bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copy number variation of the CCDC39 gene is associated with growth traits in Chinese cattle
Authors: Hu Linyong , Yu Junjian , Huang Rong , Yang Peng , Zhang Zijing , Chai Yanan , Shi Qiaoting , Chen Fuying , Liu Xian , Li Zhiming , Ru Baorui , Wang Eryao , Lei Chuzhao , Peng Wei , Huang Yongzhen 
Published: March 2022

AbstractBackgroundCopy number variation (CNV) has become an essential part of genetic structural variation. Coiled‐coil domain containing 39 (CCDC39) is a gene that related to the growth and development of organs and tissues. It is identified that it has a CNV region by animal genome resequencing.ObjectiveIn this study, we detected the phenotypic traits and different distributions of CCDC39 gene copy numbers in five Chinese cattle breeds (Qinchuan (QC) cattle, Yunling (YL) cattle, Xianan (XN) cattle, Pinan (PN) cattle and Jiaxian (JX) cattle).MethodsFive hundred and six cattle were randomly selected for CNV distribution detection. Blood samples were taken and genomic DNA was extracted. Different tissues were obtained from adult (n = 3) XN cattle, including heart, liver, kidney, skeletal muscle and lung. The genome qPCR experiment was performed with SYBR Green in triplicate. CDNA qPCR was used to detect the expression level of CCDC39 in different tissues and varieties. Using SPSS v20.0 software, the relationship between CCDC39 CNV and the growth traits of PN, XN, QC, NY and YL cattle breeds was analyzed by one‐way analysis of variance (ANOVA).ResultsThe results showed that the expression of CCDC39 in lung was higher than that in other tissues. The expression in liver and kidney was similar, but the expression in heart and muscle was less. It can be seen that the duplication type of QC cattle CCDC39 CNV is higher than the deletion or normal in the height at hip cross. The normal type of PN cattle in body length and hip width was better than duplication and deletion (p < 0.05). In XN cattle, the deletion type of CNV had superior growth characteristics in heart girth and cannon bone circumference compared with the duplication type and the normal type (p < 0.05).ConclusionThe study revealed a significant association between CNV of CCDC39 gene and growth traits in different Chinese cattle breeds.
Effect of averaging time windows on wind resource assessment of small wind turbines
Authors: Goit Jay Prakash , Taguchi Masakage , Tatsuno Junya , Kameda Takatsugu 
Published: March 2022

AbstractIn wind energy, the general practice in assessing the wind resource of a site is to employ a 10‐min averaging to measured wind data. However, small wind turbines (SWTs) with rotor diameters <15 m will have a shorter response time scale; thus, an averaging time window of 10 min is too long for accurate wind resource assessments. The current study investigates the effect of averaging time windows on wind resource assessment and power estimation of SWTs. To that end, wind data from a 1‐year measurement campaign is analysed using two short‐term averaging windows of 30 and 60 s and two long‐term averaging windows of 5 and 10 min. Although the average wind speed over the 1‐year period is 1.3 m/s with all four windows, when wind speeds higher than 3 m/s are considered, the average wind speed obtained using a 30‐s averaging window is 8% higher than that obtained using a 10‐min window. Power prediction using the 10 kW SWT shows that the predicted power using a 30‐s window is almost twice as large compared to that estimated using a 10‐min window. Finally, the rotational speed of the SWT obtained with short‐term averaging shows better agreement with that computed by direct modelling of the turbine with the measured wind speed as the input to the model. The study thus shows that the performance of SWTs will be better predicted if short‐term averaging windows are used.
On a three‐dimensional chemotaxis‐Stokes system with nonlinear sensitivity modeling coral fertilization
Authors: Zheng Pan , Yang Hanchun 
Published: March 2022

AbstractThis paper is concerned with the effects of nonlinear sensitivity on boundedness of solutions for the following chemotaxis‐Stokes system
in a smoothly bounded domain under no‐flux boundary conditions for and no‐slip boundary conditions for u, where n and m denote the densities of unfertilized sperms and eggs, respectively, c stands for the concentration of the signal, u represents the velocity of fluid, P is the pressure within the fluid and ϕ is the gravitational potential. This system describes the process of coral fertilization occurring in ocean flow. Based on the novel conditional estimates for c and u, it is proved that for all appropriately regular nonnegative initial data, this system possesses a unique globally bounded solution provided that satisfies with , which improves the known subcritical exponent under fluid‐free case.
Setting the Scene: How to Enhance the Knowledge and Practice of Transformation Literacy
Authors: Kuenkel Petra 
Published: March 2022

AbstractThis chapter looks at the scale and modes of transformations needed toward regenerative civilizations. Societal transformations have always happened in human history, and many have been consciously and actively promoted. What is new about the situation at the beginning of the twenty-first century is both scale and depth of transformations required. Institutional and political structures on which our globalized current systems are built, tend to perpetuate the status quo. It is therefore important to create new strategic and communicative structures in the form of cross-sector and cross-institutional collaboration that initiate and facilitate transformations. The chapter suggests that transformation agents need to act more consciously as part oftransformation systemsaround issues such as climate protection, regenerative pathways and economic systems change. The chapter elaborates three strategic core approaches that require conscious attention intransformation literacy:Collective stewardshipas the pro-active engagement for a regenerative future in mutually supportive strategies;visionary multiplicityas the acknowledgment of plural approaches to the quality of life; andnetwork leverageas the deliberate and reflective use of power across institutions. The chapter concludes with an overview of the different authors’ chapters.
Superpotentials of D-branes in Calabi-Yau manifolds with several moduli by mirror symmetry and blown-up
Authors: Li Xuan , Jing Yuan-Chun , Yang Fu-Zhong 
Published: March 2022

Abstract
We study B-brane superpotentials depending on several closed- and open-moduli on Calabi-Yau hypersurfaces and complete intersections. By blowing up the ambient space along a curve wrapped by B-branes in a Calabi-Yau manifold, we obtain a blow-up new manifold and the period integral satisfying the GKZ-system. Via mirror symmetry to A-model, we calculate the superpotentials and extract Ooguri-Vafa invariants for concrete examples of several open-closed moduli in Calabi-Yau manifolds.
Systematics of perturbatively flat flux vacua
Authors: Carta Federico , Mininno Alessandro , Shukla Pramod 
Published: March 2022

Abstract
In this article, we present a systematic analysis of the so-called perturbatively flat flux vacua (PFFV) for the mirror Calabi-Yau (CY) 3-folds ($$ {\overset{\sim }{X}}_3 $$

X
~

3

) with h1,1($$ {\overset{\sim }{X}}_3 $$

X
~

3

) = 2 arising from the Kreuzer-Skarke database of the four-dimensional reflexive polytopes. We consider the divisor topologies of the CY 3-folds for classifying the subsequent models into three categories; (i) models with the so-called Swiss-cheese structure, (ii) models with the K3-fibered structure, and (iii) the remaining ones which we call as models of “Hybrid type”. In our detailed analysis of PFFV we find that for a given fixed value of the D3 tadpole charge Nflux, the K3-fibered mirror CY 3-folds have significantly larger number of such PFFV as compared to those which have Swiss-cheese structure, while the Hybrid type models have a mixed behavior. We also compute the Gopakumar-Vafa invariants necessary for fixing the flat valley in the weak string-coupling and large complex-structure regime by using the non-perturbative effects, which subsequently reduce the number of physically trustworthy vacua quite significantly. Moreover, we find that there are some examples in which the PFFV are protected even at the leading orders of the non-perturbative effects due to the some underlying symmetry in the CY geometry, which we call as “Exponentially flat flux vacua”. We also present a new class of PFFV using the S-duality arguments.
Essential m-dissipativity and hypocoercivity of Langevin dynamics with multiplicative noise
Authors: Bertram Alexander , Grothaus Martin 
Published: March 2022

AbstractWe provide a complete elaboration of the $$L^2$$

L
2

-Hilbert space hypocoercivity theorem for the degenerate Langevin dynamics with multiplicative noise, studying the longtime behavior of the strongly continuous contraction semigroup solving the abstract Cauchy problem for the associated backward Kolmogorov operator. Hypocoercivity for the Langevin dynamics with constant diffusion matrix was proven previously by Dolbeault, Mouhot and Schmeiser in the corresponding Fokker–Planck framework and made rigorous in the Kolmogorov backwards setting by Grothaus and Stilgenbauer. We extend these results to weakly differentiable diffusion coefficient matrices, introducing multiplicative noise for the corresponding stochastic differential equation. The rate of convergence is explicitly computed depending on the choice of these coefficients and the potential giving the outer force. In order to obtain a solution to the abstract Cauchy problem, we first prove essential self-adjointness of non-degenerate elliptic Dirichlet operators on Hilbert spaces, using prior elliptic regularity results and techniques from Bogachev, Krylov and Röckner. We apply operator perturbation theory to obtain essential m-dissipativity of the Kolmogorov operator, extending the m-dissipativity results from Conrad and Grothaus. We emphasize that the chosen Kolmogorov approach is natural, as the theory of generalized Dirichlet forms implies a stochastic representation of the Langevin semigroup as the transition kernel of a diffusion process which provides a martingale solution to the Langevin equation with multiplicative noise. Moreover, we show that even a weak solution is obtained this way.
Surface chemistry of metal oxide nanoparticles: NMR and TGA quantification
Authors: Kunc Filip , Gallerneault Mary , Kodra Oltion , Brinkmann Andreas , Lopinski Gregory P. , Johnston Linda J. 
Published: March 2022

AbstractSurface functionalization is widely used to control the behavior of nanomaterials for a range of applications. However, methods to accurately quantify surface functional groups and coatings are not yet routinely applied to nanomaterial characterization. We have employed a combination of quantitative NMR (qNMR) and thermogravimetric analysis (TGA) to address this problem for commercial cerium, nickel, and iron oxide nanoparticles (NPs) that have been modified to add functional coatings with (3-aminopropyl)triethoxysilane (APTES), stearic acid, and polyvinylpyrrolidone (PVP). The qNMR method involves quantification of material that is released from the NPs and quantified in the supernatant after removal of NPs. Removal of aminopropylsilanes was accomplished by basic hydrolysis whereas PVP and stearic acid were removed by ligand exchange using sodium hexametaphosphate and pentadecafluorooctanoic acid, respectively. The method accuracy was confirmed by analysis of NPs with a known content of surface groups. Complementary TGA studies were carried out in both air and argon atmosphere with FT-IR of evolved gases in argon to confirm the identity of the functional groups. TGA measurements for some unfunctionalized samples show mass loss due to unidentified components which makes quantification of functional groups in surface-modified samples less reliable. XPS provides information on the presence of surface contaminants and the level of surface hydroxylation for selected samples. Despite the issues associated with accurate quantification using TGA, the TGA estimates agree reasonably well with the qNMR data for samples with high surface loading. This study highlights the issues in analysis of commercial nanomaterials and is an advance towards the development of generally applicable methods for quantifying surface functional groups.
Graphical abstract
Platelet Activation Markers in Children with Pulmonary Arterial Hypertension Associated with Congenital Heart Disease
Authors: Awad Abdulhalim , Elnemr Shimaa , Hodeib Hossam , El Amrousy Doaa 
Published: March 2022

AbstractThe study aimed to evaluate mean platelet volume (MPV), platelet distribution width (PDW), and platecrit in children with pulmonary arterial hypertension associated with congenital heart disease (PAH-CHD), to assess the predictive value of these platelet activation markers for adverse outcomes, and to correlate their levels with various data in these patients. This prospective cohort study included 60 children with PAH-CHD as group I and 60 children with CHD and no PAH as group II. Another 60 healthy children of matched age and sex served as the control group. All included children were evaluated by echocardiography. MPV, PDW, and platecrit were also measured using an automated blood counter. All patients were followed up for death or readmission for 6 months. MPV, PDW, and platecrit were significantly higher in group I compared to group II and the control group and they correlated well with increasing severity of PAH. MPV, PDW, and platecrit positively correlated with right ventricular diameter and mean pulmonary artery pressure, however they correlated negatively with right ventricular systolic and diastolic function. The best cut-off of platelet activation markers levels to predict poor prognosis in group I was > 11.2 FL with 75% sensitivity and 96.6% specificity for MPV, > 12.7 FL with 75% sensitivity and 61.5% specificity for PDW, and > 0.505% with 75% sensitivity and 93.2% specificity for platecrit. MPV, PDW, and platecrit were elevated in children with PAH-CHD and found to be good predictive markers for poor prognosis in these children.
Synovial fluid calprotectin in diagnosing periprosthetic joint infection: A meta-analysis
Authors: Hantouly Ashraf T. , Salameh Motasem , Toubasi Ahmad A. , Salman Loay A. , Alzobi Osama , Ahmed Abdulaziz F. , Hameed Shamsi , Zikria Bashir , Ahmed Ghalib 
Published: March 2022

AbstractPurposePeriprosthetic joint infection (PJI) is one of the most debilitating complications following joint replacement surgery. Synovial biomarkers, such as Calprotectin, have become valuable in the diagnosis of PJI. This meta-analysis aimed to investigate the role of synovial Calprotectin as a diagnostic test in PJI.MethodsThis meta-analysis was conducted with adherence to PRISMA guidelines. PubMed, Cochrane, Web of Science, and Google Scholar were searched until February 2022. Inclusion criteria were as follows: all studies in which the patients with joint replacements were evaluated for PJI; synovial Calprotectin was the biomarker of choice to diagnose PJI; standardized guidelines were used as the gold standard for the diagnosis; and a comparison between the guidelines and Calprotectin results was made. Diagnostic parameters such as sensitivity, specificity, diagnostic odds ratio (DOR), positive predictive value, negative predictive value, and area under the curve (AUC) were calculated for the included studies to evaluate synovial Calprotectin for PJI diagnosis.ResultsThe total number of the included patients was 618 from eight studies. The pooled sensitivity, specificity, and diagnostic odds ratio of Calprotectin test were 92% (95%CI: 84%-98%), 93% (95%CI: 84%-99%), and 187.61 (95%CI: 20.21–1741.18), respectively. The results showed that the negative and positive likelihood ratios of the Calprotectin test were 0.07 (95%CI: 0.02–0.22) and 9.91 (95%CI: 4.11–23.93), respectively. The SROC showed that the area under the curve for Calprotectin test was 0.935.ConclusionSynovial Calprotectin is a valuable biomarker as it provides a reliable and rapid diagnosis of PJI. It has the potential to be used in clinical practice due to its high sensitivity and specificity that are comparable to the other utilized biomarkers. Another advantage is its low cost relative to other biomarkers.
Variable selection in Propensity Score Adjustment to mitigate selection bias in online surveys
Authors: Ferri-García Ramón , Rueda María del Mar 
Published: March 2022

AbstractThe development of new survey data collection methods such as online surveys has been particularly advantageous for social studies in terms of reduced costs, immediacy and enhanced questionnaire possibilities. However, many such methods are strongly affected by selection bias, leading to unreliable estimates. Calibration and Propensity Score Adjustment (PSA) have been proposed as methods to remove selection bias in online nonprobability surveys. Calibration requires population totals to be known for the auxiliary variables used in the procedure, while PSA estimates the volunteering propensity of an individual using predictive modelling. The variables included in these models must be carefully selected in order to maximise the accuracy of the final estimates. This study presents an application, using synthetic and real data, of variable selection techniques developed for knowledge discovery in data to choose the best subset of variables for propensity estimation. We also compare the performance of PSA using different classification algorithms, after which calibration is applied. We also present an application of this methodology in a real-world situation, using it to obtain estimates of population parameters. The results obtained show that variable selection using appropriate methods can provide less biased and more efficient estimates than using all available covariates.
Circulating miR-200 family as predictive markers during systemic therapy of metastatic breast cancer
Authors: Fischer Chiara , Deutsch Thomas M. , Feisst Manuel , Rippinger Nathalie , Riedel Fabian , Hartkopf Andreas D. , Brucker Sara Y. , Domschke Christoph , Fremd Carlo , Michel Laura , Burwinkel Barbara , Schneeweiss Andreas , Turchinovich Andrey , Wallwiener Markus 
Published: March 2022

Abstract
Purpose
Circulating miRNAs can provide valid prognostic and predictive information for breast cancer diagnosis and subsequent management. They may comprise quintessential biomarkers that can be obtained minimally invasively from liquid biopsy in metastatic breast cancer patients. Therefore, they would be clinically crucial for monitoring therapy response, with the goal of detecting early relapse. This study investigated miRNA expression in patients with early and/or late relapse, and the predictive value for assessing overall (OS) and progression-free survival (PFS).

Methods
Forty-seven patients with metastatic breast cancer from the University Women’s Hospital Heidelberg were enrolled in this study. Expression of miR-200a, miR-200b, miR-200c, miR-141, and miR-429 was analyzed by RT-qPCR before a new line of systemic therapy and after the first cycle of a respective therapy. Tumor response was assessed every 3 months using the RECIST criteria. Statistical analysis focused on the relation of miR-200s expression and early vs. late cancer relapse in relation to systemic treatment. The association of miRNAs with PFS and OS was investigated.

Results
Before starting a new line of systemic therapy, miR-429 (p = 0.024) expression was significantly higher in patients with early relapse (PFS ≤ 4 months) than in patients with late relapse (PFS > 4 months). After one cycle of systemic therapy, miR-200a (p = 0.039), miR-200b (p = 0.003), miR-141 (p = 0.017), and miR-429 (p = 0.010) expression was higher in early than in late progressive cancer. In addition, 4 out of 5 miR-200 family members (miR-200a, miR-200b, miR-141, and miR-429) predicted PFS (p = 0.048, p = 0.008, p = 0.026, and p = 0.016, respectively). Patients with heightened miRNA levels showed a significant reduction in OS and PFS.

Conclusion
Circulating miR-200s were differentially expressed among patients with late and/or early relapse. 4 of 5 members of the miR-200 family predicted significantly early relapse after systemic treatment. Our results encourage the use of circulating miR-200s as valuable prognostic biomarkers during metastatic breast cancer therapy.
Coffee, smoking and aspirin are associated with age at onset in idiopathic Parkinson’s disease
Authors: Gabbert Carolin , König Inke R. , Lüth Theresa , Kolms Beke , Kasten Meike , Vollstedt Eva-Juliane , Balck Alexander , Grünewald Anne , Klein Christine , Trinh Joanne 
Published: March 2022

AbstractParkinson’s disease (PD) is a progressive neurodegenerative disorder. Genetic modifiers, environmental factors and gene–environment interactions have been found to modify PD risk and disease progression. The objective of this study was to evaluate the association of smoking, caffeine and anti-inflammatory drugs with age at onset (AAO) in a large PD cohort. A total of 35,963 American patients with idiopathic PD (iPD) from the Fox Insight Study responded to health and lifestyle questionnaires. We compared the median AAO between different groups using the non-parametric Mann–Whitney U test. Non-parametric Spearman’s correlation was used for correlation assessments and regression analysis was used to assess interaction between variables. We found that smoking (p < 0.0001), coffee drinking (p < 0.0001) and aspirin intake (p < 0.0001) show an exploratory association with AAO in PD, that was further supported by multivariate regression models. The association of aspirin with PD AAO was replicated in another cohort (EPIPARK) (n = 237 patients with PD).
The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants
Authors: Kwantes Michiel , Wichard Thomas 
Published: March 2022

Abstract
Main conclusion
We advanceUlva’s genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes.

Abstract
The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U. mutabilis vector-insertion mutants. In the created insertional library, we identified a null mutant with an insertion in an apoptotic protease activating factor 1 helical domain (APAF1_C)/WD40 repeat domain-encoding gene. Protein domain architecture analysis combined with phylogenetic analysis revealed that this gene is a member of a subfamily that arose early in the evolution of green plants (Viridiplantae) through the acquisition of a gene that also encoded N-terminal nucleotide-binding adaptor shared by APAF-1, certain R-gene products and CED-4 (NB-ARC) and winged helix-like (WH-like) DNA-binding domains. Although phenotypic analysis revealed no mutant phenotype, gene expression levels in control plants correlated to the presence of bacterial symbionts, which U. mutabilis requires for proper morphogenesis. In addition, our analysis led to the discovery of a putative Ulva nucleotide-binding site and leucine-rich repeat (NBS-LRR) Resistance protein (R-protein), and we discuss how the emergence of these R proteins in green plants may be linked to the evolution of the APAF1_C/WD40 protein subfamily.