bluuebunny/crossref_metadata_2025_split huggingface dataset:
An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression
Authors: Shen Ting , Ni Ting , Chen Jiaxuan , Chen Haitao , Ma Xiaopin , Cao Guangwen , Wu Tianzhi , Xie Haisheng , Zhou Bin , Wei Gang , Saiyin Hexige , Shen Suqin , Yu Peng , Xiao Qianyi , Liu Hui , Gao Yuzheng , Long Xidai , Yin Jianhua , Guo Yanfang , Wu Jiaxue , Wei Gong-Hong , Hou Jinlin , Jiang De-Ke 
Published: March 2022

AbstractMost cancer causal variants are found in gene regulatory elements, e.g., enhancers. However, enhancer variants predisposing to hepatocellular carcinoma (HCC) remain unreported. Here we conduct a genome-wide survey of HCC-susceptible enhancer variants through a three-stage association study in 11,958 individuals and identify rs73613962 (T > G) within the intronic region of PRMT7 at 16q22.1 as a susceptibility locus of HCC (OR = 1.41, P = 6.02 × 10−10). An enhancer dual-luciferase assay indicates that the rs73613962-harboring region has allele-specific enhancer activity. CRISPR-Cas9/dCas9 experiments further support the enhancer activity of this region to regulate PRMT7 expression. Mechanistically, transcription factor HNF4A binds to this enhancer region, with preference to the risk allele G, to promote PRMT7 expression. PRMT7 upregulation contributes to in vitro, in vivo, and clinical HCC-associated phenotypes, possibly by affecting the p53 signaling pathway. This concept of HCC pathogenesis may open a promising window for HCC prevention/treatment.
Mercury evidence for combustion of organic-rich sediments during the end-Triassic crisis
Authors: Shen Jun , Yin Runsheng , Algeo Thomas J. , Svensen Henrik H. , Schoepfer Shane D. 
Published: March 2022

AbstractThe sources of isotopically light carbon released during the end-Triassic mass extinction remain in debate. Here, we use mercury (Hg) concentrations and isotopes from a pelagic Triassic–Jurassic boundary section (Katsuyama, Japan) to track changes in Hg cycling. Because of its location in the central Panthalassa, far from terrigenous runoff, Hg enrichments at Katsuyama record atmospheric Hg deposition. These enrichments are characterized by negative mass independent fractionation (MIF) of odd Hg isotopes, providing evidence of their derivation from terrestrial organic-rich sediments (Δ199Hg < 0‰) rather than from deep-Earth volcanic gases (Δ199Hg ~ 0‰). Our data thus provide evidence that combustion of sedimentary organic matter by igneous intrusions and/or wildfires played a significant role in the environmental perturbations accompanying the event. This process has a modern analog in anthropogenic combustion of fossil fuels from crustal reservoirs.
A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy
Authors: Paris Josephine R. , Whiting James R. , Daniel Mitchel J. , Ferrer Obiol Joan , Parsons Paul J. , van der Zee Mijke J. , Wheat Christopher W. , Hughes Kimberly A. , Fraser Bonnie A. 
Published: March 2022

AbstractMale colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis.
The flavonoid corylin exhibits lifespan extension properties in mouse
Authors: Wang Tong-Hong , Tseng Wei-Che , Leu Yann-Lii , Chen Chi-Yuan , Lee Wen-Chih , Chi Ying-Chih , Cheng Shu-Fang , Lai Chun-Yu , Kuo Chen-Hsin , Yang Shu-Ling , Yang Sien-Hung , Shen Jiann-Jong , Feng Chun-Hao , Wu Chih-Ching , Hwang Tsong-Long , Wang Chia-Jen , Wang Shu-Huei , Chen Chin-Chuan 
Published: March 2022

AbstractIn the long history of traditional Chinese medicine, single herbs and complex formulas have been suggested to increase lifespan. However, the identification of single molecules responsible for lifespan extension has been challenging. Here, we collected a list of traditional Chinese medicines with potential longevity properties from pharmacopeias. By utilizing the mother enrichment program, we systematically screened these traditional Chinese medicines and identified a single herb, Psoralea corylifolia, that increases lifespan in Saccharomyces cerevisiae. Next, twenty-two pure compounds were isolated from Psoralea corylifolia. One of the compounds, corylin, was found to extend the replicative lifespan in yeast by targeting the Gtr1 protein. In human umbilical vein endothelial cells, RNA sequencing data showed that corylin ameliorates cellular senescence. We also examined an in vivo mammalian model, and found that corylin extends lifespan in mice fed a high-fat diet. Taken together, these findings suggest that corylin may promote longevity.
Predictors of adherence to public health behaviors for fighting COVID-19 derived from longitudinal data
Authors: Schumpe Birga M. , Van Lissa Caspar J. , Bélanger Jocelyn J. , Ruggeri Kai , Mierau Jochen , Nisa Claudia F. , Molinario Erica , Gelfand Michele J. , Stroebe Wolfgang , Agostini Maximilian , Gützkow Ben , Jeronimus Bertus F. , Kreienkamp Jannis , Kutlaca Maja , Lemay Edward P. , Reitsema Anne Margit , vanDellen Michelle R. , Abakoumkin Georgios , Abdul Khaiyom Jamilah Hanum , Ahmedi Vjollca , Akkas Handan , Almenara Carlos A. , Atta Mohsin , Bagci Sabahat Cigdem , Basel Sima , Berisha Kida Edona , Bernardo Allan B. I. , Buttrick Nicholas R. , Chobthamkit Phatthanakit , Choi Hoon-Seok , Cristea Mioara , Csaba Sara , Damnjanović Kaja , Danyliuk Ivan , Dash Arobindu , Di Santo Daniela , Douglas Karen M. , Enea Violeta , Faller Daiane , Fitzsimons Gavan J. , Gheorghiu Alexandra , Gómez Ángel , Hamaidia Ali , Han Qing , Helmy Mai , Hudiyana Joevarian , Jiang Ding-Yu , Jovanović Veljko , Kamenov Zeljka , Kende Anna , Keng Shian-Ling , Kieu Tra Thi Thanh , Koc Yasin , Kovyazina Kamila , Kozytska Inna , Krause Joshua , Kruglanski Arie W. , Kurapov Anton , Lantos Nóra Anna , Lesmana Cokorda Bagus J. , Louis Winnifred R. , Lueders Adrian , Malik Najma Iqbal , Martinez Anton P. , McCabe Kira O. , Mehulić Jasmina , Milla Mirra Noor , Mohammed Idris , Moyano Manuel , Muhammad Hayat , Mula Silvana , Muluk Hamdi , Myroniuk Solomiia , Najafi Reza , Nyúl Boglárka , O’Keefe Paul A. , Olivas Osuna Jose Javier , Osin Evgeny N. , Park Joonha , Pica Gennaro , Pierro Antonio , Rees Jonas H. , Resta Elena , Rullo Marika , Ryan Michelle K. , Samekin Adil , Santtila Pekka , Sasin Edyta , Selim Heyla A. , Stanton Michael Vicente , Sultana Samiah , Sutton Robbie M. , Tseliou Eleftheria , Utsugi Akira , van Breen Jolien A. , Van Veen Kees , Vázquez Alexandra , Wollast Robin , Yeung Victoria Wai-Lan , Zand Somayeh , Žeželj Iris Lav , Zheng Bang , Zick Andreas , Zúñiga Claudia , Leander N. Pontus 
Published: March 2022

AbstractThe present paper examines longitudinally how subjective perceptions about COVID-19, one’s community, and the government predict adherence to public health measures to reduce the spread of the virus. Using an international survey (N = 3040), we test how infection risk perception, trust in the governmental response and communications about COVID-19, conspiracy beliefs, social norms on distancing, tightness of culture, and community punishment predict various containment-related attitudes and behavior. Autoregressive analyses indicate that, at the personal level, personal hygiene behavior was predicted by personal infection risk perception. At social level, social distancing behaviors such as abstaining from face-to-face contact were predicted by perceived social norms. Support for behavioral mandates was predicted by confidence in the government and cultural tightness, whereas support for anti-lockdown protests was predicted by (lower) perceived clarity of communication about the virus. Results are discussed in light of policy implications and creating effective interventions.
Efficacy of antimicrobial and anti-viral coated air filters to prevent the spread of airborne pathogens
Authors: Watson Rowan , Oldfield Morwenna , Bryant Jack A. , Riordan Lily , Hill Harriet J. , Watts Julie A. , Alexander Morgan R. , Cox Michael J. , Stamataki Zania , Scurr David J. , de Cogan Felicity 
Published: March 2022

AbstractThe COVID-19 pandemic has demonstrated the real need for mechanisms to control the spread of airborne respiratory pathogens. Thus, preventing the spread of disease from pathogens has come to the forefront of the public consciousness. This has brought an increasing demand for novel technologies to prioritise clean air. In this study we report on the efficacy of novel biocide treated filters and their antimicrobial activity against bacteria, fungi and viruses. The antimicrobial filters reported here are shown to kill pathogens, such as Candida albicans, Escherichia coli and MRSA in under 15 min and to destroy SARS-CoV-2 viral particles in under 30 s following contact with the filter. Through air flow rate testing, light microscopy and SEM, the filters are shown to maintain their structure and filtration function. Further to this, the filters are shown to be extremely durable and to maintain antimicrobial activity throughout the operational lifetime of the product. Lastly, the filters have been tested in field trials onboard the UK rail network, showing excellent efficacy in reducing the burden of microbial species colonising the air conditioning system.
Detection of germline variants in Brazilian breast cancer patients using multigene panel testing
Authors: Guindalini Rodrigo Santa Cruz , Viana Danilo Vilela , Kitajima João Paulo Fumio Whitaker , Rocha Vinícius Marques , López Rossana Verónica Mendoza , Zheng Yonglan , Freitas Érika , Monteiro Fabiola Paoli Mendes , Valim André , Schlesinger David , Kok Fernando , Olopade Olufunmilayo I. , Folgueira Maria Aparecida Azevedo Koike 
Published: March 2022

AbstractGenetic diversity of germline variants in breast cancer (BC) predisposition genes is unexplored in miscegenated populations, such those living in Latin America. We evaluated 1663 Brazilian BC patients, who underwent hereditary multigene panel testing (20–38 cancer susceptibility genes), to determine the spectrum and prevalence of pathogenic/likely pathogenic (P/LP) variants and variants of uncertain significance (VUS). Associations between P/LP variants and BC risk were estimated in a case–control analysis of BC patients and 18,919 Brazilian reference controls (RC). In total, 335 (20.1%) participants carried germline P/LP variants: 167 (10.0%) inBRCA1/2, 122 (7.3%) in BC actionable non-BRCA genes and 47 (2.8%) in candidate genes or other cancer predisposition genes. Overall, 354 distinctive P/LP variants were identified in 23 genes. The most commonly mutated genes were:BRCA1(27.4%),BRCA2(20.3%),TP53(10.5%), monoallelicMUTYH(9.9%),ATM(8.8%),CHEK2(6.2%) andPALB2(5.1%). The Brazilian variantTP53R337H (c.1010G>A, p.Arg337His), detected in 1.6% of BC patients and 0.1% of RC, was strongly associated with risk of BC, OR = 17.4 (95% CI: 9.4–32.1; p < 0.0001); monoallelicMUTYHvariants c.1187G>A and c.536A>G, detected in 1.2% (0.9% RC) and 0.8% (0.4% RC) of the patients, respectively, were not associated with the odds of BC, the former with OR = 1.4 (95% CI: 0.8–2.4; p = 0.29) and the latter with OR = 1.9 (95% CI: 0.9–3.9; p = 0.09). The overall VUS rate was 46.1% for the entire patient population. Concluding, the use of multigene panel testing almost doubled the identification of germline P/LP variants in clinically actionable predisposition genes in BC patients. In Brazil, special attention should be given toTP53P/LP variants.
Speed-up and slow-down of a quantum particle
Authors: de la Cal X. Gutiérrez , Pons M. , Sokolovski D. 
Published: March 2022

AbstractWe study non-relativistic propagation of Gaussian wave packets in one-dimensional Eckart potential, a barrier, or a well. In the picture used, the transmitted wave packet results from interference between the copies of the freely propagating state with different spatial shifts (delays), $$x'$$

x
′

, induced by the scattering potential. The Uncertainty Principle precludes relating the particle’s final position to the delay experienced in the potential, except in the classical limit. Beyond this limit, even defining an effective range of the delay is shown to be an impracticable task, owing to the oscillatory nature of the corresponding amplitude distribution. Our examples include the classically allowed case, semiclassical tunnelling, delays induced in the presence of a virtual state, and scattering by a low barrier. The properties of the amplitude distribution of the delays, and its pole representation are studied in detail.
Near-infrared spectroscopy and machine learning-based technique to predict quality-related parameters in instant tea
Authors: Bai Xiaoli , Zhang Lei , Kang Chaoyan , Quan Bingyan , Zheng Yu , Zhang Xianglong , Song Jia , Xia Ting , Wang Min 
Published: March 2022

AbstractThe traditional method for analyzing the content of instant tea has disadvantages such as complicated operation and being time-consuming. In this study, a method for the rapid determination of instant tea components by near-infrared (NIR) spectroscopy was established and optimized. The NIR spectra of 118 instant tea samples were used to evaluate the modeling and prediction performance of a combination of binary particle swarm optimization (BPSO) with support vector regression (SVR), BPSO with partial least squares (PLS), and SVR and PLS without BPSO. Under optimal conditions, Rp for moisture, caffeine, tea polyphenols, and tea polysaccharides were 0.9678, 0.9757, 0.7569, and 0.8185, respectively. The values of SEP were less than 0.9302, and absolute values of Bias were less than 0.3667. These findings indicate that machine learning can be used to optimize the detection model of instant tea components based on NIR methods to improve prediction accuracy.
Serum catestatin levels in patients with rheumatoid arthritis
Authors: Simac Petra , Perkovic Dijana , Bozic Ivona , Matijas Marijana , Gugo Katarina , Martinovic Dinko , Bozic Josko 
Published: March 2022

AbstractCatestatin (CST) is an important peptide that influences various inflammatory diseases. Our goal was to investigate CST concentrations in patients with RA compared to healthy subjects. This cross-sectional observational study included 80 patients with RA and 80 healthy control subjects. Demographic characteristics and laboratory parameters were recorded. Serum CST levels were determined by an enzyme-linked immunosorbent assay (ELISA). Serum CST levels were significantly higher in RA patients than in the control group (10.53 ± 3.90 vs 5.24 ± 2.37 ng/mL, p < 0.001). In RA patients, there was a statistically significant correlation between CST and patient age (r = 0.418, p < 0.001) and both DAS28 (r = 0.469, p < 0.001) and HAQ scores (r = 0.483, p < 0.001). There was a statistically significant correlation between serum CST levels and RA duration (r = 0.583, p < 0.001). Multiple linear regression analysis showed that serum CST levels retained a significant association with RA duration (β ± SE, 0.13 ± 0.04, p = 0.002) and DAS28 score (0.94 ± 0.45, p = 0.039) after model adjustment for age, body mass index (BMI) and HAQ score, with serum CST levels as a dependent variable. These findings imply that CST is possibly associated with RA complex pathophysiology and disease activity. However, future larger multicentric longitudinal studies are necessary to define the role of CST in RA.
Effectiveness of behavioral sleep interventions on children’s and mothers’ sleep quality and maternal depression: a systematic review and meta-analysis
Authors: Park Jeongok , Kim Soo Yeon , Lee Kyoungjin 
Published: March 2022

AbstractThis systematic review and meta-analysis was conducted to investigate the effectiveness of behavioral sleep interventions (BSIs) on the number of child night awakenings, and maternal sleep quality and depression. The search followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA) using PubMed, CINAHL, Cochrane, and EMBASE databases and retrieved studies published until April 2021. We calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for child sleep problems, and the mean differences (MD) and 95% CI for the number of child night awakenings, and maternal sleep quality and depression. Ten studies of 1628 initial searched were included in the final analysis. Two of the 10 studies were divided into two subgroups by participants and intervention type; thus, 12 subgroups were included in the meta-analysis. BSIs significantly reduced child sleep problems (OR 0.51; 95% CI 0.37–0.69) and improved maternal sleep quality (MD − 1.30; 95% CI − 1.82 to − 0.77) in the intervention group. There were no significant differences in the number of child night awakenings and maternal depression between the two groups. More RCTs to examine the effect of BSIs considering children’s age, duration of intervention, and outcome measuring time points are needed.
Abrupt upwelling and CO2 outgassing episodes in the north-eastern Arabian Sea since mid-Holocene
Authors: Azharuddin Syed , Govil Pawan , Chalk Thomas B. , Shekhar Mayank , Foster Gavin L. , Mishra Ravi 
Published: March 2022

AbstractIdentifying the causes and consequences of natural variations in ocean acidification and atmospheric CO2 due to complex earth processes has been a major challenge for climate scientists in the past few decades. Recent developments in the boron isotope (δ11B) based seawater pH and pCO2 (or pCO2sw) proxy have been pivotal in understanding the various oceanic processes involved in air-sea CO2 exchange. Here we present the first foraminifera-based δ11B record from the north-eastern Arabian Sea (NEAS) covering the mid-late Holocene (~ 8–1 ka). Our record suggests that the region was overall a moderate to strong CO2 sink during the last 7.7 kyr. The region behaved as a significant CO2 source during two short intervals around 5.5–4 ka and 2.8–2.5 ka. The decreased pH and increased CO2 outgassing during those abrupt episodes are associated with the increased upwelling in the area. The upwelled waters may have increased the nutrient content of the surface water through either increased supply or weaker export production. This new dataset from the coastal NEAS suggests that, as a potential result of changes in the strength of the El-Nino Southern Oscillation, the region experienced short episodes of high CO2 outgassing and pre-industrial ocean acidification comparable to or even greater than that experienced during the last ~ 200 years.
The biomechanical significance of the elongated rodent incisor root in the mandible during incision
Authors: Morris Philip J. R. , Cox Philip G. , Cobb Samuel N. F. 
Published: March 2022

AbstractRodents are characterised by a distinctive masticatory apparatus which includes a single pair of enlarged and continually growing incisors. This morphology, termed diprotodonty, has also independently evolved in a number of other mammals, including the aye-aye. This study examined the functional significance of the internal “root” of the elongated rodent-like incisor. The mandibles of four rodents and an aye-aye were modelled to exhibit incrementally shorter incisor roots. Finite element analysis was used to predict stress and strain patterns across the jaw to determine whether the length of the incisor root contributes to the resistance of mechanical forces encountered in the mandible during incision. It was found that von Mises stresses increase in the region of the mandible local to where the incisor is removed, but that the stress distribution across the wider mandible is only minimally affected. Thus, the long internal incisor appears to play a small role in resisting bending forces close to the incisor alveolus, and may act with the arch-like mandibular shape to strengthen the mandible in this region. However, the impact across the whole mandible is relatively limited, suggesting the highly elongate incisor in diprotodont mammals may be principally driven by other factors such as rapid incisor wear.
An imputation approach using subdistribution weights for deep survival analysis with competing events
Authors: Gorgi Zadeh Shekoufeh , Behning Charlotte , Schmid Matthias 
Published: March 2022

AbstractWith the popularity of deep neural networks (DNNs) in recent years, many researchers have proposed DNNs for the analysis of survival data (time-to-event data). These networks learn the distribution of survival times directly from the predictor variables without making strong assumptions on the underlying stochastic process. In survival analysis, it is common to observe several types of events, also called competing events. The occurrences of these competing events are usually not independent of one another and have to be incorporated in the modeling process in addition to censoring. In classical survival analysis, a popular method to incorporate competing events is the subdistribution hazard model, which is usually fitted using weighted Cox regression. In the DNN framework, only few architectures have been proposed to model the distribution of time to a specific event in a competing events situation. These architectures are characterized by a separate subnetwork/pathway per event, leading to large networks with huge amounts of parameters that may become difficult to train. In this work, we propose a novel imputation strategy for data preprocessing that incorporates weights derived from a time-discrete version of the classical subdistribution hazard model. With this, it is no longer necessary to add multiple subnetworks to the DNN to handle competing events. Our experiments on synthetic and real-world datasets show that DNNs with multiple subnetworks per event can simply be replaced by a DNN designed for a single-event analysis without loss in accuracy.
A LexAop > UAS > QUAS trimeric plasmid to generate inducible and interconvertible Drosophila overexpression transgenes
Authors: Wendler Franz , Park Sangbin , Hill Claire , Galasso Alessia , Chang Kathleen R. , Awan Iman , Sudarikova Yulia , Bustamante-Sequeiros Mar , Liu Sichen , Sung Ethan Y-H. , Aisa-Bonoko Gabrielle , Kim Seung K. , Baena-Lopez Luis A. 
Published: March 2022

AbstractThe existence of three independent binary systems for conditional gene expression (Gal4/UAS; LexA/LexAop; QF/QUAS) has greatly expanded versatile genetic analyses in the Drosophila melanogaster; however, the experimental application of these tools is limited by the need to generate multiple collections of noninterchangeable transgenic fly strains for each inducible gene expression system. To address this practical limitation, we developed a modular vector that contains the regulatory elements from all three binary systems, enabling Gal4-, LexA- or QF-dependent expression of transgenes. Our methods also incorporate DNA elements that facilitate independent site-specific recombination and elimination of regulatory UAS, LexAop or QUAS modules with spatial and temporal control, thus offering unprecedented possibilities and logistical advantages for in vivo genetic modulation and efficient interconversion of overexpression transgenic fly lines.