bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Report on Ancient DNA analysis of 27 African Americans from Catoctin Furnace, Maryland
Authors: Harney Éadaoin , Olalde Iñigo , Bruwelheide Kari , Barca Kathryn G. , Curry Roslyn , Comer Elizabeth , Rohland Nadin , Owsley Douglas , Reich David 
Published: June 2022

SummaryCatoctin Furnace is an industrial site that functioned from 1776–1903 and was operated at least partially by an enslaved workforce until about 1850, when it shifted to paid European laborers. A cemetery including 35 graves from which the remains of 32 individuals identified with African ancestry were excavated in 1979-1980 during construction of a highway that impacted the site. Since then, the human remains have been under the stewardship of the Smithsonian’s National Museum of Natural History (NMNH). The goal of this report is to document the successful generation of ancient DNA from 27 individuals from the cemetery. The analysis of the Catoctin individuals is part of a long-term study dedicated to restoring knowledge of the identity, origins, and legacy of the enslaved and free African Americans who labored and were buried at Catoctin Furnace1.
Generation and Functional Characterization of PLAP CAR-T Cells against Cervical Cancer Cells
Authors: Yekehfallah Vahid , Pahlavanneshan Saghar , Sayadmanesh Ali , Momtahan Zahra , Ma Bin , Basiri Mohsen 
Published: June 2022

AbstractChimeric antigen receptor (CAR) T cell therapy is one of the cancer treatment modalities that has recently shown promising results in treating hematopoietic malignancies. However, one of the obstacles that need to be addressed in solid tumors is the on-target/off-tumor cytotoxicity due to the lack of specific tumor antigens with low expression in healthy cells. Placental alkaline phosphatase (PLAP) is a shared placenta/tumor-associated antigen (TAA) that is expressed in ovarian, cervical, colorectal, and prostate cancers and is negligible in normal cells. In this study, we constructed second-generation CAR T cells with a humanized scFv against PLAP antigen, then evaluated the characteristics of PLAP CAR T cells in terms of tonic signaling and differentiation in comparison with ΔPLAP CAR T cells and CD19 CAR T cells. In addition, by coculturing PLAP CAR T cells with HeLa cells, we analyzed the tumor-killing function and secretion of anti-tumor molecules. Results showed that PLAP CAR T cells not only could eliminate the cancer cells but also increase their proliferation in vitro. We also observed increased secretion of IL-2, granzyme A, and IFN-γ by PLAP CAR T cells upon exposure to the target cells. In conclusion, PLAP CAR T cells are potential candidates for further investigation in cervical cancer and potentially other solid tumors.
The cell wall polymer initiates plasma membrane partitioning in mycobacteria
Authors: Kado Takehiro , Akbary Zarina , Motooka Daisuke , Sparks Ian L. , Melzer Emily S. , Nakamura Shota , Rojas Enrique R. , Morita Yasu S. , Siegrist M. Sloan 
Published: June 2022

SummaryLateral partitioning of proteins and lipids shapes membrane function. In model membranes, partitioning can be influenced by interactions with other membranes and solid supports. While cellular membranes can departition in response to various perturbations, including disruption of bilayer-extrinsic structures, the mechanisms by which they partitionde novoare largely unknown. The plasma membrane ofMycobacterium smegmatiscan be spatially and biochemically departitioned by the fluidizing agent benzyl alcohol. By screening for mutants that are sensitive to benzyl alcohol, we show that the bifunctional cell wall synthase PonA2 promotes membrane partitioning and cell growth upon fluidizer washout. PonA2’s role in membrane repartitioning and regrowth depends solely on its conserved transglycosylase domain. We find that the cell wall polymer, but not active cell wall polymerization, is critical for membrane partitioning. Our work highlights a key initiating role for bilayer-extrinsic structures in patterning cellular membranes.
Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction
Authors: Salcedo Adriana , Tarabichi Maxime , Buchanan Alex , Espiritu Shadrielle M.G. , Zhang Hongjiu , Zhu Kaiyi , Yang Tai-Hsien Ou , Leshchiner Ignaty , Anastassiou Dimitris , Guan Yuanfang , Jang Gun Ho , Haase Kerstin , Deshwar Amit G. , Zou William , Umar Imaad , Dentro Stefan , Wintersinger Jeff A. , Chiotti Kami , Demeulemeester Jonas , Jolly Clemency , Sycza Lesia , Ko Minjeong ,   PCAWG-11 Working Group,   SMC-Het Participants, Wedge David C. , Morris Quaid D. , Ellrott Kyle , Van Loo Peter , Boutros Paul C. 
Published: June 2022

AbstractTumours are dynamically evolving populations of cells. Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumour evolution, allowing assessment of how cancers initiate, progress and respond to selective pressures. A plethora of subclonal reconstruction algorithms have been created, but their relative performance across the varying biological and technical features of real-world cancer genomic data is unclear. We therefore launched the ICGC-TCGA DREAM Somatic Mutation Calling -- Tumour Heterogeneity and Evolution Challenge. This seven-year community effort used cloud-computing to benchmark 31 containerized subclonal reconstruction algorithms on 51 simulated tumours. Each algorithm was scored for accuracy on seven independent tasks, leading to 12,061 total runs. Algorithm choice influenced performance significantly more than tumour features, but purity-adjusted read-depth, copy number state and read mappability were associated with performance of most algorithms on most tasks. No single algorithm was a top performer for all seven tasks and existing ensemble strategies were surprisingly unable to outperform the best individual methods, highlighting a key research need. All containerized methods, evaluation code and datasets are available to support further assessment of the determinants of subclonal reconstruction accuracy and development of improved methods to understand tumour evolution.
Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor
Authors: Maidment JHR , Shimizu M , Vera S , Franceschetti M , Longya A , Stevenson CEM , De la Concepcion JC , Białas A , Kamoun S , Terauchi R , Banfield MJ 
Published: June 2022

AbstractA subset of plant intracellular NLR immune receptors detect effector proteins, secreted by phytopathogens to promote infection, through unconventional integrated domains which resemble the effector’s host targets. Direct binding of effectors to these integrated domains activates plant defences. The rice NLR receptor Pik-1 binds theMagnaporthe oryzaeeffector AVR-Pik through an integrated heavy metal-associated (HMA) domain. However, the stealthy alleles AVR-PikC and AVR-PikF avoid interaction with Pik-HMA and evade host defences. Here, we exploited knowledge of the biochemical interactions between AVR-Pik and its host target, OsHIPP19, to engineer novel Pik-1 variants that respond to AVR-PikC/F. First, we exchanged the HMA domain of Pikp-1 for OsHIPP19-HMA, demonstrating that effector targets can be incorporated into NLR receptors to provide novel recognition profiles. Second, we used the structure of OsHIPP19-HMA to guide mutagenesis of Pikp-HMA to expand its recognition profile. We demonstrate that the extended recognition profiles of engineered Pikp-1 variants correlate with effector binding in planta and in vitro, and with the gain of new contacts across the effector/HMA interface. Crucially, transgenic rice producing the engineered Pikp-1 variants were resistant to blast fungus isolates carrying AVR-PikC or AVR-PikF. These results demonstrate that effector target-guided engineering of NLR receptors can provide new-to- nature disease resistance in crops.Graphical abstract
The Mediator complex regulates enhancer-promoter interactions
Authors: Ramasamy Shyam , Aljahani Abrar , Karpinska Magdalena A. , Cao T. B. Ngoc , Cruz J. Neos , Oudelaar A. Marieke 
Published: June 2022

ABSTRACTEnhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a re-distribution of the Cohesin complex on chromatin and a reduction in Cohesin occupancy specifically at enhancers. Our results indicate that enhancer-promoter interactions are dependent on an interplay between the Mediator and Cohesin complexes and provide new insights into the molecular mechanisms by which communication between enhancers and promoters is regulated.
Determinants of adaptability and its impact on the change readiness of civil servants
Authors: Yean Tan Fee , Tan Fee Cheng , Nadarajah Devika 
Published: June 2022

PurposeUnderpinned by Social Cognitive Theory (SCT), this study aimed to examine the mediating role of employees' adaptability in the relationship between the five managerial climate factors (i.e., trust, supportiveness, openness, clarity of goals and participative) and change readiness in public sector organisations.Design/methodology/approachAdopting the quantitative approach, data were collected from 379 administrative and diplomatic officers. Analysis was done using partial least squares structural equation modelling (PLS-SEM).FindingsThe results showed that trust and clarity of goals are significant motivational factors that accelerate employees' adaptability. Adaptability, in turn, was found to mediate the effect of trust and clarity of goals on employees' change readiness.Originality/valueThis study contributes to theory and practice by examining employees' adaptability as an intervening variable in the relationship between managerial climate factors and change readiness with specific reference to the public administration context.
I hate ads but not the advertised brands: a qualitative study on Internet users' lived experiences with YouTube ads
Authors: Banerjee Snehasish , Pal Anjan 
Published: June 2022

PurposeThis paper aims to explore Internet users' lived experiences with video ads, both skippable and nonskippable, while watching content on YouTube.Design/methodology/approachIn-depth interviews were conducted with 22 participants.FindingsThe participants unanimously expressed dissatisfaction with YouTube ads. The dissatisfaction was directed to the platform but did not spill over to the advertised brand/product. Ethical concerns related to privacy also emerged. Specifically, with respect to nonskippable ads, the participants expressed dislike for forced viewing and explained how they would engage in extraneous activities during the ads. Nonetheless, they appreciated the flexibility offered by skippable ads. They also elaborated on how, why and when they would skip/not skip skippable ads.Originality/valueThe findings are discussed in light of the literature on not only online advertising but also platform switching versus continuance intention, spillover effect, privacy–personalization paradox and visual attention.
A systematic review of information practices research
Authors: Zhong Huan , Han Zhengbiao , Hansen Preben 
Published: June 2022

PurposeThis systematic literature review aims to elaborate the research progress of information practices to help other researchers attain a more holistic and comprehensive understanding of the field.Design/methodology/approachFollowing a systematic review protocol, 123 research articles from nine academic databases were included in the analysis.FindingsFour separate results can be outlined. First, practice theory, social constructionist theory and activity theory are often used as the theoretical basis for the study of information practices. Second, people will engage in specific information practice activities in different external and internal contexts. The external contexts include social and needs contexts. The internal contexts include information source horizons, user's affection and user's cognition. Third, the existing information practice models can be divided into static and dynamic types. These models mainly reflected activities and influencing factors of information practices. Fourth, qualitative methods were the most used in information practice research.Research limitations/implicationsThe field of information practices is a vast, expanding research field. This research will focus only on a specific section, namely concepts, activities, contexts and models. Researchers could contribute to exploring the concepts, components and mechanisms of information practices by combining theories from various disciplines, such as sociology and behavioral science.Originality/valueThis is the first study to reveal the general picture of information practices. It also elaborates the characteristics of people's information practices and shows the potential development direction for future research.
Tourists' engagement and willingness to pay behavior during COVID-19: an assessment of antecedents, consequences and intermediate relationships
Authors: Kumar Navin , Panda Rajeev Kumar , Adhikari Kishalay 
Published: June 2022

PurposeThis study identifies antecedents and consequences of destination brand engagement (DBE) that have redefined the tourists' behavior during the COVID-19 outbreak. Specifically, it assesses the impact of social media interaction and destination authenticity on DBE and DBE's effect on tourists' willingness to pay (WTP). Further, it examines the mediating role of affective attitude and the moderating role of perceived risk between the associations of DBE and WTP.Design/methodology/approachSurvey data were collected from 436 respondents through a structured questionnaire from selected tourism destinations in India. Structural equation modeling (CB-SEM) is employed to empirically examine the formulated hypotheses. Besides, hierarchical second-order confirmatory factor analysis is also deployed to analyze certain constructs as higher-order factors.FindingsSocial media interaction and destination authenticity elevate DBE, and DBE enhances affective attitude and WTP. Affective attitude mediates the relationship between DBE and WTP. Hence, the association between tourists' engagement and spending behavior becomes crucial under elevated affective attitude conditions. Finally, perceived risk during the pandemic dampens the association between DBE and WTP.Practical implicationsThe findings may provide newer insights to the tourism companies, marketers and policymakers to create targeted strategies to minimize the risk perception and improve engagement levels of the tourists, which can yield economic returns in the long run.Originality/valueBased on the cues from protection motivation theory (PMT), this study develops a DBE framework and identifies the factors affecting its sustenance in the pandemic hit tourism sector. Further, suggesting implications to ensure safety measures in the tourism industry that may assist in establishing economic resilience.
Pericapsular nerve group block for hip fracture is feasible, safe and effective in the emergency department: A prospective observational comparative cohort study
Authors: Fahey Alan , Cripps Elinor , Ng Aloysius , Sweeny Amy , Snelling Peter J 
Published: June 2022

AbstractObjectivesThe pericapsular nerve group (PENG) block was first described for analgesia of hip fracture in 2018. We hypothesised that the PENG block is safe and effective for patients with hip fracture when provided by emergency physicians and trainees in the ED.MethodsThis was an observational study of routine care. Consecutive patients receiving regional anaesthesia for hip fracture at a single ED were prospectively enrolled. Pain scores were assessed prior to regional anaesthesia then at 15, 30 and 60 min after administration. Maximal reduction in pain scores within 60 min were assessed using the Visual Analogue Scale (at rest and on movement) or the Pain Assessment IN Advanced Dementia tool (at rest). Patients were followed for opioid use for 12 h after regional anaesthesia and adverse events over the duration of admission.ResultsThere were 67 eligible patients during the enrolment period, with 52 (78%) prospectively enrolled. Thirty‐three received femoral blocks (19 fascia iliaca compartment blocks, 14 femoral nerve blocks) and 19 received a PENG block. Inexperienced providers were able to successfully perform the PENG block. There was no difference in maximum pain score reduction between the groups. There was no difference in adverse effects between groups. Opioid use was similar between the groups. More patients were opioid‐free after a PENG block.ConclusionsThe present study demonstrated that the PENG block can be provided safely and effectively to patients with hip fracture in the ED. On the basis of this pilot study, a larger randomised controlled study should now be designed.
Effect of agave fructans on xanthan rheology: Impact on sodium caseinate emulsion properties
Authors: Sosa‐Herrera María Guadalupe , Martínez‐Padilla Laura Patricia , Delgado‐Reyes Virginia Agustina , de Avila Ortega María de los Angeles , Cruz Martínez Irene Paulina 
Published: June 2022

AbstractThe influence of agave fructans (AF) (1–10%) and xanthan (from 0.03% to 0.25%) in combination with sodium caseinate (SC) at 1% on the rheological and physicochemical properties of aqueous phases and emulsions was evaluated. Steady‐state flow behavior, particle size distribution, and stability studies were used to characterize the systems. The aqueous systems displayed the shear‐thinning behavior characteristic of xanthan solutions; however, this behavior was modified by the presence of SC and AF due to interactions between AF–SC and AF–xanthan based on predominant hydrogen bonding because of the hydroxyl groups on AF. In emulsions, an increase in viscosity due to the effect of the AF concentration reflects a probable association of fructan aggregates on the surface of SC particles that reinforce the interfacial layer of SC, while xanthan contributes to an increase in the viscosity of the continuous phase, which effectively prevents coalescence and floc formation even at higher concentrations, despite the possible existence of a depletion flocculation effect attenuated by the interaction between AF–SC and AF–xanthan.Practical ApplicationThese results can be of use, in an important way, in the design of stable functional emulsions in which there is an application for agave fructans recognized as dietary fiber, also considering their peculiar way of interacting with xanthan favoring its stabilizing functionality.
Tripeptide Hyp‐Asp‐Gly from collagen peptides inhibited platelet activation via regulation of PI3K/Akt‐MAPK/ERK1/2 signaling pathway
Authors: Song Hongdong , Yang Yijie , Li Bo 
Published: June 2022

AbstractPlatelet activation is involved in cardiovascular thrombosis. Our previous study demonstrated that oral administration of collagen peptides (CPs) inhibited platelet activation, but the mechanism of action of CPs remained to be elucidated. As a continued effort, the objective of this study was to identify the active ingredient of CPs and clarify its molecular mechanism. Simulated absorbate of CPs was prepared by simulated gastrointestinal digestion and intestinal absorption system, and then separated by C18 column. The fraction with the highest antiplatelet activity was subjected to NanoUPLC‐ESI‐MS/MS for peptide sequencing. Novel tripeptide Hyp‐Asp‐Gly (ODG) was identified. It had a broad‐spectrum inhibition of platelet activation induced by collagen, thrombin, and adenosine diphosphate (ADP). ODG could survive simulated gastrointestinal digestion and be absorbed intact. Furthermore, it showed good stability in plasma. ODG had no significant effect on the PLC‐PKC‐Ca2+ pathway, but it inhibited the PI3K/Akt‐MAPK/ERK1/2 signaling. At a dosage of 200 µmol/kg body weight, ODG had an in vivo anti‐thrombosis activity without bleeding risk. The present study provides one of the mechanisms of action of CPs and highlights its potential use as a functional component to combat cardiovascular thrombosis.Practical ApplicationThis study has suggested that tripeptide Hyp‐Asp‐Gly(ODG) derived from collagen have potent activities. This novel collagen peptide had a greatpotential to be applied to combat cardiovascular thrombosis in the foodindustry. Meanwhile, this work is expected to provide a theoretical basis forthe development of safe and effective anti‐platelet and anti‐thrombosis peptides.
Effect of ball milling‐assisted glycosylation modification on the structure and foaming property of egg white protein
Authors: Liu Lan , Wang Qia , Wu Yongyan , Wang Guoze , Geng Fang , Song Hongbo , Luo Peng , Huang Qun 
Published: June 2022

AbstractThe effect of different glycosylation degrees on molecular structure and foaming property of egg white protein (EWP) was investigated using ball milling‐assisted glycosylation. The results showed the foaming ability (FA) and foam stability (FS) of EWP improved when the degree of glycosylation was increased. In particular, FA of ball milling‐assisted glycosylation of EWP enhanced by 39.9% and 28.8%, and the FS increased by 28.7% and 24.0% compared with EWP and ball milling egg white protein (BE) at 150 min of reaction. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE) analysis could reflect the grafting degree of EWP and glucose molecules from the side. When EWP was fully grafted with glucose, endogenous fluorescence and free sulfhydryl groups indicated that tertiary structure of EWP was depolymerized, and Fourier transform infrared spectroscopy showed the secondary structure tended to change from order to disorder. The results of this study indicated that ball milling‐assisted glycosylation modification was a practical method to improve the foaming property of EWP.Practical ApplicationEWP has great FA and FS, making it indispensable in the baking industry. In this study, ball milling‐assisted glycosylation was used to improve the foaming property of EWP, and the molecular structure of EWP with different degrees of glycosylation was fully resolved. The results demonstrated that ball milling, as a physical pretreatment, can fully unfold the structure of EWP. When sugar molecules were fully grafted, the particle size of EWP reduced, solubility increased, and the stability of system improved, thus enhancing the foaming property of EWP. The results can provide theoretical basis for improving the foaming property of EWP and provide a reference value for its industrial application.