bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of late-season sheep grazing following early-season steer grazing on population dynamics of sericea lespedeza in the Kansas Flint Hills
Authors: Lemmon Jack E , Fick Walter H , Alexander Jonathan A , Gatson Garth A , Olson K C 
Published: April 2023

Abstract
Mature ewes were used in a 4-yr study to evaluate effects of intensive late-season sheep grazing on vigor of sericea lespedeza in native tallgrass prairie. Pastures (N = 8; 31 ± 3.6 ha) infested with sericea lespedeza (initial basal frequency = 1.4%) were assigned randomly to one of two treatments: early-season beef steer grazing (1.1 ha/steer; initial BW = 258 ± 34 kg) from April 15 to July 15 followed by no grazing for the rest of the year (control; STR) or steer grazing from April 15 to July 15 followed by intensive grazing by mature ewes (0.2 ha/ewe; SHP) from August 1 to October 1. Ewes (initial BW = 65 ± 3.1 kg) were assigned randomly to graze four of eight pastures; remaining pastures were not grazed from August 1 to October 1. Vegetation responses to treatment were measured along four permanent 100-m transects in each pasture. Herbivory on sericea lespedeza was monitored weekly in each pasture from July 21 to October 7. Herbivory on sericea lespedeza in SHP and STR after steer grazing and before sheep grazing was not different (P = 0.51). In contrast, sericea lespedeza herbivory following sheep grazing was greater (P &lt; 0.01) in SHP than in STR. Herbivory of individual sericea plants was greater (P &lt; 0.01) in SHP than in STR by the end of week 1 of the sheep-grazing period (10.6% vs. 0.5%); moreover, herbivory on sericea lespedeza steadily increased (P ≤ 0.01) such that 92.1% of sericea lespedeza plants were grazed in SHP compared to 1.4% in STR by week 8 of the sheep-grazing period. Whole-plant DM weight of sericea lespedeza at dormancy was less (P &lt; 0.01) in SHP than in STR. Additionally, annual seed production by sericea lespedeza was less (P &lt; 0.01) in SHP than in STR (114 vs. 864 seeds/plant). Pasture forage biomass was not different (P = 0.76) between SHP and STR after the steer-grazing period. Conversely, STR had more (P &lt; 0.01) residual forage biomass than SHP at the end of the sheep-grazing period. Growth performance of beef steers grazing from April 15 to July 15 annually was not different (P ≥ 0.59) between treatments. Our results were interpreted to suggest that intensive late-season grazing by sheep decreased vigor of sericea lespedeza. Late-season sheep grazing decreased forage biomass by 904 kg DM/ha compared with late-season rest; however, residual biomass was adequate to prevent soil-moisture loss and erosion during the dormant season.
Evolutionary repeatability of emergent properties of ecological communities
Authors: Venkataram Sandeep , Kryazhimskiy Sergey 
Published: April 2023

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics.This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory
Authors: Ruelens Philip , Wynands Thomas , de Visser J. Arjan G. M. 
Published: April 2023

What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. Additionally, pleiotropy may promote repeatability by allowing large fitness benefits of single mutations via adaptive combinations of phenotypic effects. Yet, this latter evolutionary potential may be reaped solely by specific types of mutations able to realize optimal combinations of phenotypic effects while avoiding the costs of pleiotropy. Here, we address the interaction of gene pleiotropy and mutation type on evolutionary repeatability in a meta-analysis of experimental evolution studies withEscherichia coli. We hypothesize that single nucleotide polymorphisms (SNPs) are principally able to yield large fitness benefits by targeting highly pleiotropic genes, whereas indels and structural variants (SVs) provide smaller benefits and are restricted to genes with lower pleiotropy. By using gene connectivity as proxy for pleiotropy, we show that non-disruptive SNPs in highly pleiotropic genes yield the largest fitness benefits, since they contribute more to parallel evolution, especially in large populations, than inactivating SNPs, indels and SVs. Our findings underscore the importance of considering genetic architecture together with mutation type for understanding evolutionary repeatability.This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
Identification of Iron Deficiency-Induced Chlorosis Tolerant Lines from Wild Rice Germplasm
Authors: Kumar Rahul 
Published: April 2023

AbstractThe cultivation of transplanted rice has led to depletion of groundwater levels in many parts of the world. Direct-seeded rice under aerobic conditions is an alternative production technology that requires much less water. However, under aerobic conditions, iron in the soil is oxidized from ferric to ferrous, which is not easily available for rice, resulting in iron deficiency-induced chlorosis (IDIC) and a drastic reduction in seed yield. Cultivated rice genotypes have limited variations for IDIC tolerance, therefore, wildOryzagermplasm could be a better source for IDIC tolerance. In this study, 313Oryzaaccessions were evaluated for IDIC tolerance at the tillering stage under aerobic conditions using IDIC rating, SPAD value, and iron content in leaves. Based on these parameters, twenty IDIC tolerant lines were selected. These 20 lines exhibited no chlorosis, high SPAD values, and iron content, while 8 cultivated controls showed mild to high chlorosis symptoms and low SPAD and iron content. In a subsequent year, the selected lines were evaluated again to confirm their tolerance, and they exhibited similar levels of tolerance. These accessions may be useful for developing IDIC-tolerant cultivars for aerobic rice cultivation, and future study to understand the molecular mechanism of IDIC tolerance in rice.
MOGAT: An Improved Multi-Omics Integration Framework Using Graph Attention Networks
Authors: Tanvir Raihanul Bari , Islam Md Mezbahul , Sobhan Masrur , Luo Dongsheng , Mondal Ananda Mohan 
Published: April 2023

AbstractIntegration of multi-omics data holds great promise for understanding the complex biology of diseases, particularly Alzheimer’s, Parkinson’s, and cancer. However, the integration is challenging due to the high dimensionality and complexity of the data. Traditional machine learning methods are not well-suited for handling the complex relationships between different types of omics data. Many models were proposed that utilize graph-based learning models to extract hidden representations and network structures from different omics data to enhance cancer prediction, patient categorization, etc. The existing graph neural network-based (GNN-based) multi-omics approaches for cancer subtype prediction have three shortcomings: (a) Do not consider all types of omics data, (b) Fail to determine the relative significance of the neighboring nodes (in this case, samples or patients) when it comes to downstream analyses, such as subtype classification, patient stratification, etc., and (c) Use the same approach for generating initial graphs for different omics data. To overcome these shortcomings, we present MOGAT, a novel multi-omics integration approach, leveraging a graph attention network (GAT) model that incorporates graph-based learning with an attention mechanism. MOGAT utilizes a multi-head attention mechanism that can more efficiently extract information for a specific sample by assigning unique attention coefficients to its neighboring samples. To evaluate the performance of MOGAT, we explored its capability via a case study of predicting breast cancer subtypes. Our results showed that MOGAT performs better than the state-of-the-art multi-omics integration approaches.
Developing a scale for psychological ownership in the tourism industry
Authors: Farzinfar Zohre , Konjkav Monfared Amirreza , Tabataba’i-Nasab Seyed Mohammad 
Published: April 2023

PurposeThe present study aims to identify the dimensions of destination psychological ownership (DPO) from tourists’ perspectives and to develop a reliable and valid measurement scale.Design/methodology/approachThe mixed method has been applied in this study for the development of a scale to measure psychological ownership (PO) of tourists. The first stage includes identifying the PO dimensions of tourists toward the tourist destinations through in-depth interviews with experts (university professors, managers and experts in the tourism industry). Theme analysis was applied to analyze the data in this stage. A quantitative survey was conducted among tourists during the second stage. Accordingly, a questionnaire was designed and its reliability and validity were investigated. Confirmatory factor analysis and structural equation modeling were used to examine the structural model and its validity.FindingsThe findings revealed that the DPO from tourists’ perspectives includes six dimensions for the sense of attachment, responsibility, the sense of trust, the sense of honor, the sense of gratification and self-identity toward tourist destinations. The validity of the conceptual model was confirmed according to the results of the quantitative section of the study.Originality/valueThe present study is one of the limited numbers of studies coping with PO, especially in the field of tourism, from the view of the consumer. The present study identifies the dimensions of the DPO of tourists and develops an instrument to measure them. Therefore, the developed questionnaire can be used as a valid and reliable instrument to measure the DPO in future research.
Integrating animal behaviour into research on multiple environmental stressors: a conceptual framework
Authors: Lopez Laura K. , Gil Michael A. , Crowley Philip H. , Trimmer Pete C. , Munson Amelia , Ligocki Isaac Y. , Michelangeli Marcus , Sih Andrew 
Published: April 2023

ABSTRACTWhile a large body of research has focused on the physiological effects of multiple environmental stressors, how behavioural and life‐history plasticity mediate multiple‐stressor effects remains underexplored. Behavioural plasticity can not only drive organism‐level responses to stressors directly but can also mediate physiological responses. Here, we provide a conceptual framework incorporating four fundamental trade‐offs that explicitly link animal behaviour to life‐history‐based pathways for energy allocation, shaping the impact of multiple stressors on fitness. We first address how small‐scale behavioural changes can either mediate or drive conflicts between the effects of multiple stressors and alternative physiological responses. We then discuss how animal behaviour gives rise to three additional understudied and interrelated trade‐offs: balancing the benefits and risks of obtaining the energy needed to cope with stressors, allocation of energy between life‐history traits and stressor responses, and larger‐scale escape from stressors in space or time via large‐scale movement or dormancy. Finally, we outline how these trade‐offs interactively affect fitness and qualitative ecological outcomes resulting from multiple stressors. Our framework suggests that explicitly considering animal behaviour should enrich our mechanistic understanding of stressor effects, help explain extensive context dependence observed in these effects, and highlight promising avenues for future empirical and theoretical research.
Solubility and diffusivity of hydrogen and its isotopes in the BeO system
Authors: Riot Aurélien , Virot François , Connétable Damien 
Published: April 2023

AbstractThis work revisits hydrogen insertion in the wurtzite beryllium oxide in order to fill the gap in scientific knowledge regarding the diffusion coefficients of the different chemical states of hydrogen (neutral, charged, or molecular). Both first‐principle and macroscopic models were used to this end. In the former, two exchange‐correlation functionals (PBE and SCAN) were used to compute the properties of interest and accuracy was then discussed. Regarding the behavior of interstitial insertion of hydrogen, this work is slightly different from previous works; hydrogen was mainly found in the form of charged H− or H+ ions, depending on experimental conditions. In regard to diffusivity properties, a complex migration pathway was found for hydrogen cation. Finally, the present study succeeded in producing a reliable set of diffusion coefficients for neutral, charged, and molecular hydrogen.
Processes underlying the assembly of plant communities: The role of environmental filtering heterogeneity in a competition–dispersal experiment
Authors: Alfonsi Elsa , Benot Marie‐Lise , Alard Didier 
Published: April 2023

AbstractQuestionInterspecific competition and seed dispersal are key mechanisms that may influence plant community assembly, but their relative importance remains difficult to disentangle as they can be affected by abiotic conditions (environmental filtering). We experimentally studied the balance between these processes in a Molinia wet meadow plant community in which abiotic constraints are mostly represented by flooding, while agricultural practices such as mowing prevent the dominance of a few competitive species. We hypothesized that (H1) mowing, by decreasing competitive exclusion and (H2) seed addition, by increasing immigration, both enhance plant species diversity, and that (H3) small variations in flooding intensity become secondary to these processes in determining species assembly.LocationFrench National Nature Reserve “Etang de Cousseau”, Nouvelle Aquitaine, France.MethodsIn a three‐year experiment, we added seeds of 17 species characteristic of Molinia wet meadows and managed above‐ground competition through mowing. We measured spatial variations in soil moisture as an indicator of the flooding regime. We recorded species relative cover, species richness and evenness annually, and measured light availability, linked with canopy openness, twice.ResultsFrom the beginning of the experiment, small‐scale variations in soil moisture mainly affected species richness, composition and evenness, and canopy openness. Mowing significantly increased light availability and evenness, and affected the relative cover of several species, but not species richness. The addition of seeds did not influence any of the variables monitored during the experiment.ConclusionOur study helps to disentangle processes underlying community assembly in wet meadows. It demonstrates significant and rapid effects of mowing on canopy opening and on community assembly, while seed addition had only a slight effect, possibly explained by an insufficient decrease in competitive interactions through mowing or unmeasured processes. It also shows that abiotic heterogeneity remains a primary driver of community assembly, even on a small scale. Finally, our results suggest that the respective weight of the different filters (dispersion, environment, competition) is subject to interannual variability or environmental stochasticity.
Data Supplement from Cryotherapy with Concurrent CpG Oligonucleotide Treatment Controls Local Tumor Recurrence and Modulates HER2/neu Immunity
Authors: Veenstra Jesse J. , Gibson Heather M. , Littrup Peter J. , Reyes Joyce D. , Cher Michael L. , Takashima Akira , Wei Wei-Zen 
Published: April 2023

<p>Supplementary Figure S3. (A) Experimental scheme. Sera and tumor measurements were collected from BALB/c mice on days 0, 8, 17, 24, and 30 (n= 9). (B) α-Her2 IgG levels were quantified from sera and correlated with tumor volume. Mean D2F2/E2 volume (mm3) and α-Her2 IgG (Ab5 equivalent μg/mL) are plotted on the left and right y-axis respectively. (C) Three mice were euthanized at day 17 to collect spleens for IFN-γ ELISPOT. Splenocytes were isolated and stimulated with either EKB or KB 3T3 lines for 48hr (n=3/group). **P<0.01 Unpaired t-test.</p>
All Supplementary Tables, Figures and Methods from Bicyclic Peptides as a New Modality for Imaging and Targeting of Proteins Overexpressed by Tumors
Authors: Eder Matthias , Pavan Silvia , Bauder-Wüst Ulrike , van Rietschoten Katerine , Baranski Ann-Christin , Harrison Helen , Campbell Spencer , Stace Catherine L. , Walker Edward H. , Chen Liuhong , Bennett Gavin , Mudd Gemma , Schierbaum Ursula , Leotta Karin , Haberkorn Uwe , Kopka Klaus , Teufel Daniel P. 
Published: April 2023

<p>The file contains supplemental details related to sequence information of the bicyclic peptides referred to in the text, binding data, organ distribution data, PK parameters, mouse and human plasma stability, in vivo metabolism of BCY-B2 in mice, cell binding and internalization data, additional PET imaging data. It also contains detailed methods related to protein expression, phage selection, peptide synthesis, affinity determination by fluorescence polarization and SPR, radiolabeling, internalization, confocal microscopy, plasma protein binding, plasma stability of radiolabeled compounds, ÂµPET imaging, autoradiography, immunohistochemistry, and 6 references related to these methods. Â€¢	Supplementary Tables S1 - S14: o	Table S1: Affinities and plasma stabilities of BCY-B and stabilized BCY-C. o	Table S2: Sequence information and binding data of bicyclic peptides referred to in text. o	Table S3: Surface plasmon resonance (SPR) data. o	Table S4-6: Organ distribution data, BCY-B3/B4 o	Table S7: PK parameters. o	Table S8: Selectivity data of BCY-C towards other metalloproteinases. o	Table S9-11: Organ distribution data- BCYC2/C4 o	Table S12-14: Organ distribution data- BCYD1/D2 o	Table S15: Organ distribution data- MAb Â€¢	Supplementary Figures S1-S6: o	Figure S1: Comparative HT1080 cell binding and internalization of non-stabilized BCY-B3 and stabilized BCY-C2 o	Figure S2: Organ distribution time course studies with active BCY-B3, and inactive BCY-B4 in HT1080 xenograft mice. o	Figure S3: Mouse and human plasma stability of BCY-B5, BCY-C3, BCY-D1; o	Figure S4: Pharmacokinetic profile of BCY-B2 in mouse; o	Figure S5: In vivo metabolism of BCY-B2 in mice; o	Figure S6: Confocal microscopy on HT1080 cells and BCY-C2 o	Figure S7: PET imaging. Time-resolved whole-body maximum intensity projections of 68Ga-BCY-C2 in HT1080 xenograft mouse. Â€¢	Supplementary Methods: o	Protein expression, o	Phage selection, o	Peptide synthesis, o	Affinity determination by fluorescence polarization and SPR, o	Radiolabeling, o	Internalization, o	Confocal microscopy, o	Plasma protein binding, o	Plasma stability of radiolabeled compounds, o	ÂµPET imaging, o	Autoradiography, o	Immunohistochemistry, o	6 references related to these methods.</p>
Figure S1 from Epstein–Barr Virus miRNA BART2-5p Promotes Metastasis of Nasopharyngeal Carcinoma by Suppressing RND3
Authors: Jiang Chen , Li Lei , Xiang Yan-Qun , Lung Maria Li , Zeng Tingting , Lu Jiabin , Tsao Sai Wah , Zeng Mu-Sheng , Yun Jing-Ping , Kwong Dora L.W. , Guan Xin-Yuan 
Published: April 2023

<p>Supplementary Figure 1 (a)	Two EBV (-) NPC cell lines SUNE1 and HK1 and one carcinoma cell line CNE2 were infected by lentivirus to establish stable expression of BART2-5p for following study. The abundance of BART2-5p was quantified by QPCR to confirm successful gene transduction and its expression level was comparable with that in 20 primary NPC tissues. (b)	CNE2 was transduced with Vector or BART2 by lentivirus to establish stable cell line. Migration or invasion assays were performed once Blasticidin selection finished. Migrated and invaded cells were counted and the number of which was shown in the bar chart. (c)	Matrigel coated transwell assay was performed with CNE2 cells transiently transfected with negative control, inhibitor of BART2-3p, inhibitor of BART2-5p or both inhibitors. Invaded cells were counted for subsequent statistical analysis. (d)	CNE2 transduced with Vector or BART2 were injected into the tail vein of nude mice. Lung metastasis was examined 2 months later. Cells with BART2 expression formed more and larger metastatic lesions in lung. (Left) The number of metastatic nodules on the lung surface were counted and compared statistically. (Right) (e)	Lung metastasis was examined by IHC staining. As all cells were GFP labeled, they can be easily located due to brown color. Compared with the minor metastasis formed by Vector carrying cells, BART2 expressing cells developed into larger metastatic lesions. (f)	In vivo imaging was used to visualize metastatic status in abdominal cavity of mice at the endpoint. Metastatic tumor with GFP florescence was visualized. (Left) Major organs were excised from sacrificed mice for examination of overt metastasis. Blue arrows indicated metastatic nodules on organ surface. (Right) (g)	Slides from different organs were subjected to IHC staining. Brown color indicated GFP expression. Compared with single disseminated cancer cells found in organs of control mice, cells with BART2 expression developed into more and larger metastatic colonies in these organs. (h)	Survival analysis of mice in each group during the observation period. Each group had 9 mice.</p>
Table S1 from Spatiotemporal Regulation of ΔNp63 by TGFβ-Regulated miRNAs Is Essential for Cancer Metastasis
Authors: Bui Ngoc H.B. , Napoli Marco , Davis Andrew John , Abbas Hussein A. , Rajapakshe Kimal , Coarfa Cristian , Flores Elsa R. 
Published: April 2023

<p>Table S1. List of pathways enriched in Ã¢Ë†â€ Np63-induced and -repressed gene signatures.</p>
Supplemental Tables from An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines
Authors: Dutil Julie , Chen Zhihua , Monteiro Alvaro N. , Teer Jamie K. , Eschrich Steven A. 
Published: April 2023

<p>Supplemental tables for the manuscript (S1-S8) List of supplemental tables Table S1	Common cell lines panels for cancer research. Table S2	Cell line annotations. Table S3	Number of cancer cell lines included in each panel, grouped by tissue of origin. Table S4	Cell lines pairs demonstrating excess genetic concordance. Table S5	Admixture proportions (%) for each cell line in relation with the average for 1000 Genomes reference superpopulations. Table S6	Genetic ancestral origin of cancer cell lines in the complete dataset and in cell lines grouped by membership to CCLE, COSMIC and NCI60 panels. Table S7	Genetic ancestral origin of cancer cell lines in the complete dataset and in cell lines grouped by cancer tissue of origin. Table S8	Thousand Genomes Population Abbreviations.</p>