bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel coupled RPL/OSL system to understand the dynamics of the metastable states
Authors: Jain M. , Kumar R. , Kook M. 
Published: September 2020

AbstractMetastable states form by charge (electron and hole) capture in defects in a solid. They play an important role in dosimetry, information storage, and many medical and industrial applications of photonics. Despite many decades of research, the exact mechanisms resulting in luminescence signals such as optically/thermally stimulated luminescence (OSL or TL) or long persistent luminescence through charge transfer across the metastable states remain poorly understood. Our lack of understanding owes to the fact that such luminescence signals arise from a convolution of several steps such as charge (de)trapping, transport and recombination, which are not possible to track individually. Here we present a novel coupled RPL(radio-photoluminescence)/OSL system based on an electron trap in a ubiquitous, natural, geophotonic mineral called feldspar (aluminosilicate). RPL/OSL allows understanding the dynamics of the trapped electrons and trapped holes individually. We elucidate for the first time trap distribution, thermal eviction, and radiation-induced growth of trapped electron and holes. The new methods and insights provided here are crucial for next generation model-based applications of luminescence dating in Earth and environmental sciences, e.g. thermochronometry and photochronometry.
Evaluation of plant growth promotion properties and induction of antioxidative defense mechanism by tea rhizobacteria of Darjeeling, India
Authors: Bhattacharyya Chandrima , Banerjee Srimoyee , Acharya Udita , Mitra Aroni , Mallick Ivy , Haldar Anwesha , Haldar Shyamalina , Ghosh Anupama , Ghosh Abhrajyoti 
Published: September 2020

AbstractA total of 120 rhizobacteria were isolated from seven different tea estates of Darjeeling, West Bengal, India. Based on a functional screening of in vitro plant growth-promoting (PGP) activities, thirty potential rhizobacterial isolates were selected for in-planta evaluation of PGP activities in rice and maize crops. All the thirty rhizobacterial isolates were identified using partial 16S rRNA gene sequencing. Out of thirty rhizobacteria, sixteen (53.3%) isolates belong to genus Bacillus, five (16.6%) represent genus Staphylococcus, three (10%) represent genus Ochrobactrum, and one (3.3%) isolate each belongs to genera Pseudomonas, Lysinibacillus, Micrococcus, Leifsonia, Exiguobacterium, and Arthrobacter. Treatment of rice and maize seedlings with these thirty rhizobacterial isolates resulted in growth promotion. Besides, rhizobacterial treatment in rice triggered enzymatic [ascorbate peroxidase (APX), catalase (CAT), chitinase, and phenylalanine ammonia-lyase (PAL)], and non-enzymatic [proline and polyphenolics] antioxidative defense reactions indicating their possible role in the reduction of reactive oxygen species (ROS) burden and thereby priming of plants towards stress mitigation. To understand such a possibility, we tested the effect of rhizobacterial consortia on biotic stress tolerance of rice against necrotrophic fungi, Rhizoctonia solani AG1-IA. Our results indicated that the pretreatment with rhizobacterial consortia increased resistance of the rice plants towards the common foliar pathogen like R. solani AG1-IA. This study supports the idea of the application of plant growth-promoting rhizobacterial consortia in sustainable crop practice through the management of biotic stress under field conditions.
Independent evolution of cutaneous lymphoma subclones in different microenvironments of the skin
Authors: Iyer Aishwarya , Hennessey Dylan , O’Keefe Sandra , Patterson Jordan , Wang Weiwei , Wong Gane Ka-Shu , Gniadecki Robert 
Published: September 2020

AbstractMycosis fungoides (MF) is the most common cutaneous T-cell lymphoma. Lesions of MF are formed by hematogenous seeding the skin with polyclonal (clonotypically diverse) neoplastic T-cells which accumulate numerous mutations and display a high degree of mutational, intratumoral heterogeneity (ITH). A characteristic but poorly studied feature of MF is epidermotropism, the tendency to infiltrate skin epithelial layer (epidermis) in addition to the vascularized dermis. By sequencing the exomes of the microdissected clusters of lymphoma cells from the epidermis and the dermis, we found that those microenvironments comprised different malignant clonotypes. Subclonal structure witnessed the independent mutational evolution in the epidermis and dermis. Thus, the epidermal involvement in MF could not be explained by gradual infiltration from the dermis but was caused by a separate seeding process followed by a quasi-neutral, branched evolution. In conclusion, tissue microenvironments shape the subclonal architecture in MF leading to “ecological heterogeneity” which contributes to the total ITH. Since ITH adversely affects cancer prognosis, targeting the microenvironment may present therapeutic opportunities in MF and other cancers.
Difference in persistent tuberculosis bacteria between in vitro and sputum from patients: implications for translational predictions
Authors: Faraj Alan , Clewe Oskar , Svensson Robin J. , Mukamolova Galina V. , Barer Michael R. , Simonsson Ulrika S. H. 
Published: September 2020

AbstractThis study aimed to investigate the number of persistent bacteria in sputum from tuberculosis patients compared to in vitro and to suggest a model-based approach for accounting for the potential difference. Sputum smear positive patients (n = 25) provided sputum samples prior to onset of chemotherapy. The number of cells detected by conventional agar colony forming unit (CFU) and most probable number (MPN) with Rpf supplementation were quantified. Persistent bacteria was assumed to be the difference between MPNrpf and CFU. The difference in persistent bacteria between in vitro and human sputum prior to chemotherapy was quantified using different model-based approaches. The persistent bacteria in sputum was 17% of the in vitro levels, suggesting a difference in phenotypic resistance, whereas no difference was found for multiplying bacterial subpopulations. Clinical trial simulations showed that the predicted time to 2 log fall in MPNrpf in a Phase 2a setting using in vitro pre-clinical efficacy information, would be almost 3 days longer if drug response was predicted ignoring the difference in phenotypic resistance. The discovered phenotypic differences between in vitro and humans prior to chemotherapy could have implications on translational efforts but can be accounted for using a model-based approach for translating in vitro to human drug response.
Bardoxolone conjugation enables targeted protein degradation of BRD4
Authors: Tong Bingqi , Luo Mai , Xie Yi , Spradlin Jessica N. , Tallarico John A. , McKenna Jeffrey M. , Schirle Markus , Maimone Thomas J. , Nomura Daniel K. 
Published: September 2020

AbstractTargeted protein degradation (TPD) has emerged as a powerful tool in drug discovery for the perturbation of protein levels using heterobifunctional small molecules. E3 ligase recruiters remain central to this process yet relatively few have been identified relative to the ~ 600 predicted human E3 ligases. While, initial recruiters have utilized non-covalent chemistry for protein binding, very recently covalent engagement to novel E3’s has proven fruitful in TPD application. Herein we demonstrate efficient proteasome-mediated degradation of BRD4 by a bifunctional small molecule linking the KEAP1-Nrf2 activator bardoxolone to a BRD4 inhibitor JQ1.
Characterization of the effect of cis-3-hexen-1-ol on green tea aroma
Authors: Nie Cong-ning , Gao Yuan , Du Xiao , Bian Jin-lin , Li Hui , Zhang Xiang , Wang Cong-ming , Li Shun-yu 
Published: September 2020

Abstractcis-3-Hexen-1-ol has been regarded as the main source of green aroma (or green odor) in green tea. However, no clear findings on the composition of green aroma components in tea and the effect of cis-3-hexen-1-ol on other aroma components have been reported. In this study, the main green aroma components in green tea were characterized, especially the role of cis-3-hexen-1-ol in green aroma was analyzed and how it affected other aroma components in green tea was studied. Based on the GC–MS detection, odor activity value evaluation, and monomer sniffing, 12 green components were identified. Through the chemometric analysis, cis-3-hexen-1-ol was proven as the most influential component of green aroma. Moreover, through the electronic nose analysis of different concentrations of cis-3-hexen-1-ol with 25 other aroma components in green tea, we showed that the effect of cis-3-hexen-1-ol plays a profound effect on the overall aroma based on the experiments of reconstitution solution and natural tea samples. GC–MS and CG-FID confirmed that the concentration range of the differential threshold of green odor and green aroma of cis-3-hexen-1-ol was 0.04–0.52 mg kg−1.
Urate in fingernail represents the deposition of urate burden in gout patients
Authors: Chen Haibing , Zhao Lili , Liu Fengjing , Chen Si , Hu Zhumeng , Chen Lihui , Ma Yiwen , Guo Kaifeng , Ji Aichang , Merriman Tony R. , Min Jun Zhe 
Published: September 2020

AbstractUrate in the fingernails of gout patients and healthy volunteers was successfully detected by high-performance liquid chromatography (HPLC) with ultraviolet (UV) in our previous research. This study aimed to further investigate whether nail urate could be a proxy for the burden of monosodium urate (MSU) crystals deposits in gout. To this end, we conducted a study in two parts. Firstly, we successfully detected urate in the nail by HPLC–UV and evaluated nail urate concentrations in control subjects and patients with gout. As expected, we found that levels of nail urate were significantly higher in patients with gout than in healthy controls, and the nail urate level was significantly correlated with the volume of MSU crystals deposits measured by dual-energy CT (DECT). Secondly, we found that nail urate can reflect changes in urate levels in the body during urate lowering therapy through a 3-month follow-up study. Our results provide the possibility of quantification of urate in human fingernails as a non-invasive alternative for assessing MSU crystals deposits in gout.
Machine learning-driven electronic identifications of single pathogenic bacteria
Authors: Hattori Shota , Sekido Rintaro , Leong Iat Wai , Tsutsui Makusu , Arima Akihide , Tanaka Masayoshi , Yokota Kazumichi , Washio Takashi , Kawai Tomoji , Okochi Mina 
Published: September 2020

AbstractA rapid method for screening pathogens can revolutionize health care by enabling infection control through medication before symptom. Here we report on label-free single-cell identifications of clinically-important pathogenic bacteria by using a polymer-integrated low thickness-to-diameter aspect ratio pore and machine learning-driven resistive pulse analyses. A high-spatiotemporal resolution of this electrical sensor enabled to observe galvanotactic response intrinsic to the microbes during their translocation. We demonstrated discrimination of the cellular motility via signal pattern classifications in a high-dimensional feature space. As the detection-to-decision can be completed within milliseconds, the present technique may be used for real-time screening of pathogenic bacteria for environmental and medical applications.
Quantitative proteomics identifies a plasma multi-protein model for detection of hepatocellular carcinoma
Authors: Du Zhenhua , Liu Xinyi , Wei Xiaojun , Luo Hongbo , Li Peiyao , Shi Mengting , Guo Bingqian , Cui Ying , Su Zhenglin , Zeng Jifeng , Si Anfeng , Cao Pengbo , Zhou Gangqiao 
Published: September 2020

AbstractMore efficient biomarkers are needed to facilitate the early detection of hepatocellular carcinoma (HCC). We aimed to identify candidate biomarkers for HCC detection by proteomic analysis. First, we performed a global proteomic analysis of 10 paired HCC and non-tumor tissues. Then, we validated the top-ranked proteins by targeted proteomic analyses in another tissue cohort. At last, we used enzyme-linked immunosorbent assays to validate the candidate biomarkers in multiple serum cohorts including HCC cases (HCCs), cirrhosis cases (LCs), and normal controls (NCs). We identified and validated 33 up-regulated proteins in HCC tissues. Among them, eight secretory or membrane proteins were further evaluated in serum, revealing that aldo–keto reductase family 1 member B10 (AKR1B10) and cathepsin A (CTSA) can distinguish HCCs from LCs and NCs. The area under the curves (AUCs) were 0.891 and 0.894 for AKR1B10 and CTSA, respectively, greater than that of alpha-fetoprotein (AFP; 0.831). Notably, combining the three proteins reached an AUC of 0.969, which outperformed AFP alone (P < 0.05). Furthermore, the serum AKR1B10 levels dramatically decreased after surgery. AKR1B10 and CTSA are potential serum biomarkers for HCC detection. The combination of AKR1B10, CTSA, and AFP may improve the HCC diagnostic efficacy.
Successful breeding predicts divorce in plovers
Authors: Halimubieke Naerhulan , Kupán Krisztina , Valdebenito José O. , Kubelka Vojtěch , Carmona-Isunza María Cristina , Burgas Daniel , Catlin Daniel , St Clair James J. H. , Cohen Jonathan , Figuerola Jordi , Yasué Maï , Johnson Matthew , Mencarelli Mauro , Cruz-López Medardo , Stantial Michelle , Weston Michael A. , Lloyd Penn , Que Pinjia , Montalvo Tomás , Bansal Udita , McDonald Grant C. , Liu Yang , Kosztolányi András , Székely Tamás 
Published: September 2020

AbstractWhen individuals breed more than once, parents are faced with the choice of whether to re-mate with their old partner or divorce and select a new mate. Evolutionary theory predicts that, following successful reproduction with a given partner, that partner should be retained for future reproduction. However, recent work in a polygamous bird, has instead indicated that successful parents divorced more often than failed breeders (Halimubieke et al. in Ecol Evol 9:10734–10745, 2019), because one parent can benefit by mating with a new partner and reproducing shortly after divorce. Here we investigate whether successful breeding predicts divorce using data from 14 well-monitored populations of plovers (Charadriusspp.). We show that successful nesting leads to divorce, whereas nest failure leads to retention of the mate for follow-up breeding. Plovers that divorced their partners and simultaneously deserted their broods produced more offspring within a season than parents that retained their mate. Our work provides a counterpoint to theoretical expectations that divorce is triggered by low reproductive success, and supports adaptive explanations of divorce as a strategy to improve individual reproductive success. In addition, we show that temperature may modulate these costs and benefits, and contribute to dynamic variation in patterns of divorce across plover breeding systems.
Intensity harmonization techniques influence radiomics features and radiomics-based predictions in sarcoma patients
Authors: Crombé Amandine , Kind Michèle , Fadli David , Le Loarer François , Italiano Antoine , Buy Xavier , Saut Olivier 
Published: September 2020

AbstractIntensity harmonization techniques (IHT) are mandatory to homogenize multicentric MRIs before any quantitative analysis because signal intensities (SI) do not have standardized units. Radiomics combine quantification of tumors’ radiological phenotype with machine-learning to improve predictive models, such as metastastic-relapse-free survival (MFS) for sarcoma patients. We post-processed the initial T2-weighted-imaging of 70 sarcoma patients by using 5 IHTs and extracting 45 radiomics features (RFs), namely: classical standardization (IHTstd), standardization per adipose tissue SIs (IHTfat), histogram-matching with a patient histogram (IHTHM.1), with the average histogram of the population (IHTHM.All) and plus ComBat method (IHTHM.All.C), which provided 5 radiomics datasets in addition to the original radiomics dataset without IHT (No-IHT). We found that using IHTs significantly influenced all RFs values (p-values: < 0.0001–0.02). Unsupervised clustering performed on each radiomics dataset showed that only clusters from the No-IHT, IHTstd, IHTHM.All, and IHTHM.All.C datasets significantly correlated with MFS in multivariate Cox models (p = 0.02, 0.007, 0.004 and 0.02, respectively). We built radiomics-based supervised models to predict metastatic relapse at 2-years with a training set of 50 patients. The models performances varied markedly depending on the IHT in the validation set (range of AUROC from 0.688 with IHTstd to 0.823 with IHTHM.1). Hence, the use of intensity harmonization and the related technique should be carefully detailed in radiomics post-processing pipelines as it can profoundly affect the reproducibility of analyses.
Ethnopharmacological study of native medicinal plants and the impact of pastoralism on their loss in arid to semiarid ecosystems of southeastern Iran
Authors: Sharafatmandrad Mohsen , Khosravi Mashizi Azam 
Published: September 2020

AbstractThe purpose of this study was to gather ethnopharmacological information on plants used by the pastorals of southeastern Iran. The relationships between ecological value of the plant species and ethnobotanical indices were investigated. The loss of medicinal plants and its effective factors were also determined under nomadism and sedentary pastoralism. Ethnopharmacological information of plants was collected through interviews with 85 local people including nomads (43%) and sedentary pastorals (57%). Ethnobotanical indices including relative frequency of citation (RFC), relative importance (RI), cultural value (CV), and use value (UV) were estimated. Canopy cover and density of plant species were measured at 60 sampling plots in the exclosure, nomadic rangelands and sedentary pastorals rangelands. The Importance Value Index (IVI) and Relative Loss Index (RL) were estimated for both nomadic and sedentary pastoral rangelands. Pearson correlation coefficient was used to investigate the relationship between ethnobotanical indices and IVI of plant species. The Bayesian networks was used to investigate the relationship between ethnobotanical indices and plant species loss. In total, 156 medicinal plant species of 50 families were identified in the region by locals. Positive correlation was observed between ethnobotanical indices (RFC and RI) and ecological index (IVI). The mean decline of the ecological importance of medicinal species in sedentary pastoral rangelands was approximately three times higher than in nomadic rangelands. Bayesian networks showed that cultural value, seed exploitation and aerial parts exploitation had direct relationships with species loss in both nomadic and sedentary pastoral rangelands. Bunium persicum, an ecologically and socially important species, had been extensively harvested (more than 60%) in the both nomadic and sedentary pastoral rangelands, making it a priority species in future conservation programs. Medicinal plants had high ecological value and were severely exploited, threatening sustainability of arid and semiarid ecosystems. Local pastorals not only use medicinal plants as herbal remedies but also consider them as a source of income. Popular plants with multiple medicinal uses were more susceptible to loss. Higher medicinal knowledge of pastorals did not help to mitigate medicinal plant loss, requesting new plans to aware them to the circumstances that often leads to species removal from community. Given the importance, abundance and widespread use of medicinal plants, further studies can provide a basis for their conservation and for identifying new therapeutic effects of plants in the region.
Phytoliths in selected broad-leaved trees in China
Authors: Ge Yong , Lu Houyuan , Wang Can , Gao Xing 
Published: September 2020

AbstractBroad-leaved trees are widely distributed from tropical to temperate zones in China, reference collections of phytoliths from these taxa are crucial for the precise reconstruction of paleoenvironments and the study of early plant resource exploitation. However, not much has been published on the phytoliths produced by modern broad-leaved trees. In this study, we collected samples of 110 species that cover the common species distributed in Northern and Southern China, and extracted phytoliths from leaves, twigs and fruits, in order to investigate the phytoliths types and production in these species. We found that only 58 species were phytoliths producers, and that 23 distinct phytoliths morphotypes could be recognized. The results showed that phytoliths types and production in Northern and Southern China could be similar in the two regions. Through analyzing previously published data and our data, Elongate brachiate geniculate, Polygonal tabular, Elongate facetate, Tracheary annulate/facetate geniculate and Tracheary annulate/facetate claviform have been proposed to be the potential diagnostic types for broad-leaved trees in general. This study provided a preliminary reference of phytoliths in modern broad-leaved trees, and could be used in the identification of phytoliths in sediments and archaeological contexts.
Myelodysplastic syndrome: the other cause of anemia in end-stage renal disease patients undergoing dialysis
Authors: Chang Min-Yu , Lin Sheng-Fung , Wu Shih-Chi , Yang Wen-Chi 
Published: September 2020

AbstractIn end-stage renal disease (ESRD) patients receiving dialysis, anemia is common and related to a higher mortality rate. Erythropoietin (EPO) resistance and iron refractory anemia require red blood cell transfusions. Myelodysplastic syndrome (MDS) is a disease with hematopoietic dysplasia. There are limited reports regarding ESRD patients with MDS. We aim to assess whether, for ESRD patients, undergoing dialysis is a predictive factor of MDS by analyzing data from the Taiwan National Health Insurance Research Database. We enrolled 74,712 patients with chronic renal failure (ESRD) who underwent dialysis and matched 74,712 control patients. In our study, we noticed that compared with the non-ESRD controls, in ESRD patients, undergoing dialysis (subdistribution hazard ratio [sHR] = 1.60, 1.16–2.19) and age (sHR = 1.03, 1.02–1.04) had positive predictive value for MDS occurrence. Moreover, more units of red blood cell transfusion (higher than 4 units per month) was also associated with a higher incidence of MDS. The MDS cumulative incidence increased with the duration of dialysis in ESRD patients. These effects may be related to exposure to certain cytokines, including interleukin-1, tumor necrosis factor-α, and tumor growth factor-β. In conclusion, we report the novel finding that ESRD patients undergoing dialysis have an increased risk of MDS.