bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of a Hydrothermal System to Escalating Phreatic Unrest the Case of Turrialba and Irazú in Costa Rica (2007-2012)
Authors: Rouwet Dmitri , Mora-Amador Raul , Ramirez Carlos , González-Ilama Gino , Baldoni Eleonora , Pecoraino Giovannella , Inguaggiato Salvatore , Capaccioni Bruno , Lucchi Federico , Tranne Claudio Antonio 
Published: January 2021

Abstract
This study presents the first hydrogeochemical model of the hydrothermal systems of Turrialba and Irazú volcanoes in central Costa Rica, manifested as thermal springs, summit crater lakes, and fumarolic degassing at both volcanoes. Our period of observations (2007-2012) coincides with the pre- and early syn-phreatic eruption stages of Turrialba volcano that resumed volcanic unrest since 2004, after almost 140 years of quiescence. Peculiarly, the generally stable Irazú crater lake dropped its level during this reawakening of Turrialba. The isotopic composition of discharged fluids reveals the Caribbean meteoric origin; a contribution of “andesitic water” for Turrialba fumaroles up to ~50% is suggested. Four groups of thermal springs drain the northern flanks of Turrialba and Irazú volcanoes into two main rivers. Río Sucio (i.e. “dirty river”) is a major rock remover on the North flank of Irazú, mainly fed by the San Cayetano spring group. Instead, one group of thermal springs discharges towards the south of Irazú. All thermal spring waters are of SO4-type (i.e. steam heated waters), although none of the springs has a common hydrothermal end-member. A water mass budget for thermal springs results in an estimated total output flux of 187 ± 37 L/s, with 100 ± 20 L/s accounted for by the San Cayetano springs. Thermal energy release is estimated at 110 ± 22 MW (83.9 ± 16.8 MW by San Cayetano), whereas the total rock mass removal rate by chemical leaching is ~3,000 m3/y (~2,400 m3/y by San Cayetano-Río Sucio). Despite Irazú being the currently less active volcano, it is a highly efficient rock remover, which, on the long term can have effects on the stability of the volcanic edifice with potentially hazardous consequences (e.g. flank collapse, phreatic eruptions). Moreover, the vapor output flux from the Turrialba fumaroles after the onset of phreatic eruptions on 5 January 2010 showed an increase of at least ~260 L/s above pre-eruptive background fumarolic vapor fluxes. This extra vapor loss implies that the drying of the summit hydrothermal system of Turrialba could tap deeper than previously thought, and could explain the coincidental disappearance of Irazú’s crater lake in April 2010.
Localnet: A Simple Recurrent Neural Network Model for Protein Secondary Structure Prediction Using Local Amino Acid Sequences Only
Authors: Yang Shutong , Wang Yuhong , Cruz-Gutierrez Kennie , Wu Fangling , Ding Chuan-Fan 
Published: January 2021

Abstract
BackgroundProtein secondary structure prediction (PSSP) is important for protein structure modeling and design. Over the past a few years, deep learning models have shown promising results for PSSP. However, the current good performers for PSSP often require evolutionary information such as multiple sequence alignments and even real protein structures (templates), entire protein sequences, and amino acid property profiles. ResultsIn this study, we used a fixed-size window of adjacent residues and only amino acid sequences, without any evolutionary information, as inputs, and developed a very simple, yet accurate RNN model: LocalNet. The accuracy for three states of secondary structures is as high as 85.15%, indicating that the local amino acid sequence itself contains enough information for PSSP, a well-known classical view. By comparing to other predictors, we also achieve an state-of-art accuracy on dataset of CASP11, CASP12 and CASP13.ConclusionThe well-trained models are expected to have good applications in protein structure modeling and protein design. This model can be downloaded from https://github.com/lake-chao/protein-secondary-structure-prediction.
Noninvasive Temperature Estimation Based on Texture Features of Ultrasound Images for RFA
Authors: Chen Ming , Zhao Xingqun , Yao Linfang 
Published: January 2021

Abstract
BackgroundHyperthermia is one of the most common therapy for tumor， in which temperature monitoring is essential. Invasive temperature monitoring is mostly used in clinic at present, which leads to limited points under monitoring and extra hurt to patients. Therefore, noninvasive temperature estimation is a key and tough problem in hyperthermia. In this paper, a noninvasive temperature estimation method for hyperthermia based on B-mode ultrasonic image with wavelet transform and texture analysis is proposed.MethodsAnimal tissue both in vitro and in vivo(pig kidneys in vitro and rabbit kidney in vivo) were taken as experimental materials. Ultrasound images and temperature data were collected from radio frequency ablation experiment under approved protocol. Image subtraction and wavelet transform were performed on the ultrasound images to enhance the change during ablation, after which texture features were extracted to analyze the relationship with temperature.ResultsTexture features hybrid entropy and energy extracted from gray-level gradient co-occurrence matrix of ultrasound images processed had higher linear correlation with temperature than traditional gray value method. From in vitro and in vivo experiments, the linear correlation coefficients obtained between hybrid entropy and temperature were 0.979±0.028 and -0.935±0.037, respectively, and those between energy and temperature were 0.932±0.056 and -0.915±0.034, respectively. In addition, the slopes of linear model obtained in vitro were relatively consistent, while those under in vivo condition had certain individual differences.ConclusionsThe results demonstrated that texture features hybrid entropy and energy of ultrasound image processed with the method proposed in this paper can be used for temperature estimation with a smaller error because of high linear correlation with temperature both in vitro and in vivo. Compared with most previous research which only based on biomaterial in vitro, the in vivo experiment conducted in this paper verified the feasibility of the noninvasive temperature estimation method proposed in practice.
Canons and Sparrows II*: The Enhanced Bernoulli Exact Method for Determining Statistical Significance and Effect Size in the Meta-Analysis of k 2 x 2 Tables
Authors: Paul Lawrence Marc 
Published: January 2021

Abstract
BackgroundThe use of meta-analysis to aggregate the results of multiple studies has increased dramatically over the last 40 years. For homogeneous meta-analysis, the Mantel-Haenszel technique has typically been utilized. In such meta-analyses, the effect size across the contributing studies of the meta-analysis differ only by statistical error. If homogeneity cannot be assumed or established, the most popular technique developed to date is the inverse-variance DerSimonian & Laird (DL) technique [1]. However, both of these techniques are based on large sample, asymptotic assumptions. At best, they are approximations especially when the number of cases observed in any cell of the corresponding contingency tables is small.ResultsThis research develops an exact, non-parametric test for evaluating statistical significance and a related method for estimating effect size in the meta-analysis of k 2 x 2 tables for any level of heterogeneity as an alternative to the asymptotic techniques. Monte Carlo simulations show that even for large values of heterogeneity, the Enhanced Bernoulli Technique (EBT) is far superior at maintaining the pre-specified level of Type I Error than the DL technique. A fully tested implementation in the R statistical language is freely available from the author. In addition, a second related exact test for estimating the Effect Size was developed and is also freely available.Conclusions﻿This research has developed two exact tests for the meta-analysis of dichotomous, categorical data. The EBT technique was strongly superior to the DL technique in maintaining a pre-specified level of Type I Error even at extremely high levels of heterogeneity. As shown, the DL technique demonstrated many large violations of this level. Given the various biases towards finding statistical significance prevalent in epidemiology today, a strong focus on maintaining a pre-specified level of Type I Error would seem critical.
Quantifying the Pattern of Retinal Vascular Orientation in Diabetic Retinopathy Using Optical Coherence Tomography Angiography
Authors: Ma Yanhui , Ohr Matthew , Roberts Cynthia 
Published: January 2021

Abstract
Quantitative imaging using optical coherence tomography angiography (OCTA) could provide objective tools for the detection and characterization of diabetic retinopathy (DR). In this study, we developed a novel quantitative approach using OCTA images to delineate the vessel orientation pattern of a specific region of interest, which is an orientation distribution curve depicting the probability of vessels at each angle from 0 to 360 degrees. Three quantitative metrics including vessel preferred orientation, vessel anisotropy and vessel mass were extracted from the orientation pattern and analyzed in each of eight 45° sectors at the macula. Differential retinal microvascular orientation patterns were observed between three healthy subjects and three subjects with DR. Greater variability of vessel preferred orientation (p<0.001) and vessel mass (p<0.001) was exhibited among subjects with DR than healthy in eight sectors. In the nasal-superior sector, there was a significant difference between healthy and DR subjects in preferred orientation and vessel anisotropy. The vessel mass characterized from the vascular orientation pattern was shown to be strongly correlated with the traditionally reported vessel density (p<0.00001). These preliminary results suggest the feasibility and advantage of our vessel orientation-based quantitative approach using OCTA to characterize DR-associated changes in retinal microvasculature.
A Localized Study on Reducing Total Dissolved Solids Present in Southern California Tap Water
Authors: Wang Bill 
Published: January 2021

Abstract
This study, based in San Bernardino County, Southern California, explores the feasibility of adopting non-industrial equipment and methods to reduce water hardness in local tap water. We have utilized water boiling, activated carbon and sodium bicarbonate additives, as well as electrolysis methods to investigate how water quality could be improved. The results of this study show that when water is heated to a temperature around 50 °C (122°F), there is a maximum decrease in water hardness as well as its TDS levels. When water is left to boil for more than 10 minutes, there is a significant increase in TDS, making the water unfavorable for drinking. Activated carbon is unable to lower TDS, because it is unable to bind to any impurities present in the water. However, adding less than 4 mg/L of sodium bicarbonate will further eliminate water hardness by reacting with magnesium ions and improve taste, while increasing the pH. Electrolysis is the one of the methods that are successful in eliminating TDS, resulting in a direct proportion from an increasing electrical current and duration of time lowering the amount of TDS. These results will help residents determine safer and more effective ways to lower their water hardness and control mineral levels for their health and nutritional benefits.
Genetic Diversity and Population Structure of the Parental lines of Hybrid Japonica Rice in Northern China Revealed by 8K SNP-Chips
Authors: Gao Hong , Ma Zuobin , Wang Yuanzheng , Wang Changhua , Tang Zhiqiang , Zhang Liying , Fu Liang , He Na , Wang Hui , Bai Yuanjun , Sui Guomin , Zheng Wenjing 
Published: January 2021

Abstract
BackgroundThe hybrid rice varieties have made a significant contribution to food security. Although there has been rapid development of hybrid indica rice variety, the development of hybrid japonica rice has been relatively slow. This study aimed to understand the genetic background of representative parental lines of hybrid japonica rice in northern China that were beneficial for increasing efficiency to find a superior breeding combination using a restorer line and a sterile line. ResultsWe selected 137 parental lines of hybrid japonica rice, including 90 restorer lines, 47 sterile lines, which broadly represented the recent rice breeding trends in China. These lines were genotyped using 8K SNP-Chips (China Golden Marker Biotechnology Co. Ltd.) to understand the genetic diversity, population structure, phylogenetic evolution, and indica blood content. The genetic diversity of total parental lines averaged 0.264, with values for the restorer line and sterility line as 0.287 and 0.148, respectively. Based on the model-based population structure analysis and distance-based clustering, these 137 lines were divided into 14 groups, including seven independent restorer lines groups and seven mixture groups. There were 70% restorer lines in the above-mentioned seven independent restorer lines groups, and the indica blood content was 0.348, while 30% restorer lines were genetically similar to the sterile lines and constituted the other seven mixture groups, where the indica blood content in the restorer lines and the sterility lines was 0.142 and 0.121, respectively. The results of distance-based clustering revealed that the restorer lines, Group 1 and Group 2 (containing only restorer lines), had longer genetic distances with groups containing mainly sterile lines (the genetic distance ranged from 0.672 to 0.788), which served as a potential heterotic for hybrid rice breeding. This observation was consistent with the breeding strategy of high yield hybrid japonica rice.ConclusionsThe typical japonica sterile lines were crossed with the restorer lines containing high indica components indicating a strong heterosis pattern was a feasible scheme for heterosis utilization of indica-japonica subspecies. Thus, the effective ways to further improve the rice quality of hybrid japonica rice in northern China included maintaining moderate genetic distance and indica components between the parental lines along with the excellent quality of both the parental lines.
Alteration in the Immune Microenvironment Based on APC Status in MSS/pMMR Colon Cancer Data Retrieved from TCGA
Authors: Lin Haishan , Ma Nina , Zhen Hongchao , Shang Kun , Ma Xiaoting , Cao Bangwei 
Published: January 2021

Abstract
BackgroundImmunotherapy is currently the most advanced anti-tumor treatment approach. The efficacy of anti-tumor immunotherapy is closely related to the tumor immune microenvironment, including immune cells, infiltration of immune factors, and expression of immune checkpoints. At present, the biomarkers for predicting the efficacy of colon cancer immunotherapy do not cover all colon cancer patients suitable for immunotherapy. In this study, TCGA database was used to identify tumor genotypes suitable for anti-tumor immunotherapy. MethodsWe downloaded 390 samples with RNA-sequencing data and somatic mutation status data from TCGA. We applied the ESTIMATE, Package limma, the CIBERSORT and some other algorithms to analyze the cellular immune microenvironment. And validated with immunohistochemistry in tumor tissues of colon cancer patients. ResultsWe found that some of the MSS/pMMR populations, that were initially considered unsuitable for immunotherapy, might actually be suitable. In APC-wt/MSS colon cancer, the expression of PD-1, PD-L1, CTLA4 and CYT（GZMA and PRF1）were increased. Based on calculations done by ESTIMATE and CIBERSORT algorithms, the ImmunoScore and the proportion of CT8+ T cell infiltration is increased in these patients. Enrichment analysis was done to screen signaling pathways involved in immune response, extracellular matrix, and cell adhesion. Tumors from 42 colon cancer patients, including 22 APC-mt/MSS and 20 APC-wt/MSS, were immunohistochemically evaluated for expression of CD8 and PD-L1. And APC-wt/MSS tumors showed significantly higher expression of CD8 and PD-L1 than APC-mt/MSS tumor. ConclusionsBased on the results, we found that some colon cancers of APC-wt/MSS are classified by Tumor Immune Microenvironment types (TIMTs) TMIT I. So that we speculate that APC-wt/MSS colon cancer patients could benefit from anti-tumor immunotherapy.
Combination of Palbociclib and Erlotinib Exhibits Synergistic Antitumor Effect in Colorectal Cancer Patient-Derived Xenograft (PDX) Models
Authors: Zhou Xiaohui , Gong Yeqing , Liu Xiaorong , Mao Jiaqi , Chen Zhen , Zhou Tingting , Chen Chao , Hua Yunfen , Shi Xin , Yang Liu , Lin Fan 
Published: January 2021

Abstract
Background: The heterogenetic nature of colorectal cancer (CRC) constitutes a major challenge for drug development. Simultaneous targeting multiple molecules by combination therapy provides a promising strategy, but it requires identification of more potentially useful targeted agents. Palbociclib, a selective CDK4/6 inhibitor approved for the treatment of HR/ER-positive and HER2-negative breast cancer, exhibited anti-cancer versatility in several types of cancer. In this study, we evaluated its usefulness in the treatment of CRC either by single-agent or combined with a small molecule EGFR inhibitor erlotinib. Methods: The impacts of palbociclib, erlotinib, and their combination on cell proliferation, colony formation, cell cycle, apoptosis, senescence, and ROS accumulation in CRC cells were assessed. Their efficacies were evaluated in CRC patient-derived organoids (PDO) and xenograft (PDX) models.Results: Single-agent palbociclib efficiently inhibited proliferation, suppressed the RB phosphorylation, and caused G1-phase arrest in KRAS/BRAF mutated CRC cell lines. IC50 of all cell lines were below 1 µM. Moreover, it induced ROS accumulation and consequently caused apoptosis and senescence of CRC cells. The addition of erlotinib further aggravated palbociclib-induced anti-proliferation, cell cycle arrest, ROS accumulation, apoptosis, and senescence via blocking multiple critical effectors on RB/PI3K/RAS pathways and such interaction between two agents are synergistic. Finally, both palbociclib and erlotinib demonstrated anti-CRC activities, but only their combination caused statistically meaningful inhibition of tumor growth and prolonged survival with tolerable toxicity in KRAS wildtype/mutated PDX models. Conclusion: Our work demonstrated that the palbociclib and erlotinib combination treatment is a promising therapy for CRC and worthy of further clinical evaluation.
Analysis of Acupoint Selection and Combinations in Acupuncture Treatment of Asthma Based on Data Mining
Authors: Shang Pan-Pan , Chen Cai-Tao , Cheng Mi , Shi Yang-Lin , Yang Yong-Qing , Xu Yu-Dong 
Published: January 2021

Abstract
Background: Asthma is a highly prevalent respiratory disease that remains difficult to control. Acupuncture, as an important alternative therapeutic modality in preventing and treating asthma, is widely used in the world due to its promising efficacy and safety. Although acupoint selection and combinations are critical to therapeutic effects of acupuncture, its fundamental rules for asthma have not been fully understood. Thus, using data mining, the present study aimed to discover the most effective acupoints and combinations in the acupuncture treatment of asthma..Methods: Controlled clinical trials (CCTs) of acupuncture treatment for asthma were searched and retrieved from databases including Chinese National Knowledge Infrastructure (CNKI), Wanfang, and PubMed. Data regarding the main acupoints prescribed in these clinical trials was collected and quantified. A network analysis was performed to uncover the interconnections between the acupoints. Additionally, hierarchical clustering analysis and association rule mining were conducted to discover the potential acupoint combinations. Results: A total of 183 CCTs were retrieved. Feishu (BL13), Dingchuan (EX-B1), Dazhui (GV14), Shengshu (BL23), Pishu (BL20), and Fengmen (BL12) appeared to be the most frequently used acupoints for asthma. While the Bladder Meridian of Foot Taiyang, the Governor Vessel, and the Conception Vessel, compared to other meridians, were found to be the more commonly selected meridians. In the acupoint interconnection network, Feishu (BL13), Fengmen (BL12), Dingchuan (EX-B1), and Dazhui (GV14) were defined as key node acupoints. Moreover, acupoint clustering analysis revealed the treatment principle of “facilitating the flow of the lung Qi, tonifying spleen and kidney, and treating both the symptoms and root causes”. Association rule mining analysis demonstrated that the combination of Pishu, Shenshu, Feishu, and Dingchuan, as well as that of Feishu, Dazhui, and Fengmen were potential acupoint combinations that should be selected with priority in asthma treatment.Conclusion: Based on a data mining analysis of published CCTs, this study provides valuable information regarding the selection of the most effective acupoints and combinations for clinical acupuncture practice and experimental study aimed at the prevention and treatment of asthma.
Dowry Demand and other Risk Factors for Intimate Partner Violence Against Adolescent Girls: A Cross-sectional Study in India
Authors: Srivast Shobhit , Kumar Pradeep , Govindu Manideep , T Muhammad 
Published: January 2021

Abstract
Background: Violence against women is considered a fundamental violation of women’s human rights. According to the World Health Organization, worldwide one-third of women experience some form of intimate partner violence. The present study aims to examine the association of dowry demand and other associated risk factors with physical, sexual, or emotional violence against married adolescent girls in two major states of India by using large representative data.Methods: Understanding the lives of adolescents and young adults (UDAYA) project survey data was used for this study. The effective sample size for the study was 4893 married adolescent girls. Descriptive statistics along with bivariate analysis was performed to examine the preliminary results. For analyzing the association binary logistic regression method was used.Results: The prevalence of emotional, physical, and sexual violence was 28.6%, 22.9%, and 26.1% among married adolescent girls respectively. About 44% of married adolescent girls experienced any type of violence (emotional/physical/sexual). The prevalence of violence was significantly higher among girls who reported that dowry was demanded by their husbands (emotional-54%, physical-42.1%, sexual-39.6%, and any violence-68.4%). Results show that the likelihood of any violence was 3.66 times more likely among adolescent girls who reported that dowry was demanded by their husbands than their counterparts [OR: 3.66; CI: 3.06-4.37]. Other risk factors for intimate partner violence among adolescents included justifying wife-beating, low decision-making power, having a paid job, and longer marital duration.Conclusion: The results presented in this study suggest that policies that ensure equal inheritance and property rights for women and programs that help adolescent girls retain equal power and say in their family may be necessary to reduce their vulnerability to domestic violence.