bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Chloroplast Genome Sequences of Lonicera Japonica Cv. Damaohua: Characterization and Comparative and Phylogenetic Analyses
Authors: Zhang Jiaqiang , Liu Huichun , Xu Wenting , Wan Xiao , Zhu Kaiyuan 
Published: March 2022

Abstract
Lonicera japonica is a well-known medicinal plant, and the Damaohua cultivar is one of the oldest known honeysuckle cultivars in China. The 155,151 bp chloroplast genome of this cultivar was obtained through Illumina sequencing for the first time. The genome includes a pair of inverted repeats (IRa and IRb; 23,789 bp each), a large single-copy (LSC) region (88,924 bp) and a small single-copy (SSC) region (18,649 bp). In total, 127 unique genes were identified: 80 protein-coding, 39 tRNA and 8 rRNA genes. Only ycf3 contained two introns. Eighty-nine large repetitive sequences and 54 SSRs were detected. Fifty potential RNA editing sites were predicted. Adaptive evolution analysis revealed that infA, matK, petB, petD, rbcL, rpl16, rpl2, rps3, ycf1 and ycf2 were positively selected, possibly reflecting the specific environmental adaptation of this cultivar. Sequence alignment and analysis revealed some candidate fragments for Lonicera species identification, such as the intergenic regions rpoB-petN, rbcL-accD and psaA-ycf3. IR region boundary and phylogenetic analyses showed that the L. japonica cv. Damaohua chloroplast genome was most closely related to the L. japonica genome and that the two may be sister species. Understanding of L. japonica cv. Damaohua chloroplast genomics and comparative analyses of Lonicera species will provide a scientific basis for breeding, species identification, systematic evolution analysis and chloroplast genetic engineering research on medicinal honeysuckle plants.
Deep Eutectic Solvents: green solvents for the removal of degraded gelatin on cellulose nitrate cinematographic films
Authors: LOZANO MARCO VALENTE CHAVEZ , SCIUTTO GIORGIA , PRATI SILVIA , MAZZEO ROCCO 
Published: March 2022

Abstract
Historical photographic negatives and cinematographic films with cellulose nitrate (CN) supports show deterioration mechanisms related to the thermal, photocatalytic and hydrolytic loss of nitro groups from the CN chain. To prevent their disappearance, their scanning and digitalization becomes a priority. However, degradation hinders the scanning of CN films. Since motion picture films are stocked as a reel, the backside of each frame touches the front of another one. During degradation, the decrease in pH contributes to lowering the viscosity of gelatin. In this way, the emulsion gets softer and some residues may deposit on the back of the superimposed frames, and the gelatin may also spread over the film surface and come out from the edges.Traditional approaches to clean gelatin residues from the surface of CN bases and from the sides of film rolls include mechanical removal with scalpels and the use of polar solvents. However, these methods are either slow, ineffective or could potentially damage the degraded CN support and the remaining gelatin emulsion at the other side of the film. Accordingly, we have evaluated the performance of three choline chloride and betaine-based Deep Eutectic Solvent (DES) formulations. These DES are unexpensive, easy to prepare, green (non volatile, safe towards operator and the environment), non flammable and have been previously proposed for the extraction of proteinaceous material, but their use for the restoration of photographic negatives or cinematographic films has not been reported yet.Selected areas over the frames of a real deteriorated CN cinematographic film were cleaned from gelatin accretions by rubbing a cotton swab soaked in DES. Isopropyl alcohol (IPOH) was then employed to remove the remaining DES residues.To evaluate the cleaning performance, each area was characterized and documented before and after treatment using Optical Microscopy (OM), Micro-Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (µATR-FTIR), and cross-section observation.All treatments using DES proved effective for the removal of gelatin residues and harmless towards the CN film supports at the selected application times, showing superior cleaning power compared to traditional methods. Thus, the proposed cleaning methods with DES are suitable for cinematographic and photographic film restoration.
Physical Performance Reference Values for Japanese Oldest Old: A SONIC Study
Authors: Matsumoto Kiyoaki , Gondo Yasuyuki , Masui Yukie , Yasumoto Saori , Yoshida Yuko , Ikebe Kazunori , Arai Yasumichi , Kabayama Mai , Kamide Kei , Akasaka Hiroshi , Ishizaki Tatsuro 
Published: March 2022

Abstract
Background
The oldest old, defined as those aged 90 or over, are now the fastest-growing population sector. This study aimed to determine reference values for a number of physical performance measures (PPMs) among 90-year-olds using internationally standardized measurements and to clarify the characteristics of these indices by comparing their results for 90-year-olds with those for older people ages 70 and 80.
Methods
We used data from the 90-year-olds (88–91) who participated in the Septuagenarians, Octogenarians, and Nonagenarians Investigation with Centenarians (SONIC) study. A total of 789 participants were not certified as needing nursing care and consisted of three survey waves: 2012, 2015, and 2018. For comparison, we also used SONIC respondents from different cohorts, 1,000 who were aged 70 in 2010 and 973 who were aged 80 in 2011. For our physical performance measurements, we used grip strength and score on the Short Physical Performance Battery (SPPB). In addition, we statistically analyzed sex and age differences.
Result
Simple mean ± SD hand grip strength, usual gait speed, five-times chair stand, tandem balance, and SPPB for the 90-year-old respondents were 24.1 ± 5.4 kg, 0.80 ± 0.22 m/s, 17.2 ± 6.73 s, 5.89 ± 4.42 s, and 8.3 ± 2.2, respectively, in men and 14.4 ± 4.0 kg, 0.72 ± 0.20 m/s, 17.8 ± 7.89 s, 4.72 ± 4.35 s, and 7.5 ± 2.4, respectively, in women. For all PPMs, the age 90 cohort was statistically significantly different from the age 70 and 80 cohorts (all trends P < 0.001). Grip strength decreased with a similar gradient with age cohort increase of 10 years for both sexes. In contrast, SPPB lower limb score showed a larger drop between the age 80 and 90 cohorts than between the age 70 and 80 cohorts. We also constructed sex-specific appraisal standards according to quintiles.
Conclusions
Our study yielded inclusive sex-specific reference values and appraisal standards for major physical performance measures in not certified as needing nursing care, community-dwelling, oldest old Japanese. The characteristics of age-related decline in physical performance differed between the upper and lower extremity assessments.
Novel method for producing oleophilic polyurethane foam to remove oil from open water
Authors: Dat Nguyen Huu , Tuan Vu Manh , Huynh Mai Duc , Trung Tran Huu , Trang Nguyen Thi Thu , Thang Dam Xuan , Hoa Kieu Thi Quynh , Giang Nguyen Vu 
Published: March 2022

Abstract
In this study, a novel recyclable, hydrophobicity foam with excellent oil/water separation based on polyurethane (PU) and polypropylene glycol (PPG) grafted stearic acid (PGGA) has been developed. PGGA was simply synthesized by the esterification of stearic acid and PPG, while the PU/PGGA foam was fabricated by the reaction of PPG and methyl diphenyl diisocynate (MDI) with the addition of PGGA. The PU/PGGA foam exhibits improved oil adsorption capacity, water rejection as well as oil/water selectivity with the increase of PGGA weight loadings. The presence of PGGA at high loading (≥ 5 wt.%) reduces the pore size and porosity of PU/PGGA foam due to the high viscosity of PGGA preventing the foam formation reaction. As a result, the oil adsorption capacity of PU/PGGA foam is slightly neglected, nevertheless, the oil/water selectivity is significantly enhanced compared to the original PU foam. The result in this work suggests a simple and cost-effective method with potential in oil removal at large scale application.
The crop residue conundrum: maintaining long-term soil organic carbon stocks while reinforcing the bioeconomy, compatible endeavors?
Authors: Andrade Christhel , Clivot Hugues , Albers Ariane , Zamora-Ledezma Ezequiel , Hamelin Lorie 
Published: March 2022

Abstract

Crop residues are key for supplying carbon to the bioeconomy without interfering with food security. However, it is often suggested to export no more than half of this potential to ensure the maintenance of soil organic carbon (SOC) stocks. In this study, we challenge this idea by assessing how the residues usage for the bioeconomy is intertwined with the maintenance of long-term SOC stocks and thus the amount that can safely be harvested. We considered the coproduct return to the soil from five bioeconomy scenarios: i) pyrolysis biochar, ii) gasification biochar, iii) hydrothermal liquefaction hydrochar, iv) anaerobic digestion digestate, and v) lignocellulosic ethanol molasses. To compare the long-term SOC changes from these scenarios against a business-as-usual (BAU) scenario, in which crop residues are unharvested, we developed a framework coupling a SOC model with a bioeconomy module, that we applied at high spatial resolution to cover over 60,000 combinations of crop rotations and pedoclimatic units over France, for 2020 – 2120. The adapted SOC model considers the recalcitrance to degradation of each coproduct, while the bioeconomy module determines the share of carbon from the crop residues allocated to the coproducts. Our results show that the available harvestable crop residues could be completely harvested if pyrolysis or gasification biochar returns to soils, with SOC expected to double compared to the BAU scenario. Replacing crop residues with hydrochar showed increased SOC stocks in 88% of the areas (max +8%), while the digestate scenario predicted minor SOC increases in 50% (max +0.76%) and decreases in 40% of the areas (min -4%). The molasses scenario yielded SOC losses in all the areas and is thus not recommended. Excluding these, an additional amount of 60.4 – 191 PJ of crop residues (use-dependent) could be available for the French bioeconomy compared to applying a universal removal rate of 31.5%.
Ecological Traits Affect The Seasonal Migration Patterns Of Resident Birds Along A Subtropical Altitudinal Gradient
Authors: Cheng Yuwen , Wen Zhixin , He Xingcheng , Dong Zhehan , Zhangshang Mingyu , Li Dongrui , Wang Yan , Jiang Yong , Wu Yongjie 
Published: March 2022

Abstract
Background: Altitudinal bird migration involves seasonal shifts up and down the altitude gradient annually. Asia as the place with the largest number of altitudinal migrants, has quite few related studies, especially for montane and temperate avifaunas.Method: To explore the potential drivers of seasonal altitudinal migration for birds in the middle of Hengduan Mountains, we conducted a two-year investigation on breeding and non-breeding season bird communities at eight altitude sections in the Gongga Mountains. Then, we examined the altitudinal migration patterns and relationships between seasonal distribution shifts and species’ traits, of 20 species with sufficient data recorded in both seasons.Results: We found that a large proportion of resident birds underwent altitudinal migration and showed 3 patterns (downslope shift, upslope shift, no shift). Species’ seasonal distribution shifts were mainly correlated with territoriality, nest height, diet, and temperature tolerance range. The species nesting in scrub and omnivores were more likely to present a downhill movement in the non-breeding season. In addition, territorially weaker species migrated more widely and performed multiple patterns. Notably, HWI dominated upslope shifts in altitudinal migration.Conclusion: Studying the seasonal altitudinal migration patterns of birds is essential to understanding their distributional responses to seasonal changes in climate (energy), which has important conservation implication for avian biodiversity. These results further consolidate the study of seasonal altitudinal migration in montane birds and verify that body mass is not correlated with altitudinal migration. This could be used to bridge existing knowledge gaps that currently impeding effective conservation.
Comprehensive Analysis of Differentially Expressed miRNAs in Patients with Ischemic Stroke and Development of a New Risk Prediction Nomogram
Authors: Gao Mengxi , Wang Yan , Liu Chengyuan , Meng Lingzhen , Zhang Xiaokun , Chen Li , Zhang Qin , Guo Liru 
Published: March 2022

Abstract
The aim of our study was to investigate the microRNAs (miRNA) associated with ischemic stroke (IS) and developed a new risk prediction nomogram. Gene expression profiles were obtained from public databases. Differentially expressed miRNAs (DEmiRNAs) and differentially expressed mRNAs (DEmRNAs) were identified; Then, the transcription factors (TFs) of DEmiRNAs were predicted and Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on DEmRNAs were performed; Then, the miRNA-mRNA network and the competitive endogenous RNA (ceRNA) network were constructed, and the support vector machine (SVM) model was used to further screen key miRNAs. The differential expression of the key miRNAs was verified via experiment. Finally, we combined the patients’ disease characteristics and the expression of key miRNAs to construct a risk prediction nomogram. A total of 111 DEmiRNA and 501 DEmRNA were obtained. Top 3 TFs of DEmiRNA were SP1, EGR1 and SP4. GO enrichment analysis on the DEmRNAs showed that they were mainly related to neutrophils and immune activation. Hematopoietic cell lines and cell adhesion molecules were significantly enriched KEGG pathways. MiR-140-3p, miR-34c-5p, miR-330-3p had higher degree in the networks we constructed. In the nomogram, the level of cholesterol, the level of low-density lipoprotein, hypertension, diabetes, the expression of miR-140-3p, miR-34c-5p, and miR-330-3p were related to IS. The current results indicated that hematopoietic cell lineage, cell adhesion molecules, phagosomes, and T cell receptor signaling pathways were important pathways in IS. MiR-140-3p, miR-34c-5p, and miR-330-3p may play a pivotal role in the pathogenesis and progression of IS, and may be potential new therapeutic targets for IS.
Cumulative Smoking Exposure In The Non-Demented Older People And The Risk Of Cognitive Decline (NEDICES)
Authors: Benito-León Julián , Ghosh Ritwik , Contador Israel , Lapeña José , Bermejo-Pareja Felix 
Published: March 2022

Abstract
Background: Whether cumulative smoking exposure is a risk factor for cognitive decline among older adults remains majorly unresolved. We assessed whether cumulative smoking exposure in non-demented older people was associated with a higher risk of cognitive decline.Methods: Baseline cigarette smoking habits were assessed in 2,624 non-demented elderly (≥65 years) Spanish participants. A 37-item version of the Mini-Mental State Examination (MMSE) was administered at two visits (baseline and follow-up, approximately three years later). Change in 37-MMSE (baseline 37-MMSE score − follow-up 37-MMSE score) was divided into tertiles (lower tertile ≥2 points improvement in score, higher tertile ≥2 point decline in score). We dichotomized this variable into higher (cognitive decline) vs. middle and lower tertiles for the current analyses.Results: Any cumulative smoking exposure, regardless of intensity, was associated with a higher risk of cognitive decline, with a non-linear dose-response. Multivariable-adjusted hazard ratios for higher risk of cognitive decline were 1.00 (reference) in the never smokers, 1.32 (95% confidence interval 1.0-1.74) in the lower tertile of pack-years (<19), 1.55 (1.15-2.07) in the middle tertile of pack-years (19-47), and 1.83 (1.36-2.47) in the higher tertile of pack-years (>47). Multivariable-adjusted hazard ratios for higher risk of cognitive decline were 1.00 (reference) in the never smokers, 1.37 (1.03-1.83) in former smokers, and 1.57 (1.23-2.02) in current smokers. Conclusions and relevance: The association between cumulative smoking exposure and cognitive decline in the elderly population was dose-dependent. Results underscore the cognitive health risk of smoking and the potential benefits of quitting it.
Prognostic Implication of Early Minimal Residual Disease Evaluation in Patients with Chronic Myelomonocytic Leukemia
Authors: Wang Lulu , Chen Rongrong , Li Li , Zhu Lixia , Huang Xianbo , Ye Xiujin 
Published: March 2022

Abstract
Background: This article is performed to assess the significance of minimal residual disease (MRD) after one course of therapy in patients with chronic myelomonocytic leukemia (CMML). Methods: From January 2010 to January 2022, a total of 158 patients who were newly diagnosed with CMML were enrolled, in which 58/158 (37%) patients were conducted by multiparameter flow cytometry (FCM) assessed MRD analysis after on cycle treatment and were included in this study. MRD was detected by six- to eight- colour FCM. Result: After one course of therapy, twenty-one (36%) patients achieved MRD<0.01% (MRD1-) and thirty-seven (64%) were MRD>0.01% (MRD1+). The patients in the MRD1+ group had lower platelet counts, higher 𝛽2-microglobulin, ferritin and BM1 myeloblasts (bone marrow myeloblasts after one cycle of therapy) than that of the MRD1- group (P=0.005, P=0.023, P=0.026 and P=0.007, respectively). Furthermore, a greater propotion of patients had JCK2 and SETBP1 mutation in MRD1- patients than in MRD1+ group (both P=0.037). At a median follow up time of 25.8 months (95%CI, 15.01-36.59), those patients who achieved MRD<0.01% after one course of therapy fared better prognosis in terms of both OS (overall survival, 54.9 months vs. 17.5 months; P<0.001) and PFS (progression-free survival, 52.3 months vs 11.9 months; P=0.006) than those of MRD>0.01%, and 2-year OS rate (90% vs. 30%; P<0.001) and 2-year PFS rate (70% vs. 7%; P=0.004) were also higher. MRD1 status could determine the likelihood of progression after hematopoietic stem cell transplantation (HSCT), the 2-year PFS rate (100% vs. 24%, P=0.04) was higher in MRD1+ group than MRD1- group at the post-HSCT assessment. In addition, MRD1 status were independent prognostic factor of both PFS (HR, 3.326 [95%CI, 1.340-8.259]; P=0.01) and OS (HR, 4.614 [95%CI, 1.266-16.812]; P=0.02). Conclusion: MRD is highly predictive of prognosis, and it may help identify patients at increased risk for progression to further improve the management of patients with CMML. Large-scaled investigations are warranted to validate our conclusions and its potential in clinical practice.
Uncertainty analysis of water environmental capacity based on the copula model
Authors: Li Jiaqi , Shen Zhenyao , Cai Jianying , Liu Guowangchen , Chen Lei 
Published: March 2022

Abstract
Water environmental capacity is an important factor in total pollutant control and water environmental management. Due to the uncertainty of the water environment, the uncertainty analysis of water environmental capacity is crucial. Most uncertainty analyses of water environmental capacity do not consider the correlation between various parameters that were used to calculate water environmental capacity. In this study, the copula model of discharge and water quality was constructed to analyze the uncertainty of water environmental capacity. The risk threshold of each river section was calculated when the water environmental capacity was less than 0 in the wet, normal and dry seasons. The Yitong River Basin in Changchun city was taken as a case study. The results showed that the 68.27% confidence level was considered to reduce the uncertainty of water environmental capacity by more than 54.90%. The uncertainty of water environmental capacity in the wet season was the largest, and the risk threshold was the smallest. The risk thresholds for the water environmental capacity of each river reach were all greater than 90% in the dry season. The method of this study can be extended to other basins for uncertainty analysis of water environmental capacity.
Geostatistical analysis of the water quality of an aquifer in tropical and agricultural zone
Authors: Bustos-Terrones Yaneth , García Blanca , Loaiza Juan , Rangel-Peraza Jesús , Ramírez-Pereda Blenda , Rojas-Valencia María Neftalí Neftalí 
Published: March 2022

Abstract
The objective of this study was to identify water pollution problems and obtain useful information for the sustainable extraction of water from the Culiacan River aquifer. Data from 6 sampling sites were used in the period from 2012 to 2019. A spatial geostatistical analysis was carried out to describe the water quality of the aquifer by using isoconcentration contours. Likewise, a hydrogeochemical evaluation was carried out using seven water quality indices for irrigation purposes (SAR, CSR, SSP, KR, % Na, MH, PI). Finally, a multivariate statistical analysis was obtained through the analysis of principal components, Pearson correlation and cluster analysis identified the most important water quality variables in the Culiacan River aquifer based on their variability. The water quality index showed that the aquifer water quality was good in five sampling sites and excellent in one sampling site. Based on average concentrations, the ion content was Na2+ >HCO3- >Ca2+ >Mg2+ >Cl- >SO42- >K+, which did not present any ecological or public health risk. Finally, Sample Point 1 (SP1) was the location most affected by anthropogenic contamination. This site is within an urban area and is the shallowest sampling well.
A computational framework to trace tumor tissue-of-origin of 19 cancer types based on RNA sequencing
Authors: Wang Bo , Yang Huandong , Zhang Yanxiang , Tian Geng , Yang Jialiang 
Published: March 2022

Abstract
Carcinoma of unknown primary (CUP) is a type of metastatic cancer with tissue-of-origin (TOO) unidentifiable by traditional methods. Most CUP patients have poor prognosis since no therapy targeting TOO is allowed. Thus, it’s critical to develop accurate computational methods to infer TOO. While qPCR or microarray-based methods are effective in predicting TOO for most cancer types, the overall prediction accuracy is yet to be improved. Here, we propose a computational framework to trace TOO of 19 cancer types based on RNA sequencing (RNA-seq). Specifically, we download the RNA-seq data of 7000+ tissue samples covering 19 cancer types with known TOO from TCGA. By feature selection, 90 genes are finally selected to train a random forest model for TOO inference; the 90 genes are enriched in both tissue-specific functions and tissue-general functions. The cross-validation accuracy of our framework reaches 97.55% across all cancer types. Furthermore, we collected an independent cohort of samples in GEO as testing samples. The accuracy on the independent data is 74% despite the differences in experiment procedures and pipelines. In conclusion, we develop an accurate yet robust computational framework for identifying TOO, which might be promising in clinical applications.