bluuebunny/crossref_metadata_2025 huggingface dataset:
Shifts in valence states in bimetallic MXenes revealed by electron energy-loss spectroscopy (EELS)
Authors: Foucher Alexandre C , Han Meikang , Shuck Christopher E , Maleski Kathleen , Gogotsi Yury , Stach Eric A
Published: January 2022

MXenes are an emergent class of two-dimensional materials with a very wide spectrum of promising applications. The synthesis of multiple MXenes, specifically solid-solution MXenes, allows fine tuning of their properties, expands their range of applications, and leads to enhanced performance. The functionality of solid-solution MXenes is closely related to the valence state of their constituents: transition metals, oxygen, carbon, and nitrogen. However, the impact of changes in the oxidation state of elements in MXenes is not well understood. In this work, three interrelated solid-solution MXene systems (Ti2−y
Nb
y
CT
x
, Nb2−y
V
y
CT
x
, and Ti2−y
V
y
CT
x
) were investigated with scanning transmission electron microscopy and electron energy-loss spectroscopy to determine the localized valence states of metals at the nanoscale. The analysis demonstrates changes in the electronic configuration of V upon modification of the overall composition and within individual MXene flakes. These shifts of oxidation state can explain the nonlinear optical and electronic features of solid-solution MXenes. Vanadium appears to be particularly sensitive to modification of the valence state, while titanium maintains the same oxidation state in Ti–Nb and Ti–V MXenes, regardless of stoichiometry. The study also explains Nb’s influential role in the previously observed electronic properties in the Nb–V and Nb–Ti systems.
Synthesis of Ag-decorated vertical graphene nanosheets and their electrocatalytic efficiencies
Authors: CHEN Jiali , JI Peiyu , LI Maoyang , HUANG Tianyuan , ZHUGE Lanjian , WU Xuemei
Published: January 2022

Herein we report the successful preparation of silver (Ag)-decorated vertically oriented graphene sheets (Ag/VGs) via helicon wave plasma chemical vapor deposition (HWP-CVD) and radiofrequency plasma magnetron sputtering (RF-PMS). VGs were synthesized in a mixture of argon and methane (Ar/CH4) by HWP-CVD and then the Ag nanoparticles on the prepared VGs were modified using the RF-PMS system for different sputtering times and RF power levels. The morphology and structure of the Ag nanoparticles were characterized by scanning electron microscopy and the results revealed that Ag nanoparticles were evenly dispersed on the mesoporous wall of the VGs. X-ray diffraction results showed that the diameter of the Ag particles increased with the increase in Ag loading, and the average size was between 10.49 nm and 25.9 nm, consistent with the transmission electron microscopy results. Ag/VGs were investigated as effective electrocatalysts for use in an alkaline aqueous system. Due to the uniquely ordered and interconnected wall structure of VGs, the area of active sites increased with the Ag loading, giving the Ag/VGs a good performance in the oxygen evolution reaction. The double-layer capacitance (C
dl) of the Ag/VGs under different Ag loadings were studied, and the results showed that the highest Ag content gave the best C
dl (1.04 mF cm−2). Our results show that Ag/VGs are likely to be credible electrocatalytic materials.
Fully solution-processed InSnO/HfGdO
X
thin-film transistor for light-stimulated artificial synapse
Authors: Li Jun , Wen Shengkai , Jiang Dongliang , Li Linkang , Zhang Jianhua
Published: January 2022

In recent years, the research interest in brain-inspired light-stimulated artificial synaptic electronic devices has greatly increased, due to their great potential in constructing low-power, high-efficiency, and high-speed neuromorphic computing systems. However, in the field of electronic synaptic device simulation, the development of three-terminal synaptic transistors with low manufacturing cost and excellent memory function still faces huge challenges. Here, a fully solution-processed InSnO/HfGdO
X
thin film transistor (TFT) is fabricated by a simple and convenient solution process to verify the feasibility of light-stimulated artificial synapses. This experiment investigated the electrical and synaptic properties of the device under light stimulation conditions. The device successfully achieved some important synaptic properties, such as paired-pulse facilitation, excitatory postsynaptic current and the transition from short-term memory to long-term memory. In addition, the device also exhibits brain-like memory and learning behaviors under different colors of light stimulation. This work provides an important strategy for the realization of light-stimulated artificial synapses and may have good applications in the field of artificial neuromorphic computing by light signals in the future.
Physics makes the difference: Bayesian optimization and active learning via augmented Gaussian process
Authors: Ziatdinov Maxim A , Ghosh Ayana , Kalinin Sergei V
Published: January 2022

Both experimental and computational methods for the exploration of structure, functionality, and properties of materials often necessitate the search across broad parameter spaces to discover optimal experimental conditions and regions of interest in the image space or parameter space of computational models. The direct grid search of the parameter space tends to be extremely time-consuming, leading to the development of strategies balancing exploration of unknown parameter spaces and exploitation towards required performance metrics. However, classical Bayesian optimization (BO) strategies based on the Gaussian process (GP) do not readily allow for the incorporation of the known physical behaviors or past knowledge. Here we explore a hybrid optimization/exploration algorithm created by augmenting the standard GP with a structured probabilistic model of the expected system’s behavior. This approach balances the flexibility of the non-parametric GP approach with a rigid structure of physical knowledge encoded into the parametric model. The fully Bayesian treatment of the latter allows additional control over the optimization via the selection of priors for the model parameters. The method is demonstrated for a noisy version of a standard univariate test function used to evaluate optimization algorithms and further extended to physical lattice models. This methodology is expected to be universally suitable for injecting prior knowledge in the form of physical models and past data in the BO framework.
Amorphous silica nanoparticles (nSP50) exacerbate hepatic damage through the activation of acquired cell-mediated immunity
Authors: Eto Shun-ichi , Higashisaka Kazuma , Koshida Aoi , Sato Kenta , Ogura Mao , Sakurai Miyuki , Tsujino Hirofumi , Nagano Kazuya , Tsutsumi Yasuo
Published: January 2022

Due to their innovative functions, the use of nanoparticles in various industries has been expanding. However, a key concern is whether nanoparticles induce unexpected biological effects. Although many studies have focused on innate immunity, information on whether nanoparticles induce biological responses through effects on acquired immunity is sparse. Here, to assess the effects of amorphous silica nanoparticles on acquired immunity, we analyzed changes in acute toxicities after pretreatment with amorphous silica nanoparticles (50 nm in diameter; nSP50). Pretreatment with nSP50 biochemically and pathologically exacerbated nSP50-induced hepatic damage in immunocompetent mice, while pretreatment with nSP50 did not exacerbate hepatic damage in immunodeficient mice. Consistent with this, the depletion of CD8+ cells with an anti-CD8 antibody in animals pretreated with nSP50 resulted in lower plasma levels of hepatic injury markers such as ALT and AST after an intravenous administration than treatment with an isotype-matched control antibody. Finally, stimulation of splenocytes promoted the release of IFN-γ in nSP50-pretreated mice regardless of the stimulator used. Moreover, the blockade of IFN-γ decreased plasma levels of ALT and AST levels in nSP50-pretreated mice. Collectively, these data show that nSP50-induced acquired immunity leads to exacerbation of hepatic damage through the activation of cytotoxic T lymphocytes.
The Winchcombe Meteorite: one year on
Authors: O'Brien Áine Clare , Pickersgill Annemarie , Daly Luke , Jenkins Laura , Floyd Cameron , Martin Pierre-Etienne , Hallis Lydia Jane , King Ashley , Lee Martin
Published: January 2022

It was the first UK meteorite fall for 30 years. Here we gather the story of a remarkable community hunt involving pandemic precautions, social media spikes and some very lucky guinea pigs.
Chasing change: the lasting legacy of India's 1871 eclipse
Authors: Briers Megan , Billina Mixie , Kent Deborah
Published: January 2022

The total eclipse of the Sun on 12 December 1871 offered a timely test of new astrophysical methods – and a priceless opportunity for one Indian astronomer.
Music of the spheres
Authors: Meredith Nigel P , Cunio Kim , Scarborough Diana , Wynne Amanda D
Published: January 2022

The Sounds of Space Project harvests found sounds and signals from Earth and way beyond, and gathers them into evocative sonic compositions.
Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm
Authors: Baruzzo Giacomo , Cesaro Giulia , Di Camillo Barbara
Published: January 2022

Motivation

Recently, single-cell RNA-seq (scRNA-seq) data have been used to study cellular communication. Most bioinformatics methods infer only the intercellular signaling between groups of cells, mainly exploiting ligand–receptor expression levels. Only few methods consider the entire intercellular + intracellular signaling, mainly inferring lists/networks of signaling involved genes.

Results

Here, we present scSeqComm, a computational method to identify and quantify the evidence of ongoing intercellular and intracellular signaling from scRNA-seq data, and at the same time providing a functional characterization of the inferred cellular communication. The possibility to quantify the evidence of ongoing communication assists the prioritization of the results, while the combined evidence of both intercellular and intracellular signaling increase the reliability of inferred communication. The application to a scRNA-seq dataset of tumor microenvironment, the agreement with independent bioinformatics analysis, the validation using spatial transcriptomics data and the comparison with state-of-the-art intercellular scoring schemes confirmed the robustness and reliability of the proposed method.

Availability and implementation

scSeqComm R package is freely available at https://gitlab.com/sysbiobig/scseqcomm and https://sysbiobig.dei.unipd.it/software/#scSeqComm. Submitted software version and test data are available in Zenodo, at https://dx.doi.org/10.5281/zenodo.5833298.

Supplementary information

Supplementary data are available at Bioinformatics online.
How resource sharing resists scarcity: the role of cognitive empathy and its neurobiological mechanisms
Authors: Cui Fang , Huang Xiaoxuan , Jing Yiming , Luo Yue-jia , Liu Jie , Gu Ruolei
Published: January 2022

Resource scarcity challenges individuals’ willingness to share limited resources with other people. Still, lots of field studies and laboratory experiments have shown that sharing behaviors do not disappear under scarcity. Rather, some individuals are willing to share their scarce resources with others in a similar way as when the resource is abundant, which is crucial for the maintenance and development of human society. Here, we designed a novel paradigm in which subjects decided whether (and how much) to share an amount of “relieving resources” for counteracting unpleasant noises, which mimics real-life situations that people cost their own resources to help others escape from adversity. Overall, the robustness of resource sharing under scarcity was positively correlated with individual level of the cognitive component of empathy across two independent experiments. Resource insufficiency modulated the activations of several brain regions (including the TPJ, mPFC, and PCC) as well as the functional connection (from the rTPJ to the mPFC) within the mentalizing brain network, but the modulatory effect decreased as a function of cognitive empathy. We also applied the administration of oxytocin and found significant effects on sharing behavior among individuals with a higher level of cognitive empathy, but not their low-level counterparts. These findings highlight the importance of empathy to resource sharing under scarcity and explain the underlying neurobiological mechanisms.
Rapid Detection and Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Variant in a Returning Traveler
Authors: Sexton Mary Elizabeth , Waggoner Jesse J , Carmola Ludy R , Nguyen Phuong Vi , Wang Ethan , Khosravi Dara , Taz Azmain , Arthur Robert A , Patel Mit , Edara Venkata Viswanadh , Foster Stephanie L , Moore Kathryn M , Gagne Matthew , Roberts-Torres Jesmine , Henry Amy R , Godbole Sucheta , Douek Daniel C , Rouphael Nadine , Suthar Mehul S , Piantadosi Anne
Published: January 2022

We describe rapid detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant using targeted spike single-nucleotide polymorphism polymerase chain reaction and viral genome sequencing. This case occurred in a fully vaccinated and boosted returning traveler with mild symptoms who was identified through community surveillance rather than clinical care.
New Meet-in-the-Middle Attacks on FOX Block Cipher
Authors: Dong Xiaoli , Wei Yongzhuang , Gao Wen , Chen Jie
Published: January 2022

FOX block cipher was designed with a Lai–Massey scheme, in which the round function uses the Substitution-Permutation-Substitution structure. A meet-in-the-middle (MITM) attack is one of the most important issues for the security of the block cipher, which consists of a precomputation phase for constructing a distinguisher and an online phase for key recovery. This paper studies the MITM attacks against FOX. The first MITM distinguishers of 5-round FOX64, 7-round FOX64-256 and 5-round FOX128 are presented when using the differential enumeration technique with truncated differential characteristics. Then, based on these distinguishers, the attacks for key recovery on 7-round FOX64, 11-round FOX64-256 and 7-round FOX128 are presented with the state-test and state-search techniques. It is shown that the attack on 11-round FOX64-256 is proposed for the first time; attacks on 7-round FOX64 and 7-round FOX128 can be improved with lower time and memory complexities compared with the currently known attacks.
Impact of baseline renal dysfunction on cardiac outcomes and end-stage renal disease in heart failure patients with mitral regurgitation: the COAPT trial
Authors: Beohar Nirat , Ailawadi Gorav , Kotinkaduwa Lak N , Redfors Björn , Simonato Matheus , Zhang Zixuan , Morgan Loren Garrison , Escolar Esteban , Kar Saibal , Lim David Scott , Mishell Jacob M , Whisenant Brian K , Abraham William T , Lindenfeld JoAnn , Mack Michael J , Stone Gregg W
Published: January 2022

Aims

Baseline renal dysfunction (RD) adversely impacts outcomes among patients with heart failure (HF) and severe secondary mitral regurgitation (MR). Heart failure and MR, in turn, accelerate progression to end-stage renal disease (ESRD), worsening prognosis. We sought to determine the impact of RD in HF patients with severe MR and the impact of transcatheter mitral valve repair (TMVr) on new-onset ESRD and the need for renal replacement therapy (RRT).

Methods and results

The COAPT trial randomized 614 patients with HF and severe MR to MitraClip plus guideline-directed medical therapy (GDMT) vs. GDMT alone. Patients were stratified into three RD subgroups based on baseline estimated glomerular filtration rate (eGFR, mL/min/1.73 m2): none (≥60), moderate (30–60), and severe (<30). End-stage renal disease was defined as eGFR <15 mL/min/1.73 m2 or RRT. The 2-year rates of all-cause death or HF hospitalization (HFH), new-onset ESRD, and RRT according to RD and treatment were assessed. Baseline RD was present in 77.0% of patients, including 23.8% severe RD, 6.0% ESRD, and 5.2% RRT. Worse RD was associated with greater 2-year risk of death or HFH (none 45.3%; moderate 53.9%; severe 69.2%; P < 0.0001). MitraClip vs. GDMT alone improved outcomes regardless of RD (P  interaction = 0.62) and reduced new-onset ESRD [2.9 vs. 8.1%, hazard ratio (HR) 0.34, 95% confidence interval (CI) 0.15–0.76, P = 0.008] and the need for new RRT (2.5 vs. 7.4%, HR 0.33, 95% CI 0.14–0.78, P = 0.011).

Conclusion

Baseline RD was common in the HF patients with severe MR enrolled in COAPT and strongly predicted 2-year death and HFH. MitraClip treatment reduced new-onset ESRD and the need for RRT, contributing to the improved prognosis after TMVr.
One-year incidence of sexual harassment and the contribution to poor mental health in the adult general population
Authors: Östergren Per-Olof , Canivet Catarina , Agardh Anette
Published: January 2022

Background

Sexual harassment (SH) has been highlighted as an important determinant for mental health. The aims of this study were to describe SH in terms of cumulative 1-year incidence, exposed groups, types of perpetrators and settings, and to measure the association between SH and poor mental well-being.

Methods

Data from two waves of the Scania Public Health Cohort Study, comprising 7759 randomly recruited individuals above 18 years. Exposure to SH was measured by an instrument that also recorded place of exposure and type of perpetrator. Poor mental well-being was assessed by General Health Questionnaire (GHQ)-12, 36-Item Short Form Health Survey questionnaire (SF-36) (mental health module) and self-reported use of prescribed psychotropic medication. Logistic regression was used for multivariate analyses.

Results

The cumulative 1-year incidence of SH was six times greater among women, the highest figure (17.5%) was noted for women 18–34 years of age. No difference was noted regarding educational level or country of origin. Public places, including public transportation, and unknown offenders were the most frequently reported setting of SH for both genders. Exposure to SH was associated with a doubled risk for low mental well-being, according to all three outcome definitions, and after adjustment for mental health 6 years earlier. Female gender was related to greater vulnerability to SH exposure concerning GHQ-12 and SF-36. The Population Attributable Fraction for poor mental health was calculated to 13% for women 34 years and younger.

Conclusion

The results of this study make SH an important issue for gender policy as well as for public health policy and intervention.
Apple microbial communities and differences between two main Chinese producing regions
Authors: Shen Youming , Zhang Jianyi , Nie Jiyun , Zhang Hui , Bacha Syed Asim Shah
Published: January 2022

Microbes on fresh apples are closely associated with fruit disease, preservation, and quality control. Investigation into the microbial communities on apples from different producing regions could reveal the microbial specificity and help disease prevention and quality control. In this paper, the apple surface microbes of 44 samples from two main Chinese apple-producing regions, Bohai Bay (BHB) and the Loess Plateau (LP), were investigated by sequencing fungal internal transcribed spacer and bacterial 16S rRNA hypervariable sequences. BHB and LP apples contained significantly different bacterial and fungal communities. BHB apples had a higher fungal diversity than LP apples. A total of 102 different fungal and bacterial taxonomies were obtained between apples from the two regions, in which 24 genera were predominant. BHB apples had higher phytopathogenic fungal genera, such as Tilletiopsis, Acremonium, Candida, and Phoma, indicating the higher phytopathogenic risks of apples from the humid climate of the BHB region. LP apples contained more bacterial genera identified as gut microbes, indicating the potential risks of contaminating apples with foodborne pathogens in the arid environment of the LP. This study highlighted the environment-oriented microbial specificity on apples from two main apple-producing regions, and provided a basis for further investigation.
Nutritional quality of different potassium efficiency types of vegetable soybean as affected by potassium nutrition
Authors: Liu Changkai , Wang Xue , Chen Heng , Xia Houyu , Tu Bingjie , Li Yansheng , Zhang Qiuying , Liu Xiaobing
Published: January 2022

Pot experiments were conducted in 2017, 2019, and 2020 to examine the effects of potassium nutrition on the nutritional components of vegetable soybeans with different K efficiency at immature and mature stages. Two vegetable soybean varieties with higher K efficiency and two varieties with lower K efficiency were studied in the low available K soil under the conditions of no K and normal K fertilization. The results indicated that almost all nutritional components in vegetable soybean were affected by K, genotypes, interannual differences, and their interactions. In general, no K fertilization increased protein and amino acid concentrations but decreased oil, soluble sugar, sucrose, K, Mg, and Fe concentrations in immature and mature vegetable soybean. The sensitivity of nutritional components to K nutrition differed among varieties. For instance, K high-efficiency varieties generally exhibited higher protein and amino acid concentrations without K application. K high-efficiency vegetable soybeans are low-K tolerance varieties to isoflavones. The results of this study provide insights for high yield and quality vegetable soybean breeding against soil K deficiency.
Occurrence and patterns of nutritional traits and polycyclic aromatic hydrocarbons (PAHs) in sea cucumber (Holothuria polii) tissues: benefits and risk for human health
Authors: Biandolino Francesca , Parlapiano Isabella , Spada Lucia , Di Leo Antonella , Calò Maria , Fanelli Giovanni , Prato Ermelinda , Giandomenico Santina
Published: January 2022

Objectives

The paper evaluates the benefit and risk for human health associated with consumption of sea cucumber Holothuria polii (H. polii) from Italian coasts (Central Mediterranean Sea).

Materials and Methods

Body wall (BW), internal tunic (ITu), muscle bands (MBs), alimentary canal (AC), gonad (Gd), and respiratory tree (RT) of H. polii were analyzed for proximate composition. Moreover, amino acids (AAs), fatty acids (FAs) and polycyclic aromatic hydrocarbons (PAHs) were determined with high-performance liquid chromatography coupled with ultraviolet-visible spectroscopy (UPLC UV/Vis), gas chromatography-flame ionization detector (GC-FID) and gas chromatography mass spectrometry (GC-MS), respectively.

Results

Differences in the contents of total amino acids (TAAs) occurred based on tissue and sex, with AC and MB of female and Gd of male showing higher contents (range 47.8–60.2 g/kg we weight (ww)). Glycine and glutamic acid were the most abundant. Polyunsaturated fatty acid (PUFA) was the major class of FAs and arachidonic acid and eicosapentenoic acid (EPA) were the predominant PUFA. n-3 PUFA showed higher content in Gd, AC, and RT, indicating higher quality. A favorable n-3/n-6 in the range of 1.04–1.67 was observed. PAHs showed values ranging from 23 to 207 µg/kg ww with the highest levels in Gd and AC tissues and the lower in BW. Benzo[a]pyrene, the most toxic compound, was detected in all tissues, of both sexes, at levels of 1.5–18 µg/kg ww.

Conclusion

All tissues of H. polii, although with differences among them, are valuable food and can contribute for a healthy diet. Excess cancer risk (CR) values for Gd and AC tissues were above the considerable CR threshold of one in 10 000 established by the United States Environmental Protection Agency (USEPA) for high ingestion rate of this seafood.
Effect of FOXO3 and Air Pollution on Cognitive Function: A Longitudinal Cohort Study of Older Adults in China From 2000 to 2014
Authors: Ji John S , Liu Linxin , Zeng Yi , Yan Lijing L
Published: January 2022

Forkhead Box O 3 (FOXO3) genotype is strongly associated with human longevity and may be protective against neurodegeneration. Air pollution is a risk factor for cognitive decline and dementia. We aimed to study the individual and combined effects of FOXO3 and air pollution on cognitive function in a large prospective cohort with up to 14 years of follow-up. We measured cognitive function and impairment using the Mini-Mental State Examination (MMSE). We used tagging SNPs rs2253310, rs2802292, and rs4946936 to identify the FOXO3 gene, of which roughly half of the population had the longevity-associated polymorphism. We matched annual average fine particulate matter (PM2.5) concentrations within a 1 km2 grid. We conducted cross-sectional and longitudinal analyses using multivariable linear and logistic regression models and generalized estimating equations. At baseline, carriers of the longevity-associated homozygous minor alleles of FOXO3 SNPs had a higher MMSE score than the carriers of homozygous major alleles. In the longitudinal follow-up, carriers of FOXO3 homozygous minor alleles had lower odds of cognitive impairment compared with noncarriers. Higher PM2.5 was associated with a lower MMSE score and higher odds of cognitive impairment. The positive effects of FOXO3 were the strongest in females, older people, and residents in areas with lower air pollution.
Active ocean–continent transform margins: seismic investigation of the Cayman Trough-Swan Island ridge-transform intersection
Authors: Peirce C , Grevemeyer I , Hayman N W , Van Avendonk H J A
Published: January 2022

The southern boundary of the Cayman Trough in the Caribbean is marked by the Swan Islands transform fault (SITF), which also represents the ocean–continent transition of the Honduras continental margin. This is one of the few places globally where a transform continental margin is currently active. The CAYSEIS experiment acquired an ∼165-km-long seismic refraction and gravity profile (P01) running across this transform margin, and along the ridge-axis of the Mid-Cayman Spreading Centre (MCSC) to the north. This profile reveals not only the crustal structure of an actively evolving transform continental margin, that juxtaposes Mesozoic-age continental crust to the south against zero-age ultraslow spread oceanic crust to the north, but also the nature of the crust and uppermost mantle beneath the ridge-transform intersection (RTI). The traveltimes of arrivals recorded by ocean-bottom seismographs (OBSs) deployed along-profile have been inverse and forward modelled, in combination with gravity modelling, to reveal an ∼25-km-thick continental crust that has been continuously thinned over a distance of ∼65 km to ∼10 km adjacent to the SITF, where it is juxtaposed against ∼3–4-km-thick oceanic crust. This thinning is primarily accommodated within the lower crust. Since Moho reflections are only sparsely observed, and, even then, only by a few OBSs located on the continental margin, the 7.5 km s–1 velocity contour is used as a proxy to locate the crust–mantle boundary along-profile. Along the MCSC, the crust–mantle boundary appears to be a transition zone, at least at the seismic wavelengths used for CAYSEIS data acquisition. Although the traveltime inversion only directly constrains the upper crust at the SITF, gravity modelling suggests that it is underlain by a higher density (>3000 kg m–3) region spanning the width (∼15 km) of its bathymetric expression, that may reflect a broad region of metasomatism, mantle hydration or melt-depleted lithospheric mantle. At the MCSC ridge-axis to the north, the oceanic crust appears to be forming in zones, where each zone is defined by the volume of its magma supply. The ridge tip adjacent to the SITF is currently in a magma rich phase of accretion. However, there is no evidence for melt leakage into the transform zone. The width and crustal structure of the SITF suggests its motion is currently predominantly orthogonal to spreading. Comparison to CAYSEIS Profile P04, located to the west and running across-margin and through 10 Ma MCSC oceanic crust, suggests that, at about this time, motion along the SITF had a left-lateral transtensional component, that accounts for its apparently broad seabed appearance westwards.
Oral Contraceptive Use in BRCA1 and BRCA2 Mutation Carriers: Absolute Cancer Risks and Benefits
Authors: Schrijver Lieske H , Mooij Thea M , Pijpe Anouk , Sonke Gabe S , Mourits Marian J E , Andrieu Nadine , Antoniou Antonis C , Easton Douglas F , Engel Christoph , Goldgar David , John Esther M , Kast Karin , Milne Roger L , Olsson Håkan , Phillips Kelly-Anne , Terry Mary Beth , Hopper John L , van Leeuwen Flora E , Rookus Matti A
Published: January 2022

Background

To help BRCA1 and 2 mutation carriers make informed decisions regarding use of combined-type oral contraceptive preparation (COCP), absolute risk-benefit estimates are needed for COCP-associated cancer.

Methods

For a hypothetical cohort of 10 000 women, we calculated the increased or decreased cumulative incidence of COCP-associated (breast, ovarian, endometrial) cancer, examining 18 scenarios with differences in duration and timing of COCP use, uptake of prophylactic surgeries, and menopausal hormone therapy.

Results

COCP use initially increased breast cancer risk and decreased ovarian and endometrial cancer risk long term. For 10 000 BRCA1 mutation carriers, 10 years of COCP use from age 20 to 30 years resulted in 66 additional COCP-associated cancer cases by the age of 35 years, in addition to 625 cases expected for never users. By the age of 70 years such COCP use resulted in 907 fewer cancer cases than the expected 9093 cases in never users. Triple-negative breast cancer estimates resulted in 196 additional COCP-associated cases by age 40 years, in addition to the 1454 expected. For 10 000 BRCA2 mutation carriers using COCP from age 20 to 30 years, 80 excess cancer cases were estimated by age 40 years in addition to 651 expected cases; by the age of 70 years, we calculated 382 fewer cases compared with the 6156 cases expected. The long-term benefit of COCP use diminished after risk-reducing bilateral salpingo-oophorectomy followed by menopausal hormone therapy use.

Conclusion

Although COCP use in BRCA1 and BRCA2 mutation carriers initially increases breast, ovarian, and endometrial cancer risk, it strongly decreases lifetime cancer risk. Risk-reducing bilateral salpingo-oophorectomy and menopausal hormone therapy use appear to counteract the long-term COCP-benefit.
Are regional precipitation–productivity relationships robust to decadal-scale dry period?
Authors: Hu Zhongmin , Liang Minqi , Knapp Alan , Xia Jianyang , Yuan Wenping
Published: January 2022

Precipitation (PPT) is the primary climatic determinant of plant growth and aboveground net primary productivity (ANPP) for many of the world’s major terrestrial ecosystems. Thus, relationships between PPT and productivity can provide insight into how changes in climate may alter ecosystem functions globally. Spatial PPT–ANPP relationships for grasslands are found remarkably similar around the world, but whether and how they change during periods of extended climatic anomalies remain unknown. Here, we quantified how regional-scale PPT-ANPP relationships vary between an extended wet and a dry period by taking advantage of a 35-year record of PPT and NDVI (as a surrogate for ANPP) at 1700 sites in the temperate grasslands of northern China. We found a sharp decrease in the strength of the spatial PPT–ANPP relationship during an 11-year period of below average PPT. We attributed the collapse of this relationship to asynchrony in the responses of different grassland types to this decadal period of increased aridity. Our results challenge the robustness of regional PPT–productivity if aridity in grasslands is increased globally by climate change.
Mock catalogues of emission-line galaxies based on the local mass density in dark-matter only simulations
Authors: Osato Ken , Nishimichi Takahiro , Takada Masahiro
Published: January 2022

The high-precision measurement of spatial clustering of emission-line galaxies (ELGs) is a primary objective for upcoming cosmological spectroscopic surveys. The source of strong emission of ELGs is nebular emission from surrounding ionized gas irradiated by massive short-lived stars in star-forming galaxies. As a result, ELGs are more likely to reside in newly formed haloes and this leads to a non-linear relation between ELG number density and matter density fields. In order to estimate the covariance matrix of cosmological observables, it is essential to produce many independent realizations to simulate ELG distributions for large survey volumes. To this end, we present a novel and fast scheme to populate ELGs in dark-matter only N-body simulations based on local density field. This method enables fast production of mock ELG catalogues suitable for verifying analysis methods and quantifying observational systematics in upcoming spectroscopic surveys and can populate ELGs in moderately high-density regions even though the halo structure cannot be resolved due to low resolution. The power spectrum of simulated ELGs is consistent with results of hydrodynamical simulations up to fairly small scales ($\lesssim 1 h \, \mathrm{Mpc}^{-1}$), and the simulated ELGs are more likely to be found in filamentary structures, which is consistent with results of semi-analytic and hydrodynamical simulations. Furthermore, we address the redshift-space power spectrum of simulated ELGs. The measured multipole moments of simulated ELGs clearly exhibit a weaker Finger-of-God effect than those of matter due to infalling motions towards halo centre, rather than random virial motions inside haloes.
Strong conformity and assembly bias: towards a physical understanding of the galaxy–halo connection in SDSS clusters
Authors: Zu Ying , Song Yunjia , Shao Zhiwei , Chen Xiaokai , Zheng Yun , Gao Hongyu , Yu Yu , Shan Huanyuan , Jing Yipeng
Published: January 2022

Understanding the physical connection between cluster galaxies and massive haloes is key to mitigating systematic uncertainties in next-generation cluster cosmology. We develop a novel method to infer the level of conformity between the stellar mass of the bright central galaxies (BCGs) $M_*^{\texttt {BCG}}$ and the satellite richness λ, defined as their correlation coefficient ρcc at fixed halo mass, using the abundance and weak lensing of SDSS clusters as functions of $M_*^{\texttt {BCG}}$ and λ. We detect a halo mass-dependent conformity as ρcc = 0.60 + 0.08ln (Mh/3 × 1014h−1M⊙). The strong conformity successfully resolves the ‘halo mass equality’ conundrum discovered in Zu et al. – when split by $M_*^{\texttt {BCG}}$ at fixed λ, the low- and high-$M_*^{\texttt {BCG}}$ clusters have the same average halo mass despite having a 0.34-dex discrepancy in average $M_*^{\texttt {BCG}}$. On top of the best-fitting conformity model, we develop a cluster assembly bias (AB) prescription calibrated against the CosmicGrowth simulation and build a conformity + AB model for the cluster weak lensing measurements. Our model predicts that with an ${\sim }20{{\ \rm per\ cent}}$ lower halo concentration c, the low-$M_*^{\texttt {BCG}}$ clusters are ${\sim }10{{\ \rm per\ cent}}$ more biased than the high-$M_*^{\texttt {BCG}}$ systems, in good agreement with the observations. We also show that the observed conformity and assembly bias are unlikely due to projection effects. Finally, we build a toy model to argue that while the early-time BCG–halo co-evolution drives the $M_*^{\texttt {BCG}}$-c correlation, the late-time dry merger-induced BCG growth naturally produces the $M_*^{\texttt {BCG}}$-λ conformity despite the well-known anticorrelation between λ and c. Our method paves the path towards simultaneously constraining cosmology and cluster formation with future cluster surveys.
Comprehensive profiling of mRNA splicing indicates that GC content signals altered cassette exon inclusion in Ewing sarcoma
Authors: Graham Garrett T , Selvanathan Saravana P , Zöllner Stefan K , Stahl Emily , Shlien Adam , Caplen Natasha J , Üren Aykut , Toretsky Jeffrey A
Published: January 2022

Ewing sarcoma (EwS) is a small round blue cell tumor and is the second most frequent pediatric bone cancer. 85% of EwS tumors express the fusion oncoprotein EWS-FLI1, the product of a t(11;22) reciprocal translocation. Prior work has indicated that transcription regulation alone does not fully describe the oncogenic capacity of EWS-FLI1, nor does it provide an effective means to stratify patient tumors. Research using EwS cell lines and patient samples has suggested that EWS-FLI1 also disrupts mRNA biogenesis. In this work we both describe the underlying characteristics of mRNA that are aberrantly spliced in EwS tumor samples as well as catalogue mRNA splicing events across other pediatric tumor types. Here, we also use short- and long-read sequencing to identify cis-factors that contribute to splicing profiles we observe in Ewing sarcoma. Our analysis suggests that GC content upstream of cassette exons is a defining factor of mRNA splicing in EwS. We also describe specific splicing events that discriminate EwS tumor samples from the assumed cell of origin, human mesenchymal stem cells derived from bone marrow (hMSC-BM). Finally, we identify specific splicing factors PCBP2, RBMX, and SRSF9 by motif enrichment and confirm findings from tumor samples in EwS cell lines.
Adaptive and powerful microbiome multivariate association analysis via feature selection
Authors: Banerjee Kalins , Chen Jun , Zhan Xiang
Published: January 2022

The important role of human microbiome is being increasingly recognized in health and disease conditions. Since microbiome data is typically high dimensional, one popular mode of statistical association analysis for microbiome data is to pool individual microbial features into a group, and then conduct group-based multivariate association analysis. A corresponding challenge within this approach is to achieve adequate power to detect an association signal between a group of microbial features and the outcome of interest across a wide range of scenarios. Recognizing some existing methods’ susceptibility to the adverse effects of noise accumulation, we introduce the Adaptive Microbiome Association Test (AMAT), a novel and powerful tool for multivariate microbiome association analysis, which unifies both blessings of feature selection in high-dimensional inference and robustness of adaptive statistical association testing. AMAT first alleviates the burden of noise accumulation via distance correlation learning, and then conducts a data-adaptive association test under the flexible generalized linear model framework. Extensive simulation studies and real data applications demonstrate that AMAT is highly robust and often more powerful than several existing methods, while preserving the correct type I error rate. A free implementation of AMAT in R computing environment is available at https://github.com/kzb193/AMAT.
Prediction and analysis of functional RNA structures within the integrative genomics viewer
Authors: Rouse Warren B , Andrews Ryan J , Booher Nicholas J , Wang Jibo , Woodman Michael E , Dow Ernst R , Jessop Theodore C , Moss Walter N
Published: January 2022

In recent years, interest in RNA secondary structure has exploded due to its implications in almost all biological functions and its newly appreciated capacity as a therapeutic agent/target. This surge of interest has driven the development and adaptation of many computational and biochemical methods to discover novel, functional structures across the genome/transcriptome. To further enhance efforts to study RNA secondary structure, we have integrated the functional secondary structure prediction tool ScanFold, into IGV. This allows users to directly perform structure predictions and visualize results—in conjunction with probing data and other annotations—in one program. We illustrate the utility of this new tool by mapping the secondary structural landscape of the human MYC precursor mRNA. We leverage the power of vast ‘omics’ resources by comparing individually predicted structures with published data including: biochemical structure probing, RNA binding proteins, microRNA binding sites, RNA modifications, single nucleotide polymorphisms, and others that allow functional inferences to be made and aid in the discovery of potential drug targets. This new tool offers the RNA community an easy to use tool to find, analyze, and characterize RNA secondary structures in the context of all available data, in order to find those worthy of further analyses.
Cigarette Prices and Smoking Among Youth in 16 African Countries: Evidence From the Global Youth Tobacco Survey
Authors: Filby Samantha , van Walbeek Corne
Published: January 2022

Introduction

African countries have among the lowest excise taxes in the world. This paper provides new evidence on the association between cigarette prices and youth smoking in 16 African countries.

Aims and Methods

We use Global Youth Tobacco Survey (GYTS) cross-country data from approximately 67 500 participants. The relationship between prices and youth smoking in Africa is estimated using probit models for smoking participation and generalized linear models for conditional cigarette demand. Each model is estimated using local-brand and foreign-brand cigarette prices.

Results

Higher prices are associated with lower demand across African countries, for both smoking prevalence and the intensity of cigarette consumption by smokers. The estimated price elasticity of participation is −0.70 [95% CI: −1.28 to −0.12] for local-brand cigarettes and −0.71 [95% CI: −0.98 to −0.44] for foreign-brand cigarettes. The price elasticity of conditional cigarette demand is −0.44 [95% CI: −0.76 to −0.12] for local brands and −0.75 [95% CI: −0.96 to −0.53] for foreign brands. The total price elasticity of demand for youth in our sample is −1.14 for local brands and −1.46 for foreign brands.

Conclusions

Higher cigarette prices significantly decrease the likelihood of smoking and decrease the intensity of cigarette consumption among African youths. Increases in the excise tax that increase the retail price of cigarettes will play an important role in reducing youth tobacco use on the continent. Governments are encouraged to increase excise taxes in order to improve public health.

Implications

Evidence on the association between cigarette prices and youth smoking in African countries is limited. The Global Youth Tobacco Survey (GYTS) was first introduced in 1999. In 2012, the Centers for Disease Control and Prevention revised the GYTS questionnaire, which removed some questions and introduced new questions into the survey. To the best of our knowledge, there are no published estimates of the relationship between cigarette prices and demand that have used this more recent individual-level GYTS data for African countries. In conducting this analysis, we add to the limited literature on the association between cigarette prices and youth smoking in Africa.
Possible role of type 1 and type 2 taste receptors on obesity-induced inflammation
Authors: Koh Gar Yee , Rowling Matthew J , Pritchard Samantha K
Published: January 2022

Obesity is characterized by chronic low-grade inflammation that could lead to other health complications, such as cardiovascular disease, diabetes, and various forms of cancer. Emerging evidence has shown that taste perception is altered during the development of obesity. Moreover, suppression of taste receptor or taste signaling molecules potentiate the inflammatory response, and the progression of inflammation attenuates the expression of taste receptors in vivo. Together, these findings suggest a possible interplay between taste signaling and inflammation. This review summarizes the interactions between type 1 (T1Rs) and type 2 taste receptors (T2Rs) and inflammation, as well as the impact of obesity on T1R- and T2R-mediated signaling. Furthermore, we evaluate the possible role that taste receptors play in regulating the inflammatory response during obesity as a therapeutic target to prevent the progression of comorbidities associated with obesity.
Dominant Currencies: How Firms Choose Currency Invoicing and Why it Matters
Authors: Amiti Mary , Itskhoki Oleg , Konings Jozef
Published: January 2022

We analyze how firms choose the currency of invoicing and the implications of this choice for exchange rate pass-through into export prices and quantities. Using a new data set for Belgian firms, we find currency invoicing to be an active firm-level decision, shaped by the firm’s size, exposure to imported inputs, and the currency choices of its competitors. Our results show that a firm’s currency choice, in turn, has a direct causal effect on the exchange rate pass-through into prices and quantities. Moreover, the differential price response of similar firms that invoice in different currencies is large, persists beyond a one-year horizon, and gradually wanes in the long run. This results in allocative expenditure-switching effects on export quantities, which build up over time, suggesting a role for quantity adjustment frictions in addition to price stickiness. Our findings shed light on the mechanisms that make or break a dominant currency and the consequences it has for the international transmission of shocks.
Does Retirement Change What Makes Us Satisfied With Life? An Examination of Response Shift With a Matched Control Group Design
Authors: Wetzel Martin , Wünsche Jenna , Spuling Svenja M
Published: January 2022

Research has shown that life satisfaction depends on a person’s resources and that retirement is associated with resource gains and losses. We examine if these resources contribute equally to life satisfaction before and after the retirement transition. Coming from the psychological concept of response shifts, we conceptualize an adjustment process to major life changes in which also the association between different resources and life satisfaction could be subject of change with retirement. Data from the English Longitudinal Study of Ageing (2004–2016, every 2 years) were used to study people who retired over the course of 2 consecutive waves. Using propensity score matching, we identified n = 991 retirees and a matched control group of n = 991 people with similar sociodemographic characteristics but who were continuously working. We then used a seemingly unrelated regression model to examine how the association between life satisfaction and economic (income, assets), personal (morbidity, functional limitations, club membership), and social-relational resources (network size, partner, parenthood, grandparenthood) changed from the pre- to postretirement wave. Retirement was associated with a slight increase in life satisfaction and only moderate to minor declines in income and club memberships. We found retirement-related changes in the predictor strength for financial resources (i.e., decline for income, increase for assets) but not for the other resources. In sum, the study provides some evidence that retirees reprioritize the importance of economic resources only for their overall life satisfaction at retirement. We discuss the findings in light of (economic) social inequality which points to potential for further research.