bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resilience of soil nematodes to logging residue inputs following clear-cutting is site-dependent: a case study in rubber plantations on the Ivory Coast
Authors: Aymard KOUAKOU Kouakou , Trap Jean , Diakhaté Sidy , Kolo Yeo , Perron Thibaut , Gay Frédéric 
Published: February 2022

Abstract
Aims The effect of tree plantations on soil biological functions when they replace tropical forests is detrimental. However, the current trend is to repeat tree plantations on the same land after clear-cutting, with a probable strong disturbance of soil functions. We addressed this question in rubber plantations, one of the world’s most important tropical perennial crops, using soil nematode communities as an indicator of soil functioning. We hypothesised that (i) the restitution of logging residues from previous plantations will foster the resilience of the soil nematode community and (ii) this resilience will depend on soil type.Methods An experimental design with different levels of logging residues for the previous rubber plantation and legumes (Pueraria phaseoloides) was set up in two rubber plantations on the Ivory Coast with contrasting soil types. The response of nematodes to clear-cutting was monitored every 6 months over 24 months.Results At both sites, we observed significant decreases in nematode abundance, diversity, taxonomic composition, and ecological nematode index six months after rubber tree logging. At the clay site, practices with logging residues led to higher resilience of the total nematode abundance. The ecological indices (enrichment index) in the sandy site were more resilient with logging residue input than without over time. Conclusions Logging residues and legumes input was the most efficient practice for promoting soil nematode biodiversity and mitigating the negative impact of clear-cutting in rubber monocultures after a 40-year rotation. However, soil type determined both the level of resistance and resilience of the nematode community.
Steps to a Good Night’s Sleep: The Association Between Physical Activity and Sleep in early Adolescence
Authors: Fontanellaz-Castiglione Chiara E. G. , Timmers Tammy T. , Lerch Stefan , Hamman Christoph , Kaess Michael , Tarokh Leila 
Published: February 2022

Abstract
Purpose
Research to date suggests that physical activity is associated with improved sleep, but studies have predominantly relied on self-report measures and have not accounted for school day/free day variability.
Methods
To address these gaps in the literature, the aim of the present study was to describe the number of steps in adolescents using long-term daily actigraphy measurement (5,989 days in total; average of 119 ± 40 days per participant; range = 39–195 days) and examine the association between actigraphically assessed steps and sleep behavior (i.e., total sleep time, bedtime, rise time and sleep efficiency) in a sample of healthy adolescents (N = 50). We use multilevel modeling to disentangle the within subject and between subject effects of physical activity on sleep.
Results
Within a subject more steps on school and free days were associated with later bed times as well as later rise times on school days. On the other hand, comparing between subjects’ effects, steps were associated with lower sleep efficiency on free and school days. No other significant associations were found for the other sleep variables.
Conclusion
Our results obtained through objective and long-term measurement of both sleep and steps challenge previous findings showing a positive effect of physical activity on sleep. We emphasize the importance of the methodology and the separation of within subject from between subject features when examining the relationship between physical activity and sleep.
A multidisciplinary care pathway improves quality of life and pain in patients with fibrous dysplasia/McCune-Albright syndrome: a multicenter prospective observational study
Authors: Meier Maartje Ekwia , Hagelstein-Rotman Marlous , de Ven Annenienke C van , Geest Ingrid CM van der , Donker Olav , Pichardo Sarina EC , Muller Petra CE Hissink , Meeren Stijn W Van der , Dorleijn Desirée MJ , Winter Elizabeth M , de Sande Michiel AJ van , Appelman-Dijkstra Natasha M 
Published: February 2022

Abstract
Background: Fibrous dysplasia/McCune-Albright syndrome (FD/MAS) may cause pain, impaired ambulation and decreased quality of life (QoL). International guidelines advocate management of FD/MAS in a tertiary multidisciplinary care pathway, but no longitudinal data are available to support this recommendation. This multicenter prospective observational study aimed to evaluate effects of 1 year of treatment in the FD/MAS care pathway in 2 tertiary clinics on QoL and pain, assessed by change in Short Form 36 and Brief Pain Inventory between baseline and follow-up. Patients completing baseline questionnaires <1 year after intake were classified as new referrals, others as under chronic care. Results: 92 patients were included, 61 females (66%). 22 patients (24%) had monostotic disease, 16 (17%) isolated craniofacial FD, 27 (40%) polyostotic FD and 17 (19%) MAS. 26 were new referrals (28%) and 66 chronic patients (72%). Median age at baseline was 47 years (Q1-Q3 36-56). Skeletal burden correlated with baseline Physical Function (rs=-0.281,p=0.007). QoL was in all domains lower compared to the general population. New referrals reported clinically important differences (CID) over time in domains Physical Function (mean 67±SD24 to 74±21, effect size (ES) 0.31, p=0.020), Role Physical (39±41 to 53±43, ES 0.35, p=0.066), Social Functioning (64±24 to 76±23, ES 0.49, p=0.054), and Health Change (39±19 to 53±24, ES 0.76, p=0.016), chronic patients in Physical Function (52±46 to 66±43, ES 0.31, p=0.023) and Emotional Wellbeing (54±27 to 70±15, ES 0.59, p<0.001). New referrals reported a CID of 1 point in maximum pain, average pain and pain interference, chronic patients reported stable scores. Change in pain interference and Role Physical were correlated (rs=-0.472,p<0.001). Patients with limited disease extent improved more than patients with severe disease. Patients receiving FD-related therapy had lower baseline scores than patients not receiving therapy and reported improvements in QoL after 1 year. Yet also patients without FD-related therapy improved in Physical Function. Conclusions: All FD-subtypes may induce pain and reduced QoL. A multidisciplinary care pathway for FD/MAS may improve pain and QoL, mainly in new referrals without MAS comorbidities with low baseline scores. Therefore we recommend referral of patients with all subtypes of FD/MAS to specialized academic centers.
Identification of molecular subtypes and a novel prognostic model of diffuse large B-cell lymphoma based on a metabolism-associated gene signature
Authors: He Jing , Chen Ziwei , Xue Qingfeng , Sun Pingping , Wang Yuan , Zhu Cindy（Xinyi） , Shi Wenyu 
Published: February 2022

Abstract
Background:Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma in adults. Metabolic reprogramming in tumors is closely related to the immune microenvironment. This study aimed to explore the interactions between metabolism-associated genes (MAGs) and DLBCL prognosis and their potential associations with the immune microenvironment. Methods:Gene expression and clinical data on DLBCL patients were obtained from the GEO database. Metabolism-associated molecular subtypes were identified by consensus clustering. A prognostic risk model containing 14 MAGs was established using Lasso-Cox regression in the GEO training cohort. It was then validated in the GEO internal testing cohort and TCGA external validation cohort. GO, KEGG and GSVA were used to explore the differences in enriched pathways between high- and low-risk groups. ESTIMATE, CIBERSORT, and ssGSEA analyses were used to assess the immune microenvironment. Finally, WGCNA analysis was used to identify two hub genes among the 14 model MAGs, and they were preliminarily verified in our tissue microarray (TMA) using multiple fluorescence immunohistochemistry (mIHC).Results：Consensus clustering divided DLBCL patients into two metabolic subtypes with significant differences in prognosis and the immune microenvironment. Poor prognosis was associated with an immunosuppressive microenvironment. A prognostic risk model was constructed based on 14 MAGs and it was used to classify the patients into two risk groups; the high-risk group had poorer prognosis and an immunosuppressive microenvironment characterized by low immune score, low immune status, high abundance of immunosuppressive cells, and high expression of immune checkpoints. Cox regression, ROC curve analysis, and a nomogram indicated that the risk model was an independent prognostic factor and had a better prognostic value than the International Prognostic Index (IPI) score. The risk model underwent multiple validations and the verification of the two hub genes in TMA indicated consistent results with the bioinformatics analyses.Conclusions:The molecular subtypes and a risk model based on MAGs proposed in our study are both promising prognostic stratification tools in DLBCL, which may provide novel insights for developing accurate targeted cancer therapies.
Near Infrared Molecular Imaging of Breast Cancer Cell Lines Using a Novel ER Targeted Fluorescent Dye
Authors: Pillai Vinay Jha , Jose Iven 
Published: February 2022

Abstract
Hormone-targeted contrast agents bind with functional groups associated with the physiology of breast cancer leading to improved prognosis. We have synthesized a novel estrogen receptor (ER) targeted near-infrared fluorescent dye referred to as Novel Dye Conjugate (nDC). It is a conjugate of 17β-estradiol with a derivative of indocyanine green dye, bis-1,1-(4-sulfobutyl) indotricarbocyanine-5-carboxylic acid, sodium salt. Structural and photophysical characterizations of nDC followed with breast cancer cell lines (MCF-7 and MDA MB 231) stained with novel dye were carried out. The target, MCF-7 cells (ER-positive) showed specific high-affinity binding sites of novel dye onto the nucleus and membrane of ER-positive cells, in contrast, the control, MDA MB 231 (ER-negative) showed only plasma membrane staining. Similar results were obtained when ER expressing cancerous tissues (viz. Non-Invasive Ductal Carcinoma, Non-Invasive Lobular Carcinoma, Non-Invasive Adenocarcinoma, and Non-Invasive Medullary Carcinoma) were stained with novel dye. Approximately 70% of breast cancer cases are ER-positive, therefore nDC being ER binding properties can unambiguously improve the specificity and sensitivity of breast cancer imaging.
Associations of head circumference trajectories and growth-sensitive periods during the first two years of life with adolescent cognitive, emotional and behavioral health: A birth cohort in rural western China
Authors: Zhu Zhonghai , Shen Jiali , Zhu Yingze , Wang Liang , Qi Qi , Wang Xueyao , Li Chao , Andegiorgish Amanuel Kidane , Elhoumed Mohamed , Cheng Yue , Dibley Michael J , Zeng Lingxia 
Published: February 2022

Abstract
Purpose The associations of early-life head circumference (HC) with child cognition and emotional and behavioral health among generally healthy population remain unclear. We aimed to examine the associations of early-life HC trajectories with adolescent neurodevelopmental and mental health and to identify HC growth-sensitive period. MethodsWe conducted a prospective, community-based birth cohort in rural western China, and 745 adolescents aged 10-14 years were followed between June to December 2016. We repeatedly assessed child HC for eight times during the first two years of life, and adolescent cognitive and emotional and behavioral outcomes using Wechsler Intelligence Scale for Children and Youth Self-Report, respectively. We applied group-based trajectory modeling to identify HC trajectories and used conditional growth to derive sensitive periods. ResultsWe identified five distinct HC trajectories characterized as Start below average-then decrease (7.8% of the sample), Start below average-then increase (6.8%), Start average-then decrease (33.4%), Consistently average (37.9%), and Consistently above average (14.1%). Infants in the trajectory of consistently above average had higher cognitive scores at early adolescence as compared to those from suboptimal trajectories, with adjusted mean differences ranging from -2.84 to -8.99 points. The conditional gains show that the sensitive HC growth period appeared to be between 0-6 months. While we found null associations between HC measures and adolescent emotional and behavioral health.ConclusionsRoutine HC measurements especially during the first 6 months were recommended for monitoring child cognition but for mental health. Integrated prenatal and postnatal interventions should be pursued to promote child development.
Interlocking Directorate and Firm Performance: Distance, Size, and Endogeneity
Authors: Buccellato Tullio , Busin Riccardo , Casarin Roberto , Corò Giancarlo 
Published: February 2022

Abstract
BackgroundThis paper contributes to the literature on interlocking directorates (ID) by providing a new solution to the two inference issues arising in the joint analysis of interlocks and firm performance which are the endogenous nature of ID and sample selection bias due to the exclusion of isolated firms.Method Some key determinants of ID network formation are identified and used to control for endogeneity. The instruments for eigen-centrality and clustering coefficient are based on the features of the degree-neighbors of a firm. The estimated the Mills ratio is used as a regressor in the second stage of the two-stage least square to deal with the sample selection bias. We analyze the impact of the positioning in the network on firms’ performance and inspect how the impact varies across firms of different sizes drawing on information relating to 37,324 firms in the interlocking network which, to our knowledge, is the widest dataset ever used in approaching the study of IDResultsOur results, made robust for endogeneity and sample selection bias, suggest that eigenvector centrality and the clustering coefficient have a positive and significant impact on all the performance measures and that this effect is more pronounced for small firms.ConclusionA new inference framework is provided to assess the impact of the positioning of the firm in the network on its performance while controlling for endogeneity in the network structure. An application of the proposed framework to an original ID dataset provides new empirical results on the firm positing within the ID network.
One of the main culprits of Morchella (Morohellaceae: Morchella) pileus rot disease: Pestalotiopsis trachicarpicola
Authors: liang zhen , li linhui 
Published: February 2022

Abstract
We found some diseased fruiting bodies when cultivating Morchella. The infected ascomata were covered by white mycelia mainly on the pileus, and the infection cause the fruiting body to rot and die. A total of 5 fungi were separated from symptomatic tissue. One of them was proved to be pathogenic by Koch’s postulates. The pathogen was identified as Pestalotiopsis trachicarpicola based on its morphology and Multi-gene (ITS,β-tubulin and tef1) analysis. This is the first report of pileus rot disease on cultivated Morchella caused by P. trachicarpicola in China, which is of positive significance for the quarantine of cultivated soil of Morchella.
CDMPred: A Tool for Predicting Cancer Driver Mutations with High-Quality Passenger Mutations and Ensemble Learning
Authors: Wang Lihua , Sun Haiyang , Yue Zhenyu , Xia Junfeng , Li Xiaoyan 
Published: February 2022

Abstract
Background
Benchmark datasets are of great importance for model construction and must be representative of the phenomenon being investigated. Currently available computational methods for predicting driver mutations have been trained with positive sample data, typically derived from cancer-related databases such as the Catalogue of Somatic Mutations in Cancer (COSMIC) database, whereas negative samples are generally based on statistical methods or putative samples. Obviously, negative samples are not enough for modelling the broad spectrum of passenger mutations that occur.
Results
To address these problems, we constructed a balanced dataset with driver mutations from the COSMIC database and high-quality passenger mutations from the Cancer Passenger Mutation database (dbCPM). We then encoded the features of these mutations. According to feature correlation analysis, we constructed a cancer driver missense mutations predictor (CDMPred) with feature selection via the Extreme Gradient Boosting (XGBoost) classifier ensemble learning method. The proposed CDMPred method, with the top 10 features and XGBoost, achieved area under the receiver operating characteristic curve values of 0.83 and 0.80 by 10-fold cross-validation of the training and independent test sets, respectively. Moreover, CDMPred outperformed several state-of-the-art mutation prediction methods for cancer-specific and general diseases in terms of AUC and area under the precision-recall curve.
Conclusions
High-quality passenger mutations of training data and ensemble learning are benefit to CDMPred. We expect that CDMPred can serve as a valuable method for prediction of cancer driver mutations which can further lead to deeper understanding on personal therapy.
Discovery of European frogbit (Hydrocharis morus-ranae L.) in Oconto County, Wisconsin: A summary of physical and plant community changes at a Lake Michigan coastal marsh
Authors: Rutherford Ryne Douglas , Hartsock Jeremy , Danz Nicholas 
Published: February 2022

Abstract
Located in Oconto County, Wisconsin, Oconto Marsh #2 is a Great Lakes Coastal Wetland Monitoring Program (CWMP) study site that borders the shoreline of Lake Michigan. Plant communities were characterized at Oconto Marsh #2 along three fixed transects in 2011, 2016, 2017 and 2021, a period when Lake Michigan water levels increased by two meters. Transects were placed to intersect with three vegetation zones: submergent, emergent, and wet meadow. Here, we highlight physical landscape changes and the vegetation composition changes that occurred from 2011 to 2021. From satellite imagery, we estimate the vegetated wetland area decreased by 50 percent. High energy wave action and ice scour penetrating farther inland are likely most responsible for causing these changes. Using multivariate ordination and PERMANOVA, we show plant composition in 2011 and 2021 was different from years 2016 and 2017. While invasive Phragmites australis was treated with herbicide in 2014 (herbicide treatment completed by non-CWMP groups), disturbance from progressively increasing water levels has facilitated considerable species turnover since monitoring began. Despite successful treatment of P. australis, the establishment of additional non-native species has caused site-wide mean coefficient of conservatism scores to decline from a calculated score of 4.2 in 2011 to 3.3 in 2021. Of critical importance, we discovered the highly invasive species European frogbit (EFB) (Hydrocharis morus-ranae L) near the research transects in 2021. This is the first documented occurrence of EFB in Wisconsin. The newly discovered EFB range spans 31 km along the general shoreline from Marinette to Oconto, WI.
Glyphosate-Induced Oxidative Stress, Genotoxic Effect and Differential Expression of P53, Bax and Bcl2 in Different Mice Tissues
Authors: Locatelli Claudriana , Zancanaro Vilmair , Bellaver Emyr , Baratto César 
Published: February 2022

Abstract
Glyphosate is one of the most widely used herbicides in Brazil and worldwide for controlling weeds in various agricultural crops, which raises concern on possible environmental impacts and human health. The present study aimed at assessing the induction of mutagenic changes and oxidative stress in different tissues of animals exposed to glyphosate and Trop®. Male Swiss mice were submitted to gavage treatment with glyphosate and Trop® at the concentrations of 50 and 200 mg/kg for 5 days. After the treatments the animals were euthanized and their bone marrow, liver, lung, and kidney were collected. The bone marrow was used for micronucleus. The liver, lung and kidney were submitted to biochemical analyzes of thiobarbituric acid reactive substances (TBARS), catalase enzyme, total antioxidant, in addition to evaluating the expression of Bax, Bcl2 and p53 proteins, as well as the expression of p53 gene transcription. The animals were weighed before and after the treatments. The results showed a significant weight reduction in the animals treated for 5 days. The occurrence of micronuclei was significant in the bone marrow. A significant increase in lipid peroxidation, besides changes in both, the catalase enzyme and total antioxidant levels were seen in all tissues. There was a decrease in p53 gene and Bax protein expression, and an increase of the Bcl2 protein expression. These results might suggest that the exposure to glyphosate and the consumption of antioxidant defenses can cause oxidative stress. In addition, changes in cellular biomarkers regarding glyphosate and Trop® were similar.
Cu and Ni Co-Sputtered Heteroatomic Thin Film for Enhanced Nonenzymatic Glucose Detection
Authors: Barbee Brianna , Muchharla Baleeswaraiah , Adedeji Adetayo , Karoui Abdennaceur , Sadasivuni Kishor Kumar , Sha Mizaj Shabil , Abdullah Aboubakr M. , Slaughter Gymama , kumar bijandra 
Published: February 2022

Abstract
In this work, we report a wafer-scale and chemical-free fabrication of nickel (Ni) and copper (Cu) heteroatomic Cu-Ni thin films using RF magnetron sputtering technique for non-enzymatic glucose sensing application. The as-prepared wafer-scale Cu-Ni thin films exhibits excellent electrocatalytic activity toward glucose oxidation with a 1.86 µM detection limit in the range of 0.01 mM to 20 mM range. The Cu-Ni film shows 1.3- and 5.4-times higher glucose oxidation activity in comparison to the Cu and Ni electrodes, respectively. The improved electrocatalytic activity is attributed to the synergistic effect of the bimetallic catalyst and high density of grain boundaries. The Cu-Ni electrodes also possessed excellent anti-interference characteristics. These results indicate that Cu-Ni heteroatomic thin film can be a potential candidate for the development of non-enzymatic glucose biosensor because of its chemical free synthesis, excellent reproducibility, reusability, and long-term stability.