bluuebunny/crossref_metadata_2025_split huggingface dataset:
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy
Authors: Salgado-Albarrán Marisol , Späth Julian , González-Barrios Rodrigo , Baumbach Jan , Soto-Reyes Ernesto 
Published: February 2022

AbstractHigh-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment, and chemoresistance. Improving the diagnosis and the development of targeted therapies is still needed. The molecular pathomechanisms driving HGSC progression are not fully understood though crucial for effective diagnosis and identification of novel targeted therapy options. The oncogene CTCFL (BORIS), the paralog of CTCF, is a transcriptional factor highly expressed in ovarian cancer (but in rarely any other tissue in females) with cancer-specific characteristics and therapeutic potential. In this work, we seek to understand the regulatory functions of CTCFL to unravel new target genes with clinical relevance. We used in vitro models to evaluate the transcriptional changes due to the presence of CTCFL, followed by a selection of gene candidates using de novo network enrichment analysis. The resulting mechanistic candidates were further assessed regarding their prognostic potential and druggability. We show that CTCFL-driven genes are involved in cytoplasmic membrane functions; in particular, the PI3K-Akt initiators EGFR1 and VEGFA, as well as ITGB3 and ITGB6 are potential drug targets. Finally, we identified the CTCFL targets ACTBL2, MALT1 and PCDH7 as mechanistic biomarkers to predict survival in HGSC. Finally, we elucidated the value of CTCFL in combination with its targets as a prognostic marker profile for HGSC progression and as putative drug targets.
Epigenetic study of early breast cancer (EBC) based on DNA methylation and gene integration analysis
Authors: Zhang Wenshan , Wang Haoqi , Qi Yixin , Li Sainan , Geng Cuizhi 
Published: February 2022

AbstractBreast cancer (BC) is one of the leading causes of cancer-related deaths in women. The purpose of this study is to identify key molecular markers related to the diagnosis and prognosis of early breast cancer (EBC). The data of mRNA, lncRNA and DNA methylation were downloaded from The Cancer Genome Atlas (TCGA) dataset for identification of differentially expressed mRNAs (DEmRNAs), differentially expressed lncRNAs (DElncRNAs) and DNA methylation analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyzes were used to identify the biological functions of DEmRNAs. The correlation analysis between DNA methylation and DEmRNAs was carried out. Then, diagnostic analysis and prognostic analysis of identified DEmRNAs and DElncRNAs were also performed in the TCGA database. Subsequently, methylation state verification for identified DEmRNAs was performed in the GSE32393 dataset. In addition, real-time polymerase chain reaction (RT-PCR) in vitro verification of genes was performed. Finally, AC093110.1 was overexpressed in human BC cell line MCF-7 to verify cell proliferation and migration. In this study, a total of 1633 DEmRNAs, 750 DElncRNAs and 8042 differentially methylated sites were obtained, respectively. In the Venn analysis, 11 keys DEmRNAs (ALDH1L1, SPTBN1, MRGPRF, CAV2, HSPB6, PITX1, WDR86, PENK, CACNA1H, ALDH1A2 and MME) were we found. ALDH1A2, ALDH1L1, HSPB6, MME, MRGPRF, PENK, PITX1, SPTBN1, WDR86 and CAV2 may be considered as potential diagnostic gene biomarkers in EBC. Strikingly, CAV2, MME, AC093110.1 and AC120498.6 were significantly actively correlated with survival. Methylation state of identified DEmRNAs in GSE32393 dataset was consistent with the result in TCGA. AC093110.1 can affect the proliferation and migration of MCF-7. ALDH1A2, ALDH1L1, HSPB6, MME, MRGPRF, PENK, PITX1, SPTBN1, WDR86 and CAV2 may be potential diagnostic gene biomarkers of EBC. Strikingly, CAV2, MME, AC093110.1 and AC120498.6 were significantly actively correlated with survival. The identification of these genes can help in the early diagnosis and treatment of EBC. In addition, AC093110.1 can regulate SPTBN1 expression and play an important role in cell proliferation and migration, which provides clues to clarify the regulatory mechanism of EBC.
Thin films of the $$\alpha$$-quartz $$Si_xGe_{1-x}O_2$$ solid solution
Authors: Zhou Silang , Antoja-Lleonart Jordi , Ocelík Václav , Noheda Beatriz 
Published: February 2022

Abstract$$SiO_2$$SiO2with the$$\alpha$$α-quartz structure is one of the most popular piezoelectrics. It is widely used in crystal oscillators, bulk acoustic wave (BAW) devices, surface acoustic wave (SAW) devices, and so on.$$GeO_2$$GeO2can also be crystallized into the$$\alpha$$α-quartz structure and it has better piezoelectric properties, with higher piezoelectric coefficient and electromechanical coupling coefficients, than$$SiO_2$$SiO2. Experiments on bulk crystals and theoretical studies have shown that these properties can be tuned by varying the Si/Ge ratio in the$$Si_xGe_{1-x}O_2$$SixGe1-xO2solid solution. However, to the best of our knowledge, thin films of$$Si_xGe_{1-x}O_2$$SixGe1-xO2quartz have never been reported. Here we present the successful crystallization of$$Si_xGe_{1-x}O_2$$SixGe1-xO2thin films in the$$\alpha$$α-quartz phase on quartz substrates ($$SiO_2$$SiO2) with x up to 0.75. Generally, the films grow semi-epitaxially, with the same orientation as the substrates. Interestingly, the$$Si_{0.75}Ge_{0.25}O_2$$Si0.75Ge0.25O2composition grows fully strained by the quartz substrates and this leads to the formation of circular quartz domains with an ordered Dauphiné twin structure. These studies represent a first step towards the optimization of piezoelectric quartz thin films for high frequency (> 5 GHz) applications.
Increased nodular P level induced by intercropping stimulated nodulation in soybean under phosphorus deficiency
Authors: Qin Xiaomin , Pan Haonan , Xiao Jingxiu , Tang Li , Zheng Yi 
Published: February 2022

AbstractLow P availability is a vital constraint for nodulation and efficient N2 fixation of legume, including soybean. To elucidate the mechanisms involved in nodule adaption to low P availability under legume/cereal intercropping systems, two experiments consisting of three cropping patterns (monocropped soybean, monocropped maize, soybean/maize intercropping) were studied under both sufficient- and deficient-P levels. Our results demonstrated that intercropped soybean with maize showed a higher nodulation and N2 fixation efficiency under low P availability than monocropped soybean as evidenced by improvement in the number, dry weight and nitrogenase activity of nodules. These differences might be attributed to increase in P level in intercropping-induced nodules under low P supply, which was caused by the elevated activities of phytase and acid phosphatases in intercropping-induced nodules. Additionally, the enhanced expression of phytase gene in nodules supplied with deficient P level coincided with an increase in phytase and acid phosphatase activities. Our results revealed a mechanism for how intercropped maize stimulated nodulation and N2 fixation of soybean under P deficient environments, where enhanced synthesis of phytase and acid phosphatases in intercropping-induced nodules, and stimulated nodulation and N2 fixation.
A pilot study for the prediction of liver function related scores using breath biomarkers and machine learning
Authors: Patnaik Rakesh Kumar , Lin Yu-Chen , Agarwal Ashish , Ho Ming-Chih , Yeh J. Andrew 
Published: February 2022

AbstractVolatile organic compounds (VOCs) present in exhaled breath can help in analysing biochemical processes in the human body. Liver diseases can be traced using VOCs as biomarkers for physiological and pathophysiological conditions. In this work, we propose non-invasive and quick breath monitoring approach for early detection and progress monitoring of liver diseases using Isoprene, Limonene, and Dimethyl sulphide (DMS) as potential biomarkers. A pilot study is performed to design a dataset that includes the biomarkers concentration analysed from the breath sample before and after study subjects performed an exercise. A machine learning approach is applied for the prediction of scores for liver function diagnosis. Four regression methods are performed to predict the clinical scores using breath biomarkers data as features set by the machine learning techniques. A significant difference was observed for isoprene concentration (p < 0.01) and for DMS concentration (p < 0.0001) between liver patients and healthy subject’s breath sample. The R-square value between actual clinical score and predicted clinical score is found to be 0.78, 0.82, and 0.85 for CTP score, APRI score, and MELD score, respectively. Our results have shown a promising result with significant different breath profiles between liver patients and healthy volunteers. The use of machine learning for the prediction of scores is found very promising for use of breath biomarkers for liver function diagnosis.
Parent–offspring conflict and its outcome under uni-and biparental care
Authors: Sahm Jacqueline , Prang Madlen A. , Steiger Sandra 
Published: February 2022

AbstractConflicts over parental investment are predicted to be common among family members, especially between parents and their offspring. Parent–offspring conflict has been studied in many brood-caring organisms, but whether its outcome is closer to the parental or offspring optimum is usually unknown, as is whether the presence of a second parent, a caring male partner, can affect the outcome. Here, we manipulated the initial brood size of single and paired female burying beetles to examine how many offspring are necessary to maintain parental care in the current brood. We found that mothers continued to invest in small broods even if their reproductive output would have been higher if they had discontinued their care and produced a second brood instead. Consequently, our data suggests that the offspring have the upper hand in the conflict. However, our results further show that paired females laid a second egg clutch more often and produced more offspring than single females, suggesting that the presence of a male partner shifts the conflict outcome towards the parental optimum. This latter result not only is a novel aspect of parent–offspring theory, but also represents an additional factor that might explain the evolution of biparental care.
Changes in the acoustic activity of beaked whales and sperm whales recorded during a naval training exercise off eastern Canada
Authors: Stanistreet Joy E. , Beslin Wilfried A. M. , Kowarski Katie , Martin S. Bruce , Westell Annabel , Moors-Murphy Hilary B. 
Published: February 2022

AbstractExperimental research has shown that beaked whales exhibit strong avoidance reactions to naval active sonars used during antisubmarine warfare training exercises, including cessation of echolocation and foraging activity. Behavioural responses to sonar have also been linked to strandings and mortality. Much of the research on the responses of beaked whales and other cetaceans to naval active sonar has occurred on or near U.S. naval training ranges, and the impacts of sonar in other regions remain poorly understood, particularly as these impacts, including mortality, are likely to go unobserved in offshore areas. In September 2016 the multinational naval exercise ‘CUTLASS FURY 2016’ (CF16) was conducted off eastern Canada. We used passive acoustic recordings collected in the region to quantify the occurrence and characteristics of sonar signals, measure ambient noise levels, and assess changes in the acoustic activity of beaked and sperm whales. The number of hours per day with echolocation clicks from Cuvier’s beaked whales and sperm whales were significantly reduced during CF16, compared to the pre-exercise period in 2016 (sperm whales) and to control data from 2015 (both species). Clicks from an unidentified Mesoplodont beaked whale species, sporadically detected prior to CF16, were absent during the exercise and for 7 days afterward. These results suggest that beaked and sperm whales ceased foraging in the vicinity of CF16 and likely avoided the affected area. Such disturbance may have energetic, health, and fitness consequences.
Insulin-like growth factor 2 and autophagy gene expression alteration arise as potential biomarkers in Parkinson’s disease
Authors: Sepúlveda Denisse , Grunenwald Felipe , Vidal Alvaro , Troncoso-Escudero Paulina , Cisternas-Olmedo Marisol , Villagra Roque , Vergara Pedro , Aguilera Carlos , Nassif Melissa , Vidal Rene L. 
Published: February 2022

AbstractInsulin-like growth factor 2 (IGF2) and autophagy-related genes have been proposed as biomolecules of interest related to idiopathic Parkinson’s disease (PD). The objective of this study was to determine the IGF2 and IGF1 levels in plasma and peripheral blood mononuclear cells (PBMCs) from patients with moderately advanced PD and explore the potential correlation with autophagy-related genes in the same blood samples. IGF1 and IGF2 levels in patients' plasma were measured by ELISA, and the IGF2 expression levels were determined by real-time PCR and Western blot in PBMCs. The expression of autophagy-related genes was evaluated by real-time PCR. The results show a significant decrease in IGF2 plasma levels in PD patients compared with a healthy control group. We also report a dramatic decrease in IGF2 mRNA and protein levels in PBMCs from PD patients. In addition, we observed a downregulation of key components of the initial stages of the autophagy process. Although IGF2 levels were not directly correlated with disease severity, we found a correlation between its levels and autophagy gene profile expression in a sex-dependent pattern from the same samples. To further explore this correlation, we treated mice macrophages cell culture with α-synuclein and IGF2. While α-synuclein treatment decreased levels Atg5, IGF2 treatment reverted these effects, increasing Atg5 and Beclin1 levels. Our results suggest a relationship between IGF2 levels and the autophagy process in PD and their potential application as multi-biomarkers to determine PD patients' stages of the disease.
Estimating the population at risk with soil transmitted helminthiasis and annual drug requirements for preventive chemotherapy in Ogun State, Nigeria
Authors: Mogaji Hammed Oladeji , Johnson Olatunji Olugoke , Adigun Abbas Bolaji , Adekunle Oladunni Nimota , Bankole Samuel , Dedeke Gabriel Adewunmi , Bada Babatunde Saheed , Ekpo Uwem Friday 
Published: February 2022

AbstractSoil transmitted helminth (STH) infections are among the most common human infections worldwide with over 1 billion people affected. Many estimates of STH infection are often based on school-aged children (SAC). This study produced predictive risk-maps of STH on a more finite scale, estimated the number of people infected, and the amount of drug required for preventive chemotherapy (PC) in Ogun state, Nigeria. Georeferenced STH infection data obtained from a cross-sectional survey at 33 locations between July 2016 and November 2018, together with remotely-sensed environmental and socio-economic data were analyzed using Bayesian geostatistical modelling. Stepwise variable selection procedure was employed to select a parsimonious set of predictors to predict risk and spatial distribution of STH infections. The number of persons (pre-school ages children, SAC and adults) infected with STH were estimated, with the amount of tablets needed for preventive chemotherapy. An overall prevalence of 17.2% (95% CI 14.9, 19.5) was recorded for any STH infection. Ascaris lumbricoides infections was the most predominant, with an overall prevalence of 13.6% (95% CI 11.5, 15.7), while Hookworm and Trichuris trichiura had overall prevalence of 4.6% (95% CI 3.3, 5.9) and 1.7% (95% CI 0.9, 2.4), respectively. The model-based prevalence predictions ranged from 5.0 to 23.8% for Ascaris lumbricoides, from 2.0 to 14.5% for hookworms, and from 0.1 to 5.7% for Trichuris trichiura across the implementation units. The predictive maps revealed a spatial pattern of high risk in the central, western and on the border of Republic of Benin. The model identified soil pH, soil moisture and elevation as the main predictors of infection for A. lumbricoides, Hookworms and T. trichiura respectively. About 50% (10/20) of the implementation units require biannual rounds of mass drug administration. Approximately, a total of 1.1 million persons were infected and require 7.8 million doses. However, a sub-total of 375,374 SAC were estimated to be infected, requiring 2.7 million doses. Our predictive risk maps and estimated PC needs provide useful information for the elimination of STH, either for resource acquisition or identifying priority areas for delivery of interventions in Ogun State, Nigeria.
Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics
Authors: Wang Jen-Hung , Choong Wai-Kok , Chen Ching-Tai , Sung Ting-Yi 
Published: February 2022

AbstractIdentifying peptides and proteins from mass spectrometry (MS) data, spectral library searching has emerged as a complementary approach to the conventional database searching. However, for the spectrum-centric analysis of data-independent acquisition (DIA) data, spectral library searching has not been widely exploited because existing spectral library search tools are mainly designed and optimized for the analysis of data-dependent acquisition (DDA) data. We present Calibr, a spectral library search tool for spectrum-centric DIA data analysis. Calibr optimizes spectrum preprocessing for pseudo MS2 spectra, generating an 8.11% increase in spectrum–spectrum match (SSM) number and a 7.49% increase in peptide number over the traditional preprocessing approach. When searching against the DDA-based spectral library, Calibr improves SSM number by 17.6–26.65% and peptide number by 18.45–37.31% over two state-of-the-art tools on three different data sets. Searching against the public spectral library from MassIVE, Calibr improves state-of-the-art tools in SSM and peptide numbers by more than 31.49% and 25.24%, respectively, for two data sets. Our analyses indicate higher sensitivity of Calibr results from the use of various spectral similarity measures and statistical scores, coupled with machine learning-based statistical validation for FDR control. Calibr executable files including a graphical user-interface application are available at https://ms.iis.sinica.edu.tw/COmics/Software_CalibrWizard.html and https://sourceforge.net/projects/comics-calibr.
Integrating population genetics and species distribution modelling to guide conservation of the noble crayfish, Astacus astacus, in Croatia
Authors: Lovrenčić Leona , Temunović Martina , Gross Riho , Grgurev Marin , Maguire Ivana 
Published: February 2022

AbstractThe noble crayfish,Astacus astacus,is an indigenous European freshwater species. Its populations show significant declines caused by anthropogenic pressure on its habitats, climate change and the spread of invasive species. Diminishing populations’ trends and loss of genetic diversity highlight the need for effective conservation that will ensure their long-term survival. We combined population genetics and species distribution modelling (SDM) to reveal the impact of climate change and invasive species on the noble crayfish, and to guide future conservation programs of current populations. Our study showed that Croatian populations ofA. astacusharbour an important part of species genetic diversity and represent significant genetic reservoir at the European level. The SDM results predicted substantial reductions of suitable habitats forA. astacusby the 2070; only 13% of its current potential distribution is projected to remain stable under pessimistic Representative Concentration Pathway (RCP 8.5) emission scenario. Moreover, most of the populations with high genetic diversity are located in the areas predicted to become unsuitable, and consequently have a high probability of being lost in the future. Further, SDM results also indicated considerable decrease of future habitat suitability for invasive crayfish species in Croatia, suggesting that climate change poses a major threat to already endangeredA. astacus. The obtained results help in the identification of populations and areas with the highest conservation value which should be given the highest priority for protection. In order to preserve present diversity in areas that are predicted as suitable, we propose assisted migration and repopulation approaches, for enhancing populations’ size and saving maximum genetic variability. The result of our research emphasizes once again the benefits of multidisciplinary approach in the modern biodiversity conservation.
Mathematical modelling to determine the greatest height of trees
Authors: Kanahama Tohya , Sato Motohiro 
Published: February 2022

AbstractThis study aimed to analyse the critical height of a column whose weight varies vertically in order to obtain a simple scaling law for a tree where the weight distribution considered. We modelled trees as cantilevers that were fixed to the ground and formulated a self-buckling problem for various weight distributions. A formula for calculating the critical height was derived in a simple form that did not include special functions. We obtained a theoretical clarification of the effect of the weight distribution of heavy columns on the buckling behaviour. A widely applicable scaling law for trees was obtained. We found that an actual tree manages to distribute the weight of its trunk and branches along its vertical extent in a manner that adequately secures its critical height. The method and findings of this study are applicable to a wide range of fields, such as the simplification of complicated buckling problems and the study of tree shape quantification.
Two-dimensional biocompatible plasmonic contact lenses for color blindness correction
Authors: Roostaei N. , Hamidi S. M. 
Published: February 2022

AbstractColor blindness, or color vision deficiency (CVD), is an ocular disease that suppresses the recognition of different colors. Recently, tinted glasses and lenses have been studied as hopeful devices for color blindness correction. In this study, 2D biocompatible and flexible plasmonic contact lenses were fabricated using polydimethylsiloxane (PDMS) and a low-cost, and simple design based on the soft nano-lithography method and investigated for correction of red–green (deuteranomaly) color blindness. In addition, the stability test of the fabricated plasmonic contact lenses was investigated into the phosphate buffered saline (PBS) solution and the proposed lens offers an excellent stability into the PBS solution. The plasmonic contact lens proposed herein is based on the plasmonic surface lattice resonance (SLR) phenomenon and offers a good color filter for color blindness correction. The biocompatibility, low cost, stability, and simple fabrication of these contact lenses can offer new insights for applications of color blindness correction.