bluuebunny/crossref_metadata_2025 huggingface dataset:
Distributional changes in synonym sets
Authors: Pettersson-Traba Daniela
Published: January 2022

This chapter analyzes the diachronic development in 19th-
and 20th-century American English of the synonyms fragrant,
perfumed, and scented, which denote the
concept sweet-smelling. Their distributional patterns are examined
by means of conditional inference trees and collocational networks in order
to (1) uncover distinctions in meaning between the synonyms and (2)
determine the changes that the concept sweet-smelling has
experienced and their effect on the relationship between the synonyms.
Results indicate a significant split between entities denoting natural and
artificial smells, associated with fragrant and
perfumed, respectively. In turn,
scented is common in both senses. Moreover, a
significant increase of scented at the expense of
fragrant and perfumed emerges over
time, a fact which can be accounted for in terms of processes of attraction,
differentiation, and ongoing replacement.
Pejorative Suffixes and Combining Forms in English
Authors: Sánchez Fajardo José A.
Published: January 2022

The book is a research monograph that reviews and revises the concept of linguistic pejoration, and explores the role of 15 suffixes and combining forms, such as -ie, -o, -ard, -holic, -rrhea, -itis, -porn, -ish, in the formation of English pejoratives. The examination of the inner structure of the resulting derivatives is based on an innovative methodology that encompasses the theories and approaches of Construction Morphology, Componential Analysis, and Morphopragmatics. Following the principles of this methodology, pejorative words collected from dictionaries and corpora (a total of approximately 950 words) are abstracted into generalizations (or constructional schemas) where structural and functional similarities are used to cognitively trace the ways in which negative (or derisive) meaning is connected with a specific form. Through this multifaceted methodology, my analysis showcases the fact that the universal properties of ‘diminution’, ‘excess’, ‘resemblance’, and ‘metonymization’ are what underlie the making of pejorative meaning. These generalizations, along with the schematic representations of formatives, can help linguists, or linguistics enthusiasts in general, to understand the conventions and intricacy of lexical pejoration.

This book has been awarded 'Best Book in English Language and Linguistics 2022' by AEDEAN!
Detection and quantification of the vacuolar H+ATPase using the Legionella effector protein SidK
Authors: Maxson Michelle E. , Abbas Yazan M. , Wu Jing Ze , Plumb Jonathan D. , Grinstein Sergio , Rubinstein John L.
Published: January 2022

Acidification of secretory and endocytic organelles is required for proper receptor recycling, membrane traffic, protein degradation, and solute transport. Proton-pumping vacuolar H+ ATPases (V-ATPases) are responsible for this luminal acidification, which increases progressively as secretory and endocytic vesicles mature. An increasing density of V-ATPase complexes is thought to account for the gradual decrease in pH, but available reagents have not been sufficiently sensitive or specific to test this hypothesis. We introduce a new probe to localize and quantify V-ATPases. The probe is derived from SidK, a Legionella pneumophila effector protein that binds to the V-ATPase A subunit. We generated plasmids encoding fluorescent chimeras of SidK1-278, and labeled recombinant SidK1-278 with Alexa Fluor 568 to visualize and quantify V-ATPases with high specificity in live and fixed cells, respectively. We show that V-ATPases are acquired progressively during phagosome maturation, that they distribute in discrete membrane subdomains, and that their density in lysosomes depends on their subcellular localization.
The transcription factor HIF-1α mediates plasticity of NKp46+ innate lymphoid cells in the gut
Authors: Krzywinska Ewelina , Sobecki Michal , Nagarajan Shunmugam , Zacharjasz Julian , Tambuwala Murtaza M. , Pelletier Abigaelle , Cummins Eoin , Gotthardt Dagmar , Fandrey Joachim , Kerdiles Yann M. , Peyssonnaux Carole , Taylor Cormac T. , Sexl Veronika , Stockmann Christian
Published: January 2022

Gut innate lymphoid cells (ILCs) show remarkable phenotypic diversity, yet microenvironmental factors that drive this plasticity are incompletely understood. The balance between NKp46+, IL-22–producing, group 3 ILCs (ILC3s) and interferon (IFN)-γ–producing group 1 ILCs (ILC1s) contributes to gut homeostasis. The gut mucosa is characterized by physiological hypoxia, and adaptation to low oxygen is mediated by hypoxia-inducible transcription factors (HIFs). However, the impact of HIFs on ILC phenotype and gut homeostasis is not well understood. Mice lacking the HIF-1α isoform in NKp46+ ILCs show a decrease in IFN-γ–expressing, T-bet+, NKp46+ ILC1s and a concomitant increase in IL-22–expressing, RORγt+, NKp46+ ILC3s in the gut mucosa. Single-cell RNA sequencing revealed HIF-1α as a driver of ILC phenotypes, where HIF-1α promotes the ILC1 phenotype by direct up-regulation of T-bet. Loss of HIF-1α in NKp46+ cells prevents ILC3-to-ILC1 conversion, increases the expression of IL-22–inducible genes, and confers protection against intestinal damage. Taken together, our results suggest that HIF-1α shapes the ILC phenotype in the gut.
On the duality of Schwarzschild–de Sitter spacetime and moving mirror
Authors: Fernández-Silvestre Diego , Foo Joshua , Good Michael R R
Published: January 2022

The Schwarzschild–de Sitter (SdS) metric is the simplest spacetime solution in general relativity with both a black hole event horizon and a cosmological event horizon. Since the Schwarzschild metric is the most simple solution of Einstein’s equations with spherical symmetry and the de Sitter metric is the most simple solution of Einstein’s equations with a positive cosmological constant, the combination in the SdS metric defines an appropriate background geometry for semi-classical investigation of Hawking radiation with respect to past and future horizons. Generally, the black hole temperature is larger than that of the cosmological horizon, so there is heat flow from the smaller black hole horizon to the larger cosmological horizon, despite questions concerning the definition of the relative temperature of the black hole without a measurement by an observer sitting in an asymptotically flat spacetime. Here we investigate the accelerating boundary correspondence of the radiation in SdS spacetime without such a problem. We have solved for the boundary dynamics, energy flux and asymptotic particle spectrum. The distribution of particles is globally non-thermal while asymptotically the radiation reaches equilibrium.
The covariance matrix transformation method in all-earth integrated navigation considering coordinate frame conversion
Authors: Zhang Yongjian , Luo Hui , Yu Xudong , Wei Guo , Gao Chunfeng , Wang Lin
Published: January 2022

In the exploration of polar regions, navigation is one of the most important issues to be resolved. To avoid the limitations of a single navigation coordinate frame, navigation systems usually use different navigation coordinate frames in polar and nonpolar regions, such as the north-oriented geographic frame and the grid frame. However, the error states and covariance matrix are related to the definition of the navigation coordinate frame, since coordinate frame conversion will cause overshoot of the integrated navigation Kalman filter and error discontinuity. To solve this problem, the transformation relationship of error states defined in different frames is deduced, whereby the covariance matrix transformation relationship is also analyzed. On this basis, covariance transformation-based open-loop and closed-loop Kalman filter integrated navigation algorithms are proposed. The effectiveness of the algorithms is verified by flight tests with a rotational strapdown inertial navigation system/global navigation satellite system integrated navigation system.
Monte Carlo investigation of electron fluence perturbation in MRI-guided radiotherapy beams using six commercial radiation detectors
Authors: Cervantes Yunuen , Duane Simon , Bouchard Hugo
Published: January 2022

With the integration of treatments with MRI-linacs to the clinical workflow, the understanding and characterization of detector response in reference dosimetry in magnetic fields are required. The external magnetic field perturbs the electron fluence. The degree of perturbation depends on the irradiation conditions and on the detector type. The purpose of this study is to evaluate the magnetic field impact on the electron fluence spectra in several detectors to provide a deeper understanding of detector response in these conditions. Monte Carlo calculations of the electron fluence are performed in six detectors (solid-state: PTW60012 and PTW60019, ionization chambers: PTW30013, PTW31010, PTW31021, and PTW31022) in water and irradiated by a 7 MV FFF photon beam with a small and a reference field, at 0 and 1.5 T. Three chamber axis orientations are investigated: parallel or perpendicular (either the Lorentz force pointing towards the stem or the tip) to the magnetic field and always perpendicular to the photon beam. One orientation for the solid-state detector is studied: parallel to the photon beam and perpendicular to the magnetic field. Additionally, electron fluence spectra are calculated in modified detector geometries to identify the underlying physical mechanisms behind the fluence perturbations. The total electron fluence in the Farmer chamber varies up to 1.24% and 5.12% at 1.5 T, in the parallel and perpendicular orientation, respectively. The interplay between the gyration radius and the Farmer chamber cavity length significantly affects the electron fluence in the perpendicular orientation. For the small-cavity chambers, the maximal variation in total electron fluence is 0.19% in the parallel orientation for the reference field. Significant small-field effects occur in these chambers; the magnetic field reduces the total electron fluence (with respect to the no field case) between 9.86% and 14.50%, depending on the orientation. The magnetic field strongly impacted the solid-state detectors in both field sizes, probably due to the high-Z components and cavity density. The maximal reductions of total electron fluence are 15.06 ± 0.09% (silicon) and 16.00 ± 0.07% (microDiamond). This work provides insights into detector response in magnetic fields by illustrating the interplay between several factors causing dosimetric perturbation effects: (1) chamber and magnetic field orientation, (2) cavity size and shape, (3) extracameral components, (4) air gaps and their asymmetry, (5) electron energy. Low-energy electron trajectories are more susceptible to change in magnetic fields, and are associated with detector response perturbation. Detectors with higher density and high-Z extracameral components exhibit more significant perturbations in the presence of a magnetic field, regardless of field size.
TBS-BAO: fully automated beam angle optimization for IMRT guided by a total-beam-space reference plan
Authors: Schipaanboord B W K , Heijmen B J M , Breedveld S
Published: January 2022

Properly selected beam angles contribute to the quality of radiotherapy treatment plans. However, the beam angle optimization (BAO) problem is difficult to solve to optimality due to its non-convex discrete nature with many local minima. In this study, we propose TBS-BAO, a novel approach for solving the BAO problem, and test it for non-coplanar robotic CyberKnife radiotherapy for prostate cancer. First, an ideal Pareto-optimal reference dose distribution is automatically generated using a priori multi-criterial fluence map optimization (FMO) to generate a plan that includes all candidate beams (total-beam-space, TBS). Then, this ideal dose distribution is reproduced as closely as possible in a subsequent segmentation/beam angle optimization step (SEG/BAO), while limiting the number of allowed beams to a user-selectable preset value. SEG/BAO aims at a close reproduction of the ideal dose distribution. For each of 33 prostate SBRT patients, 18 treatment plans with different pre-set numbers of allowed beams were automatically generated with the proposed TBS-BAO. For each patient, the TBS-BAO plans were then compared to a plan that was automatically generated with an alternative BAO method (Erasmus-iCycle) and to a high-quality manually generated plan. TBS-BAO was able to automatically generate plans with clinically feasible numbers of beams (∼25), with a quality highly similar to corresponding 91-beam ideal reference plans. Compared to the alternative Erasmus-iCycle BAO approach, similar plan quality was obtained for 25-beam segmented plans, while computation times were reduced from 10.7 hours to 4.8/1.5 hours, depending on the applied pencil-beam resolution in TBS-BAO. 25-beam TBS-BAO plans had similar quality as manually generated plans with on average 48 beams, while delivery times reduced from 22.3 to 18.4/18.1 min. TBS reference plans could effectively steer the discrete non-convex BAO.
Gyro-average method for global gyrokinetic particle simulation in realistic tokamak geometry
Authors: Duan Yihao , Xiao Yong , Lin Zhihong
Published: January 2022

Gyro-average is a crucial operation to capturing the essential finite Larmor radius (FLR) effect in gyrokinetic simulation. In order to simulate strongly shaped plasmas, an innovative multi-point average method based on non-orthogonal coordinates has been developed to improve the accuracy of the original multi-point average method in gyrokinetic particle simulation. This new gyro-average method has been implemented in the gyrokinetic toroidal code (GTC). Benchmarks have been carried out to prove the accuracy of this new method. In the limit of concircular tokamak, ion temperature gradient (ITG) instability is accurately recovered for this new method and consistency is achieved. The new gyro-average method is also used to solve the gyrokinetic Poisson equation, and its correctness is confirmed in the long-wavelength limit for realistically shaped plasmas. The improved GTC code with the new gyro-average method is used to investigate the ITG instability with EAST magnetic geometry. The simulation results show that the correction induced by this new method in the linear growth rate is more significant for short-wavelength modes where the FLR effect becomes important. Due to its simplicity and accuracy, this new gyro-average method can find broader applications in simulating shaped plasmas in realistic tokamaks.
Preparation of N-TiO2/SiO2 composites by solvothermal method and their photocatalytic properties
Authors: Wu Chunli , Dong Xiaohao , Wang Lan , Zhang Lei , Liu Xiaotong
Published: January 2022

In order to improve the visible light catalytic activity of titanium dioxide (TiO2) and ensure its long-term stability on the surface of concrete, an N-TiO2/SiO2 composite was prepared using tetrabutyl titanate, nitric acid, and modified SiO2 nanospheres as the precursors by a solvothermal method. The effect of nitric acid on the phase composition, morphology and photoelectric properties of the synthesized photocatalytic composites was systematically studied by various characterization methods. The results show that the optimum nitric acid/butyl titanate volume ratio is 1/6. The nitrogen-doped TiO2 nanoparticles were uniformly dispersed on the surface of spherical SiO2 with a diameter of 200 nm. The degradation rate of simulated pollutants (RhB) with pH 5 and 7 exceeded 95% within 30 min and the catalytic effect remained excellent after five repetitions without much weakening. The excellent visible photocatalytic performance can be attributed to the doping of N replacing part of the oxygen atoms in TiO2, forming the energy level of N 2p at the O 2p energy level and reducing the TiO2 energy band gap to 2.99 eV. At the same time, the better dispersion of N-TiO2/SiO2 prepared by this new synthesis method also plays an important role in the improvement of visible light photocatalytic activity.
Performance of air plasma sprayed Cr3C2–25NiCr and NiCrMoNb coated X8CrNiMoVNb16–13 alloy subjected to high temperature corrosion environment
Authors: Subramani P , Sathishkumar M , Manikandan M , Selvaraj Senthil Kumaran , Sreenivasulu V , Arivazhagan N , Rajkumar S
Published: January 2022

Thermal barrier coating plays a vital role in protecting materials’ surfaces from high-temperature environment conditions. This work compares the demeanour of uncoated and air plasma sprayed Cr3C2–25NiCr and NiCrMoNb coated X8CrNiMoVNb16–13 substrates subjected to air oxidation and molten salt (Na2SO4 + 60%V2O5) environment condition at 900 °C for 50 cycles. Coating characteristics have been analyzed through microstructure, thickness, porosity, hardness, and bond strength. SEM, EDS and XRD analysis were used to analyze corrosion’s product at the end of the 50th cycle. Coating microstructures showed a uniform laminar structure that is adherent and denser with a coating thickness of 150 ± 20 μm and porosity less than 3.5%. The Microhardness of both the coated substrates were higher than that of the bare substrate. Cr3C2–25NiCr and NiCrMoNb coating bond strength was 38.9 MPa and 42.5 MPa. Thermogravimetric analysis showed the parabolic rate law of oxidation for all the substrates in both environments. In the molten salt environment, all the substrates exhibited higher weight gain compared to the air oxidation environment. In both environmental conditions, the uncoated X8CrNiMoVNb16–13 alloy exhibited higher weight gain than the coated substrates. The formation of Cr2O3, NiO and spinel oxide NiCr2O4 offers good resistance to corrosion to all the substrates in both the environmental condition. However, the presence of Mo and Nb significantly accelerated the corrosion of the substrate, thereby increasing the weight of the NiCrMoNb substrate. It is observed that Cr3C2–25NiCr and NiCrMoNb coating over the X8CrNiMoVNb16–13 substrate significantly protected the substrate against the hot corrosion than the bare alloy exposed to similar environmental conditions.
Steering the current flow in twisted bilayer graphene
Authors: Arturo Sánchez-Sánchez Jesús , Navarro-Espino Montserrat , Betancur-Ocampo Yonatan , Barrios-Vargas José Eduardo , Stegmann Thomas
Published: January 2022

A nanoelectronic device made of twisted bilayer graphene (TBLG) is proposed to steer the direction of the current flow. The ballistic electron current, injected at one edge of the bottom layer, can be guided predominantly to one of the lateral edges of the top layer. The current is steered to the opposite lateral edge, if either the twist angle is reversed or the electrons are injected in the valence band instead of the conduction band, making it possible to control the current flow by electric gates. When both graphene layers are aligned, the current passes straight through the system without changing its initial direction. The observed steering angle exceeds well the twist angle and emerges for a broad range of experimentally accessible parameters. It is explained by the twist angle and the trigonal shape of the energy bands beyond the van Hove singularity due to the Moiré interference pattern. As the shape of the energy bands depends on the valley degree of freedom, the steered current is partially valley polarized. Our findings show how to control and manipulate the current flow in TBLG. Technologically, they are of relevance for applications in twistronics and valleytronics.
Weak generics
Authors: Almotahari Mahrad
Published: January 2022

Some generic sentences seem to be true despite the fact that almost all the members of the relevant kind are exceptions. It’s controversial whether generics of this type express relatively weak generalizations or relatively strong ones. If the latter, then we’re systematically mistaken about their truth, but they make no trouble for our semantic theorizing. In this brief note, I present several arguments for the former: sentences of the relevant type are weak generics.
Molecular insights into luminescence system of the pelagic shrimp Lucensosergia lucens
Authors: Kanie Shusei , Komatsu Mami , Mitani Yasuo
Published: January 2022

Lucensosergia lucens is a luminous marine shrimp that has been suggested to use a coelenterazine-dependent luminescence system. However, the genetic information related to the luminescence system is lacking. Our RNA-Seq analysis of this shrimp did not show the existence of known or homologous coelenterazine-dependent luciferase genes. Subsequent biochemical analyses suggested that the shrimp possessed unknown proteinaceous components for coelenterazine luminescence.
Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes
Authors: Rubio Alejandro , Jimenez Juan , Pérez-Pulido Antonio J
Published: January 2022

Bacterial genomes are massively sequenced, and they provide valuable data to better know the complete set of genes of a species. The analysis of thousands of bacterial strains can identify both shared genes and those appearing only in the pathogenic ones. Current computational gene finders facilitate this task but often miss some existing genes. However, the present availability of different genomes from the same species is useful to estimate the selective pressure applied on genes of complete pangenomes. It may assist in evaluating gene predictions either by checking the certainty of a new gene or annotating it as a gene under positive selection. Here, we estimated the selective pressure of 19 271 genes that are part of the pangenome of the human opportunistic pathogen Acinetobacter baumannii and found that most genes in this bacterium are subject to negative selection. However, 23% of them showed values compatible with positive selection. These latter were mainly uncharacterized proteins or genes required to evade the host defence system including genes related to resistance and virulence whose changes may be favoured to acquire new functions. Finally, we evaluated the utility of measuring selection pressure in the detection of sequencing errors and the validation of gene prediction.
AlzCode: a platform for multiview analysis of genes related to Alzheimer’s disease
Authors: Lin Cui-Xiang , Li Hong-Dong , Deng Chao , Erhardt Shannon , Wang Jun , Peng Xiaoqing , Wang Jianxin
Published: January 2022

Motivation

Alzheimer’s disease (AD) is a complex brain disorder with risk genes incompletely identified. The candidate genes are dominantly obtained by computational approaches. In order to obtain biological insights of candidate genes or screen genes for experimental testing, it is essential to assess their relevance to AD. A platform that integrates different types of omics data and approaches would facilitate the analysis of candidate genes and is in great need.

Results

We report AlzCode, a platform for multiview analysis of genes related to AD. First, this platform integrates a rich collection of functional genomic data, including expression data of AD samples (gene expression, single-cell RNA-seq data and protein expression), AD-specific biological networks (co-expression networks and functional gene networks), neuropathological and clinical traits (CERAD score, Braak staging score, Clinical Dementia Rating, cognitive function and clinical severity) and general data such as protein–protein interaction, regulatory networks, sequence similarity and miRNA-target interactions. These data provide basis for analyzing genes from different views. Second, the platform integrates multiple approaches designed for the various types of data. We implement functions to analyze both individual genes and gene sets. We also compare AlzCode with two existing platforms for AD analysis, which are Agora and AD Atlas. We pinpoint the features of each platform and highlight their differences. This platform would be valuable to the understanding of AD genetics and pathological mechanisms.

Availability and implementation

AlzCode is freely available at: http://www.alzcode.xyz.

Supplementary information

Supplementary data are available at Bioinformatics online.
Proteomic analysis of spermatozoa reveals caseins play a pivotal role in preventing short-term periods of subfertility in stallions
Authors: Griffin Róisín Ann , Swegen Aleona , Baker Mark A , Ogle Rachel Ann , Smith Nathan , Aitken Robert John , Skerrett-Byrne David Anthony , Fair Sean , Gibb Zamira
Published: January 2022

Stallions experience transient fluctuations in fertility throughout the breeding season. Considering pregnancy diagnoses cannot be ascertained until ~14 days postbreeding, the timely detection of decreases in stallion fertility would enhance industry economic and welfare outcomes. Therefore, this study aimed to identify the proteomic signatures reflective of short-term fertility fluctuations and to determine the biological mechanisms governing such differences. Using liquid chromatography–mass spectrometry (LC-MS/MS), we compared the proteomic profile of semen samples collected from commercially “fertile” stallions, during high- and low-fertility periods. A total of 1702 proteins were identified, of which, 38 showed a significant change in abundance (P ≤ 0.05). Assessment of intra- and interstallion variability revealed that caseins (namely κ-, α-S1-, and α-S2-casein) were significantly more abundant during “high-fertility” periods, while several epididymal, and seminal plasma proteins (chiefly, epididymal sperm binding protein 1 [ELSPbP1], horse seminal plasma protein 1 [HSP-1], and clusterin), were significantly more abundant during “low-fertility” periods. We hypothesized that an increased abundance of caseins offers greater protection from potentially harmful seminal plasma proteins, thereby preserving cell functionality and fertility. In vitro exposure of spermatozoa to casein resulted in decreased levels of lipid scrambling (Merocyanine 540), higher abundance of sperm-bound caseins (α-S1-, α-S2-, and κ-casein), and lower abundance of sperm-bound HSP-1 (P ≤ 0.05). This study demonstrates key pathways governing short-term fertility fluctuations in the stallion, thereby providing a platform to develop robust, fertility assessment strategies into the future.
Treatment and survival of patients with pancreatic ductal adenocarcinoma: 15-year national cohort
Authors: Nymo Linn Såve , Myklebust Tor Åge , Hamre Hanne , Møller Bjørn , Lassen Kristoffer
Published: January 2022

Background

Improvement in survival from pancreatic ductal adenocarcinoma (PDAC) has been reported in trial settings but is less explored in unselected cohorts. The aim of this study was to assess trends in provision of treatments and survival in Norway over a 15-year period following the implementation of hepato-pancreato-biliary (HPB) multidisciplinary teams, centralization of surgery, and implementation of modern chemotherapy (CTx) regimens.

Methods

A population-based observational study was conducted by analysing all patients diagnosed with PDAC between 2004 and 2018 using coupled data from the Cancer Registry of Norway and the National Patient Registry.

Results

A total of 10 630 patients were identified, of whom 1492 (14.0 per cent) underwent surgical resection. The resection rate, median age of those resected, and provision of perioperative CTx all increased over time. Median overall survival after resection improved from 16.0 months in the period 2004 to 2008 to 25.1 months in the period 2014 to 2018 (P < 0.001). For non-resected patients there was a rise in the provision of palliative chemotherapy, but little survival gain over time (median overall survival for 2004 to 2008 was 3.2 months versus 4.2 months for 2014 to 2018; P < 0.001). The rate of patients who did not receive any tumour-directed treatment (neither CTx nor surgery) was 44.3 per cent (2481 of 5603 patients) and decreased from 52.9 per cent in 2010 to 37.9 per cent in 2018 (P < 0.001). The median overall survival for all patients with PDAC increased from 3.7 months for 2004 to 2008 to 5.8 months for 2014 to 2018 (P < 0.001).

Conclusion

Survival after resection increased substantially, as did national resection rates. Little development in the provision of CTx or survival was observed for non-resected patients.
Phylogenetic relationships and biogeography of Psoraleeae (Fabaceae)
Authors: Bello Abubakar , Stirton Charles H , Chimphango Samson Bm , Muasya A Muthama
Published: January 2022

Psoraleeae consist of c. 228 species in ten genera, distributed worldwide but mostly in the temperate biome. Here, we reconstruct the phylogenetic history of Psoraleeae using eight molecular markers (rpl32-trnL, trnQ-rps16, trnS-trnG, matK, rbcLa, rpoB-trnC, trnL-trnF and ITS) to test the monophyly and previous hypotheses on generic relationships and to reconstruct the biogeographical history (distribution pattern, potential ancestral area and biome). The monophyly of Psoraleeae is supported. The African Otholobium and Psoralea form a strongly supported clade that is sister to the rest of Psoraleeae. However, Otholobium is not monophyletic; the American taxa of the genus are resolved as closer to Bituminaria, whereas Psoralea is a clade derived from within African Otholobium. South African Otholobium is subsumed into Psoralea, the latter having priority, with a synopsis of species level nomenclature provided here. An expanded sampling of Cullen reveals three clades comprising Mediterranean (Cullen americanum), African (Cullen obtusifolium and Cullen biflorum) and Eurasian (Cullen corylifolium and Cullen drupaceum) taxa, whereas Australian Cullen are a derived clade (BS = 95%, PP = 1.00). Biogeographic reconstructions show that Psoraleeae probably originated in the Mediterranean south biome of Africa in the Late Miocene, c. 8.2 Mya, and then dispersed into the succulent biome of the Americas, Mediterranean north biome, temperate grasslands of Africa and Australia to the temperate forest of Eurasia. Climate changes in the Late Miocene, changes induced by ocean currents during the Quaternary and environmental heterogeneity are proposed as the major drivers of speciation in Psoraleeae.
Increased circulating PD-1hiCXCR5− peripheral T helper cells are associated with disease activity of ANCA-associated vasculitis
Authors: Liu Zhenyu , Li Xueqin , Fan Ningning , Wang Hong , Xia Wenli , Li Wenjie , Tang Sha , Zhou Xinyuan , Wu Yuzhang , Zou Liyun , Li Jingyi , Zhang Jingbo
Published: January 2022

Newly identified PD-1hiCXCR5–CD4+ T-cells, termed as peripheral helper T-cells (Tph), have been found elevated and playing a pathogenic role in some autoimmune diseases like systemic lupus erythematosus (SLE) and rheumatic arthritis (RA). However, the potential role of Tph-cells in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) remains unclear. Here, we explored the potential clinical significance of circulating Tph-cells in the pathogenesis of AAV. Comparing 32 active AAV patients and 18 age- and sex-matched healthy controls (HCs), we found that the frequency of circulating Tph-cells was significantly expanded in active AAV patients. Besides, programmed death 1 (PD-1) expression on the surface of Tph-cells was significantly up-regulated in active AAV patients. Importantly, the frequency of circulating Tph-cells was greatly decreased in AAV patients after receiving treatment. Tph-cells frequency was positively correlated with the Birmingham Vasculitis Activity Score (BVAS), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), neutrophil lymphocyte ratio (NLR), and cellular crescent in active AAV patients, but negatively correlated with fibrosus crescent. Tph-cells frequency was also positively correlated with naïve B-cells, serum concentration of MPO-ANCAs, serum tumor necrosis factor-α (TNF-α), IL-4, IL-21, and IL-12. However, serum IL-10 exhibited a negative correlation with circulating Tph-cells in active AAV patients. These results demonstrate that circulating Tph-cells are greatly expanded in active AAV patients and are positively associated with serum MPO-ANCAs and disease activity, thus contributing to the pathogenesis of AAV.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Dynamics and Immune Responses in a Household of Vaccinated Persons
Authors: Liu Jamin , Laurie Matthew T , Rubio Luis , Vazquez Sara E , Sunshine Sara , Mitchell Anthea M , Hapte-Selassie Matthias , Mann Sabrina A , Pilarowski Genay , Black Douglas , Marquez Carina , Rojas Susana , Lionakis Michail S , Petersen Maya , Whitman Jeffrey D , Jain Vivek , Anderson Mark , Havlir Diane , DeRisi Joseph
Published: January 2022

While SARS-CoV-2 vaccines prevent severe disease effectively, postvaccination “breakthrough” COVID-19 infections and transmission among vaccinated individuals remain ongoing concerns. We present an in-depth characterization of transmission and immunity among vaccinated individuals in a household, revealing complex dynamics and unappreciated comorbidities, including autoimmunity to type 1 interferon in the presumptive index case.
Stability and compatibility of antibiotics in peritoneal dialysis solutions
Authors: So Simon Wai Yin , Chen Lu , Woo Alex Yuk Hei , Ng Derek Man Him , Wong Jennifer Ka Wah , Chow Kai Ming , Runnegar Naomi , Johnson David W , Li Philip Kam-Tao
Published: January 2022

Intraperitoneal (IP) administration of antibiotics is a preferred treatment of peritoneal dialysis (PD)-related peritonitis. Given the treatment duration of up to 2–3 weeks, it is important that robust data on antibiotic stability and compatibility are available to achieve notable treatment success. This article provides a comprehensive review of recent stability and compatibility studies pertaining to a wide range of antibiotics admixed in various PD solutions.
Two-Party Signing For ISO/IEC Digital Signature Standards
Authors: Tang Guofeng , Zhang Zhenfeng
Published: January 2022

Two-party signing can be used to provide a high level of key protection especially in the blockchain systems where the safety of money relies on the safety of the signing key. With a two-party signing protocol, the signing key is distributed among two devices, thus the funds are safe as long as one device remains uncorrupted. In this paper, we study the two-party signing protocols for all ISO/IEC signature standards. The mechanisms based on elliptic curve discrete logarithm in ISO/IEC can be divided into three types: Schnorr-type, Elliptic Curve Digital Signature Algorithm (ECDSA)-type and SM2-type. There have already been efficient two-party protocols based on Schnorr signature scheme which can be easily extended into all Schnorr-type standards. However, it is particularly hard to construct efficient distributed SM2-type and ECDSA-type protocols due to their nonlinear signing equations. In this paper, we present the first secure and efficient two-party protocol over SM2-type signature standard. We prove its security in the generic group model. We then construct a more efficient two-party ECDSA protocol that is secure in the generic group model and outperforms all previous works.
Single step estimation of ARMA roots for nonfundamental nonstationary fractional models
Authors: Lobato Ignacio N , Velasco Carlos
Published: January 2022

We propose a single step estimator for the autoregressive and moving average roots (without imposing causality or invertibility restrictions) of a nonstationary Fractional ARMA process. These estimators employ an efficient tapering procedure, which allows for a long memory component in the process, but avoids estimating the nonstationarity component, which can be stochastic and/or deterministic. After selecting automatically the order of the model, we robustly estimate the AR and MA roots for trading volume for the thirty stocks in the Dow Jones Industrial Average Index in the last decade. Two empirical results are found. First, there is strong evidence that stock market trading volume exhibits nonfundamentalness. Second, noncausality is more common than noninvertibility.
Trend, predictors, and outcomes of combined mitral valve replacement and coronary artery bypass graft in patients with concomitant mitral valve and coronary artery disease: a National Inpatient Sample database analysis
Authors: Ullah Waqas , Gul Sajjad , Saleem Sameer , Syed Mubbasher Ameer , Khan Muhammad Zia , Zahid Salman , Minhas Abdul Mannan Khan , Virani Salim S , Mamas Mamas A , Fischman David L
Published: January 2022

Aims

Combined mitral valve replacement (MVR) and coronary artery bypass graft (CABG) procedures have been the norm for patients with concomitant mitral valve disease (MVD) and coronary artery disease (CAD) with no large-scale data on their safety and efficacy.

Methods and results

The National Inpatient Sample database (2002–18) was queried to identify patients undergoing MVR and CABG. The major adverse cardiovascular events (MACE) and its components were compared using a propensity score-matched (PSM) analysis to calculate adjusted odds ratios (OR). A total of 6 145 694 patients (CABG only 3 971 045, MVR only 1 933 459, MVR + CABG 241 190) were included in crude analysis, while a matched cohort of 724 237 (CABG only 241 436, MVR only 241 611 vs. MVR + CABG 241 190) was selected in PSM analysis. The combined MVR + CABG procedure had significantly higher adjusted odds of MACE [OR 1.13, 95% confidence interval (CI) 1.11–1.14 and OR 1.96, 95% CI 1.93–1.99] and in-hospital mortality (OR 1.29, 95% CI 1.27–1.31 and OR 2.1, 95% CI 2.05–2.14) compared with CABG alone and MVR alone, respectively. Similarly, the risk of post-procedure bleeding, major bleeding, acute kidney injury, cardiogenic shock, sepsis, need for intra-aortic balloon pump, mean length of stay, and total charges per hospitalization were significantly higher for patients undergoing the combined procedure. These findings remained consistent on yearly trend analysis favouring the isolated CABG and MVR groups.

Conclusion

Combined procedure (MVR + CABG) in patients with MVD and CAD appears to be associated with worse in-hospital outcomes, increased mortality, and higher resource utilization compared with isolated CABG and MVR procedures. Randomized controlled trials are needed to determine the relative safety of these procedures in the full spectrum of baseline valvular and angiographic characteristics.
The 2020 ESC atrial fibrillation guidelines for atrial fibrillation catheter ablation, CABANA, and EAST
Authors: Arbelo Elena , Dagres Nikolaos
Published: January 2022

Prior randomised clinical trials (RCTs) have suggested that rhythm control offers no benefit compared to accepting AF and instituting rate control in terms of all-cause mortality, CV mortality and sudden death; as a consequence, the ESC AF guidelines have recommended rhythm control for reducing AF-related symptoms and improving quality of life. The Early Treatment of Atrial Fibrillation for Stroke Prevention Trial (EAST-AFNET 4) evaluated whether a more up-to-date rhythm control management strategy provides a benefit in mortality or stroke rates while the Catheter Ablation vs Antiarrhythmic Drug Therapy for Atrial Fibrillation (CABANA) trial evaluated whether catheter ablation was better than drug therapy in preventing a composite of death, disabling stroke, serious bleeding or cardiac arrest. This document critically reviews the recommendations of the 2020 ESC guidelines for the management of AF in the light of these two landmark trials, both of which have underlined the safety of contemporary rhythm control treatment. Considering the safety of the different strategies in modern AF treatment, a personalized approach taking into account the specific patient profile and preferences of the individual patient is needed.
Supportive interactions with primary care doctors are associated with better mental health among transgender people: results of a nationwide survey in Aotearoa/New Zealand
Authors: Treharne Gareth J , Carroll Rona , Tan Kyle K H , Veale Jaimie F
Published: January 2022

Background

Past research has established that transgender people experience significant disparities in mental health outcomes and healthcare dissatisfaction compared with cisgender people, but more research is needed on how supportive healthcare interactions relate to the mental health of transgender people.

Objectives

The 2 main aims of our analyses were: (i) to establish the most common negative experiences in healthcare and the most common supportive experiences specifically with primary care doctors for transgender people; and (ii) to examine the association of supportive experiences with mental health variables after controlling for demographic factors.

Methods

Data from the 2018 Counting Ourselves nationwide survey of transgender people were analysed using regression modelling. The 948 participants with a primary care doctor or general practitioner were included in analyses. Participants were aged 14–83 years old (mean 30.20).

Results

The most common supportive experiences involved primary care doctors treating transgender people equitably, with competence, and with respect. Participants with more negative healthcare experiences had higher psychological distress as well as higher likelihood of reporting nonsuicidal self-injury and suicidality. Conversely, participants with more experiences of supportive primary care doctors had lower psychological distress and were less likely to have attempted suicide in the past 12 months.

Conclusion

When transgender people receive supportive care from their primary care providers they experience better mental health, despite ongoing negative healthcare experiences. Future research is needed to confirm ways of supporting positive trajectories of mental health for transgender people but these findings demonstrate the importance of positive aspects of care.
Cost-effectiveness of an occupational therapy-led self-management support programme for multimorbidity in primary care
Authors: Gillespie Paddy , Hobbins Anna , O’Toole Lynn , Connolly Deirdre , Boland Fiona , Smith Susan M
Published: January 2022

Background

Multimorbidity is a major public health concern. Complex interventions, incorporating individualized care plans, may be appropriate for patients with multimorbidity given their individualized and variable needs. There is a dearth of evidence on the cost-effectiveness of complex multimorbidity interventions.

Objective

This study examines the cost-effectiveness of a 6-week occupational therapy-led self-management support programme (OPTIMAL) for adults with multimorbidity.

Methods

Economic evaluation, from a healthcare perspective, was conducted alongside a randomized controlled trial of 149 adults with multimorbidity. Intervention was the OPTIMAL programme with a comparison of usual primary care. Incremental costs, quality-adjusted life years (QALYs) gained, and expected cost-effectiveness were estimated at 6 months and uncertainty was explored using cost-effectiveness acceptability curves.

Results

The intervention was associated with a mean improvement in QALYs gained of 0.031 per patient (P-value: 0.063; 95% confidence intervals [CIs]: −0.002 to 0.063) and a mean reduction in total costs of €2,548 (P-value: 0.114; 95% CIs: −5,606 to 509) per patient. At cost-effectiveness threshold values of €20,000 and €45,000 per QALY, the probability of the intervention being cost-effective was estimated to be 0.951 and 0.958, respectively. The results remained consistent across all subgroups examined.

Conclusions

This study adds to the limited evidence base on the cost-effectiveness of complex interventions for multimorbidity, and highlights the potential for the OPTIMAL programme to be cost-effective. Further studies are warranted to explore the clinical and cost-effectiveness of complex interventions for the multimorbidity patient population, and for subgroups within it.

Trial registration

Trial number: ISRCTN67235963.
Combination of salicylic acid and ultrasonication for alleviating chilling injury symptoms of longkong
Authors: Noonim Paramee , Venkatachalam Karthikeyan
Published: January 2022

Objectives

Chilling injury is a prominent physiological disorder in longkong fruit pericarp when stored under 13 °C for a prolonged period. This study aimed to investigate the effects of individual salicylic acid (SA) and ultrasonication (US) treatments and of the combination salicylic acid and ultrasonication (SA-US) on alleviating the chilling injury symptoms in longkong fruit pericarp when in prolonged cold storage.

Materials and methods

SA (1 mmol/L) and US (40 kHz, 10 min at 90% amplitude, 350 W) were used as individual and combined (SA-US) treatments to control the chilling injury in longkong pericarp. The various quality measures were checked every 2 days in longkong for up to 18 days of cold storage (13 °C, 90% relative humidity).

Results

The results revealed that the control fruits treated with water exhibited severe chilling injury symptoms followed in rank order by US, SA, and SA-US cases. Treatments such as US and SA alone were more effective in controlling chilling injuries than control, while only minimal significant differences were noticed between them. On the other hand, the longkong pericarp treated with the SA-US combination had significantly increased antioxidant enzyme (superoxide dismutase and catalase) activities and decreased levels of membrane lytic (phospholipase D and lipoxygenase) enzymes and browning-inducing enzymes (phenylalanine ammonia lyase and polyphenol oxidase). Consequently, in the longkong pericarp, the chilling injury index, electrolytic leakage, respiration rate, weight loss, firmness, malondialdehyde content, changes in unsaturated and saturated fatty acid contents, and reactive oxygen species were significantly controlled by this treatment.

Conclusions

The present study concludes that longkong fruit treatment with a combination of US and SA is an excellent alternative for controlling the chilling injury symptoms and extending the shelf-life.
Dietary fiber in plant cell walls—the healthy carbohydrates
Authors: An Yi , Lu Weitai , Li Wenze , Pan Langlang , Lu Mengzhu , Cesarino Igor , Li Zheng , Zeng Wei
Published: January 2022

Dietary fiber (DF) is one of the major classes of nutrients for humans. It is widely distributed in the edible parts of natural plants, with the cell wall being the main DF-containing structure. DF content varies significantly in different plant species and organs, and the processing procedure can have a dramatic effect on the DF composition of plant-based foods. Given the considerable nutritional value of DF, a deeper understanding of DF in food plants, including its composition and biosynthesis, is fundamental to the establishment of a daily intake reference of DF and is also critical to molecular breeding programs for modifying DF content. In the past decades, plant cell wall biology has seen dramatic progress, and such knowledge is of great potential to be translated into DF-related food science research and may provide future research directions for improving the health benefits of food crops. In this review, to spark interdisciplinary discussions between food science researchers and plant cell wall biologists, we focus on a specific category of DF—cell wall carbohydrates. We first summarize the content and composition of carbohydrate DF in various plant-based foods, and then discuss the structure and biosynthesis mechanism of each carbohydrate DF category, in particular the respective biosynthetic enzymes. Health impacts of DF are highlighted, and finally, future directions of DF research are also briefly outlined.