bluuebunny/crossref_metadata_2025_split huggingface dataset:
Durable antibody responses in staff at two long-term care facilities, during and post SARS-CoV-2 outbreaks
Authors: Gallichotte Emily N. , Nehring Mary , Young Michael C. , Pugh Sierra , Sexton Nicole R. , Fitzmeyer Emily , Quicke Kendra M. , Richardson Megan , Pabilonia Kristy L. , Ehrhart Nicole , Fosdick Bailey K. , VandeWoude Sue , Ebel Gregory D. 
Published: May 2021

AbstractSARS-CoV-2 has had a disproportionate impact on non-hospital healthcare settings such as long-term care facilities (LTCFs). The communal nature of these facilities, paired with the high-risk profile of residents, has resulted in thousands of infections and deaths and a high case fatality rate. To detect pre-symptomatic infections and identify infected workers, we performed weekly surveillance testing of staff at two LTCFs which revealed a large outbreak at one of the sites. We collected serum from staff members throughout the study and evaluated it for binding and neutralization to measure seroprevalence, seroconversion, and type and functionality of antibodies. At the site with very few incident infections, we detected that over 40% of the staff had preexisting SARS-CoV-2 neutralizing antibodies, suggesting prior exposure. At the outbreak site, we saw rapid seroconversion following infection. Neutralizing antibody levels were stable for many weeks following infection, suggesting a durable, long-lived response. Receptor-binding domain antibodies and neutralizing antibodies were strongly correlated. The site with high seroprevalence among staff had two unique introductions of SARS-CoV-2 into the facility through seronegative infected staff during the period of study but these did not result in workplace spread or outbreaks. Together our results reveal that high seroprevalence rate among staff can contribute to herd immunity within a workplace and protect against subsequent infection and spread within a facility.
Breaking the fibrinolytic speed limit with microwheel co-delivery of tissue plasminogen activator and plasminogen
Authors: Disharoon Dante , Trewyn Brian G. , Herson Paco S. , Marr David W.M. , Neeves Keith B. 
Published: May 2021

AbstractFibrinolysis is the enzymatic degradation of fibrin, the biopolymer that gives blood clots their mechanical integrity. To reestablish blood flow in vessels occluded by clots, tissue plasminogen activator (tPA) can be used; however, its efficacy is limited by transport to and into a clot and by the depletion of its substrate, plasminogen. To overcome these rate limitations, we design a platform to co-deliver tPA and plasminogen based on microwheels (μwheels), wheel-like assemblies of superparamagnetic colloidal beads that roll along surfaces at high speeds and carry therapeutic payloads in applied magnetic fields. By experimentally measuring fibrinolysis of plasma clots at varying concentrations of tPA and plasminogen, the biochemical speed limit was first determined. These data, in conjunction with measurements of μwheel translation, activity of immobilized tPA on beads, and plasminogen release kinetics from magnetic mesoporous silica nanoparticles (mMSN), were used in a mathematical model to identify the optimal tPA:plasminogen ratio and guide the coupling of plasminogen-loaded mMSN to tPA functionalized superparamagnetic beads. Once coupled, particle-bead assemblies form into a co-delivery vehicle that rolls to plasma clot interfaces and lyses them at rates comparable to the biochemical speed limit. With the addition of mechanical action provided by rotating μwheels to penetrate clots, this barrier was exceeded by rates 40-fold higher lysis by 50 nM tPA. This co-delivery of an immobilized enzyme and its substrate via a microbot capable of mechanical work has the potential to target and rapidly lyse clots that are inaccessible by mechanical thrombectomy devices or recalcitrant to systemic tPA delivery.
Strategic infarct locations for post-stroke depressive symptoms: a lesion- and disconnection-symptom mapping study
Authors: Weaver Nick A. , Lim Jae-Sung , Schilderinck Janniek , Biessels Geert Jan , Kang Yeonwook , Kim Beom Joon , Kuijf Hugo J. , Lee Byung-Chul , Lee Keon-Joo , Yu Kyung-Ho , Bae Hee-Joon , Biesbroek J. Matthijs 
Published: May 2021

AbstractBackgroundDepression is the most common neuropsychiatric complication after stroke. Infarct location is associated with post-stroke depressive symptoms (PSDS), but it remains debated which brain structures are critically involved. We performed a large-scale lesion-symptom mapping study to identify infarct locations, and white matter disconnections, associated with PSDS.MethodsWe included 553 patients (age 69±11 years, 42% female) with acute ischemic stroke. PSDS were measured using the 30-item Geriatric Depression Scale (GDS-30). Multivariable support vector regression (SVR)-based analyses were performed both at the level of individual voxels (SVR-VLSM) and predefined regions of interest (SVR-ROI) to relate infarct location to PSDS. We externally validated our findings in an independent stroke cohort (N=459). Finally, disconnectome-based analyses were performed using SVR-VLSM, in which white matter fibers disconnected by the infarct were analyzed instead of the infarct itself.Results:Infarcts in the right amygdala, right hippocampus and right pallidum were consistently associated with PSDS (permutation-based p<0.05) in SVR-VLSM and SVR-ROI. External validation (N=459) confirmed the association between infarcts in the right amygdala and pallidum, but not the right hippocampus, and PSDS. Disconnectome-based analyses revealed that disconnections in the right parahippocampal white matter, right thalamus and pallidum, and right anterior thalamic radiation were significantly associated (permutation-based p<0.05) with PSDS.ConclusionsInfarcts in the right amygdala and pallidum, and disconnections of right limbic and frontal cortico-basal ganglia-thalamic circuits, are associated with PSDS. Our findings provide a comprehensive and integrative picture of strategic infarct locations for PSDS, and shed new light on pathophysiological mechanisms of depression after stroke.
Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
Authors: Zuzic Lorena , Samsudin Firdaus , Shivgan Aishwary T. , Raghuvamsi Palur V. , Marzinek Jan K , Boags Alister , Pedebos Conrado , Tulsian Nikhil Kumar , Warwicker Jim , MacAry Paul , Crispin Max , Khalid Syma , Anand Ganesh S. , Bond Peter J 
Published: May 2021

ABSTRACTThe recent global COVID-19 pandemic has prompted a rapid response in terms of vaccine and drug development targeting the viral pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this work, we modelled a complete membrane-embedded SARS-CoV-2 spike (S) protein, the primary target of vaccine and therapeutics development, based on available structural data and known glycan content. We then used molecular dynamics (MD) simulations to study the system in the presence of benzene probes designed to enhance discovery of cryptic, potentially druggable pockets on the S protein surface. We uncovered a novel cryptic pocket with promising druggable properties located underneath the 617-628 loop, which was shown to be involved in the formation of S protein multimers on the viral surface. A marked multi-conformational behaviour of this loop in simulations was validated using hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, supportive of opening and closing dynamics. Interestingly, the pocket is also the site of the D614G mutation, known to be important for SARS-CoV-2 fitness, and within close proximity to mutations in the novel SARS-CoV-2 strains B.1.1.7 and B.1.1.28, both of which are associated with increased transmissibility and severity of infection. The pocket was present in systems emulating both immature and mature glycosylation states, suggesting its druggability may not be dependent upon the stage of virus maturation. Overall, the predominantly hydrophobic nature of the cryptic pocket, its well conserved surface, and proximity to regions of functional relevance in viral assembly and fitness are all promising indicators of its potential for therapeutic targeting. Our method also successfully recapitulated hydrophobic pockets in the receptor binding domain and N-terminal domain associated with detergent or lipid binding in prior cryo-electron microscopy (cryo-EM) studies. Collectively, this work highlights the utility of the benzene mapping approach in uncovering potential druggable sites on the surface of SARS-CoV-2 targets.
Evidence for high intergenic sequence variation in heterozygous Italian ryegrass (Lolium multiflorumLam.) genome revealed by a high-quality draft diploid genome assembly
Authors: Copetti Dario , Yates Steven A. , Vogt Maximilian M. , Russo Giancarlo , Grieder Christoph , Kölliker Roland , Studer Bruno 
Published: May 2021

AbstractBackgroundOver the last decade, progress in DNA sequencing technologies and assembly methods allowed plant scientists to move beyond the use of model organisms and work directly on the genomes of the major crops. Forage grass research can also benefit from this revolution, enabling progress in population genetic studies, functional biology, and genomics-assisted breeding. Due to its large genome size and high repeat content, so far only incomplete and fragmented assemblies are available for the grasses of theLoliumandFestucaspecies complex.FindingsHere, we report a highly contiguous draft assembly of Italian ryegrass (L. multiflorumLam.), spanning 4.5 Gb and with a N50 of 3 Mb, containing ~70,000 gene models. Thanks to its relatedness to barley, 78% of the assembly was anchored on seven pseudomolecules. The high heterozygosity of the plant allowed obtaining a diploid assembly – i.e. across 95% of the assembly, both alleles were assembled on separate sequences. This feature allowed unraveling a very high amount of intergenic sequence variation between allelic sequences.ConclusionsWe present a nearly complete genome assembly of a genotype used in contemporary Swiss forage grass breeding programs. This work shows how genomic research has improved, allowing to decode the genetic code of large, complex, and heterozygous plants. It also allows the functional characterization of the ryegrass gene repertoire and the large-scale development of molecular markers. Furthermore, it paves the road for a reference-based characterization and exploitation of the genetic variation within theLoliumandFestucaspecies complex.
Affective contagion: how attitudes expressed by others influence our perception of actions
Authors: Di Cesare G. , Pelosi A. , Aresta S. , Lombardi G. , Sciutti A. 
Published: May 2021

AbstractVitality forms represent a fundamental aspect of social interactions, characterizinghowactions are performed andhowwords are pronounced, on the basis of the agent’s attitude. The same action, such as a handshake, has a different impact on the receiver when it is performed kindly or vigorously, and the same happens with a gentle or rude tone of voice. In the present study, we carried out two experiments which aimed to investigate whether and how vocal requests conveying different vitality forms can influence the perception of goal-directed actions and to measure the duration of this effect over time. More specifically, participants listened to an actor voice pronouncing “give me” in a rude or gentle way, and then they were asked to observe the initial part of a rude or gentle passing action, continue it mentally and estimate its conclusion. Results showed that the perception of different vitality forms expressed by vocal requests influenced the estimated action duration. Moreover, we found that this effect was limited to a certain time interval, after which it started to decay.
Probing the biogenesis pathway and dynamics of thylakoid membranes
Authors: Huokko Tuomas , Ni Tao , Dykes Gregory F. , Simpson Deborah M. , Brownridge Philip , Conradi Fabian D. , Beynon Robert J. , Nixon Peter J. , Mullineaux Conrad W. , Zhang Peijun , Liu Lu-Ning 
Published: May 2021

AbstractHow thylakoid membranes are generated to form the metabolically active membrane network and how thylakoid membranes orchestrate the insertion and localization of protein complexes for efficient electron flux remain elusive. Here, we develop a method to modulate thylakoid biogenesis in the rod-shaped cyanobacteriumSynechococcus elongatusPCC 7942 by modulating light intensity during cell growth, and probe the spatial-temporal stepwise biogenesis process of thylakoid membranes in cells. Our results reveal that the plasma membrane and regularly arranged concentric thylakoid layers have no physical connections. The newly synthesized thylakoid membrane fragments emerge between the plasma membrane and pre-existing thylakoids. Photosystem I monomers appear in the thylakoid membranes earlier than other mature photosystem assemblies, followed by generation of Photosystem I trimers and Photosystem II complexes. Redistribution of photosynthetic complexes during thylakoid biogenesis ensures establishment of the spatial organization of the functional thylakoid network. This study provides insights into the dynamic biogenesis process and maturation of the functional photosynthetic machinery.
Cancer mutational processes vary in their association with replication timing and chromatin accessibility
Authors: Yaacov Adar , Vardi Oriya , Blumenfeld Britny , Greenberg Avraham , Massey Dashiell J. , Koren Amnon , Adar Sheera , Simon Itamar , Rosenberg Shai 
Published: May 2021

AbstractBackgroundCancer somatic mutations are the product of multiple mutational and repair processes, which are tightly associated with DNA replication. Distinctive patterns of somatic mutations accumulation in tumors, termed mutational signatures, are indicative of processes the tumors underwent. While tumor mutational load is correlated with late replicating regions and spatial genome organization, much is unknown about the association of many different mutational processes and replication timing, and the interplay with chromatin structure remains an open question.MethodsWe systematically analyzed the mutational landscape of 2,787 WGS tumors from 32 different tumor types separately for early and late replicating regions. We used sequence context normalization and chromatin data to account for sequence and chromatin accessibility differences between early and late replicating regions. Moreover, we expanded the signature analyses to doublet base substitutions and small insertions and deletions by developing an artificial genomes-based approach to account for sequence differences between various genomic regions.ResultsWe revealed the replication timing (RT) association of single base, doublet base and small insertions and deletions mutational signatures. The association is signature specific: some are associated with early or late replication (such as UV-exposure signatures SBS7b and SBS7a, respectively) and others have no association. Most associations exist even after normalizing for genome accessibility. We further developed a focused mutational signature identification approach, which uses RT information to improve signature identification, and found that SBS16, which is biased towards early replication, is strongly associated with better survival rates in liver cancer.ConclusionsOur comprehensive analyses enabled a more robust classification of RT association of single base, doublet base and indels signatures. By doing so, we demonstrated a variation in the association with RT, as many mutational processes biased towards either early or late replication timing, and others have an equal RT distribution. These associations were independent from chromatin accessibility in most cases. This work highlights that restricting signatures analyses to concise genomic regions improves identification of signatures, such as SBS16, and demonstrates its clinically relevance as a predictor of improved survival of liver cancer patients.
Heparin protects human neural progenitor cells from Zika Virus-induced cell death and preserves their differentiation into mature neural-glia cells
Authors: Pagani Isabel , Ottoboni Linda , Podini Paola , Ghezzi Silvia , Brambilla Elena , Bezukladova Svetlana , Corti Davide , Bianchi Marco Emilio , Capobianchi Maria Rosaria , Yates Edwin A , Martino Gianvito , Vicenzi Elisa 
Published: May 2021

AbstractZika virus (ZIKV) is an arbovirus member of the Flaviviridae family that causes severe congenital brain anomalies in infected fetuses. Human neural progenitor cells (hNPCs) are highly permissive to ZIKV infection, causing inhibition of cell proliferation concomitant with an induction of cell death. We previously demonstrated that pharmaceutical-grade heparin inhibited virus-induced cell death with minor effects onin vitrovirus replication in ZIKV-infected hNPCs. Here we show that heparin prevented ZIKV-induced intracellular vacuoles, a signature characteristic of paraptosis, but also inhibited necrosis and apoptosis of hNPCs when grown as neurospheres (NS). Furthermore, heparin preserved the differentiation of both ZIKV-infected human-induced pluripotent stem cells (hiPSC) derived-NPCs and fetus-derived NPCs into neural-glial cells. Collectively, these results highlight the potential neuroprotective effect of heparin that could be re-purposed and exploited to drive the development of novel agents for preventing ZIKV damage.
Variance in student and teacher roles in the contemporary Australasian architecture design studio context
Authors: Iftikhar Naima , Crowther Philip , Osborne Burton Lindy 
Published: May 2021

PurposeThis study aims to expose the various roles that teachers and students adopt in the architecture design studio. It highlights how these roles change over time, through three distinct phases, which relate to the stages of the design project. This understanding of how roles change over the semester will guide academics in understanding how to better relate to students.Design/methodology/approachThrough a series of interviews and surveys, this study utilised a modified Delphi method to establish a consensus of opinion, both within and across the three stakeholder groups of students, tutors and coordinators/lecturers. Two rounds of data collection were conducted, with “expert” perceptions of the three stakeholder roles being established.FindingsThe roles that are adopted and perceived by students, tutors and coordinators/lecturers vary over time and respond to the stages of the design project. While there is general agreement between the perceptions of students and their teachers, there are some notable differences at key times.Originality/valueThis research builds upon previous studies into the roles of students and their teachers in the architecture design studio. It provides a nuanced map of how roles change and how interactions happen, over the duration and through the phases, of the architecture design project.
Female directors and acquisition outcomes: a reflection on replicating Levi, Li and Zhang (2014)
Authors: Bachmann Rebecca Lorena , Spiropoulos Helen 
Published: May 2021

Purpose
In this pitch research letter (PRL), the authors reflect on their research journey in replicating Levi, Li and Zhang (2014) for the AFAANZ Finance SIG 2020 Shark Tank Pitch event.

Design/methodology/approach
The authors outline their experience in using the pitch template and discuss some issues and considerations one might encounter when replicating a study using Australian data.

Findings
They found the pitch template useful for planning our replication and for developing a thorough understanding of the different aspects involved in completing the project (such as data and methodology considerations as well as motivation and contribution to existing knowledge).

Originality/value
This PRL highlights the benefits of replicating an existing study using Australian data, and outlines some potential challenges (and solutions) one may encounter along the way. This experience is expected to be useful to early career researchers and those beginning to work with Australian data.
Quality control (QC) of an institutional repository: a hands-on
Authors: Ahammad Nur 
Published: May 2021

Purpose
The purpose of this paper is to show the quality control process and techniques of an open-source digital library (DL)/institutional repository (IR) in an institution. It will also demonstrate the challenges for quality control of a digital library in an institution.

Design/methodology/approach
It will explain metadata quality control and structural quality control and some matters that are important for an ideal IR. It also describes data migration from one repository to another.

Findings
Metadata without quality is just junk. Library personnel should have adequate library science educational qualifications to do the DL work. Non-professionals may create junk in the IR. Quality control can ensure the standard of a digital IR.

Originality/value
This study drowns upon the practical experience of DSpace quality control of a private university library in Bangladesh.
Exploring the role of organizational slack in the COVID-19 pandemic: an empirical study of the manufacturing industry
Authors: Li Zonghui 
Published: May 2021

Purpose
Drawing on the behavioral theory of the firm (BTF), this study aims to understand the role of organizational slack in the manufacturing industry during the COVID-19 pandemic.

Design/methodology/approach
Using panel data of publicly traded manufacturing firms in the USA over a 12-quarter time period, this study uses generalized least squares modeling to test the hypothesized relationships.

Findings
Results show that the COVID-19 pandemic has a negative impact on manufacturing firms’ performance and organizational slack weakens the negative relationship between the COVID-19 pandemic and firm performance. In addition, when a positive performance aspirational gap (PAG) exists, the negative relationship between COVID-19 pandemic and firm performance in firms with high levels of organizational slack is further weakened.

Originality/value
This study contributes to organizational studies by investigating the contingent impact of organizational slack in the setting of COVID-19 pandemic. This study also contributes to the BTF by investigating how firm PAG, combined with the abundance of organizational slack, moderates the impact of COVID-19 pandemic on firm performance.