in the daily work with residents, but efforts primarily focused on individual behavior and motivation. Findings points to several challenges and barriers, including ambivalent attitudes towards smoking and beliefs that health promotion undermines self-determination and empowerment. To build supportive environments for people with mental and IDs, we need to focus on the attitudes, values and competences of managers and employees to tackle misconceptions about smoking, raise awareness about the wider determinants and promote structural changes.