bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

SUMMARY
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 (&gt;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

Abstract

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

Abstract
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

ABSTRACT
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

ABSTRACT
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

ABSTRACTEwing 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

ABSTRACTThe 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

ABSTRACT
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.