bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Assessment of the Binding and Neutralisation Activity of Bispecific Antibodies Against SARS-CoV-2 Variants
Authors: Dean Alexis Q , Stauft Charles B , Twomey Julianne D , Tan Joshua , Varani Luca , Wang Tony T , Zhang Baolin 
Published: December 2022

AbstractBackgroundNeutralising antibodies against SARS-CoV-2 are a vital component in the fight against COVID-19 pandemic, having the potential of both therapeutic and prophylactic applications. Bispecific antibodies (BsAbs) against SARS-CoV-2 are particularly promising, given their ability to bind simultaneously to two distinct sites of the receptor-binding domain (RBD) of the viral spike protein. Such antibodies are complex molecules associated with multi-faceted mechanisms of action that require appropriate bioassays to ensure product quality and manufacturing consistency.MethodsWe developed procedures for biolayer interferometry (BLI) and a cell-based virus neutralisation assay, the focus reduction neutralisation test (FRNT). Using both assays, we tested a panel of five BsAbs against different spike variants (Ancestral, Delta and Omicron) to evaluate the use of these analytical methods in assessing binding and neutralisation activities of anti-SARS-CoV-2 therapeutics.ResultsWe found comparable trends between BLI-derived binding affinity and FRNT-based virus neutralisation activity. Antibodies that displayed high binding affinity against a variant were often followed by potent neutralisation at lower concentrations, whereas those with low binding affinity also demonstrated reduced neutralisation activity.ConclusionThe results support the utility of BLI and FRNT assays in measuring variant-specific binding and virus neutralisation activity of anti-SARS-CoV-2 antibodies.
Modeling Intra- and Inter-individual Changes in L2 Classroom Engagement
Authors: Zhou Shiyao Ashlee , Hiver Phil , Zheng Yongyan 
Published: December 2022

Abstract
In this study, we investigated how student engagement and disengagement change over the course of a semester in the L2 classroom. We modeled change at the inter- and intra-individual levels, using time-variant predictors to examine differences in student classroom engagement and disengagement trajectories. In addition to these temporal dynamics, we also examined what motivational antecedents are related to these changes in engagement and disengagement over time. We collected data from 686 students enrolled in general-purpose English courses at two publicly funded universities in mainland China at three waves in a 17-week semester, and tested a series of multi-level, mixed-effects growth models. Our analyses showed that students who reported higher initial classroom engagement or disengagement levels had lower growth rates than their counterparts as the semester proceeded. Students’ classroom engagement in language learning dipped to its lowest point around the middle of the semester and peaked toward the end of the semester. Motivational antecedents were also strong predictors of student engagement and disengagement in the language classroom at both within- and between-person levels. We discuss the implications of these temporal dynamics of learner engagement in the language classroom.
Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning
Authors: Zhu Xi-Liang , Bao Lin-Xia , Xue Min-Qi , Xu Ying-Ying 
Published: December 2022

Abstract
With the improvement of single-cell measurement techniques, there is a growing awareness that individual differences exist among cells, and protein expression distribution can vary across cells in the same tissue or cell line. Pinpointing the protein subcellular locations in single cells is crucial for mapping functional specificity of proteins and studying related diseases. Currently, research about single-cell protein location is still in its infancy, and most studies and databases do not annotate proteins at the cell level. For example, in the human protein atlas database, an immunofluorescence image stained for a particular protein shows multiple cells, but the subcellular location annotation is for the whole image, ignoring intercellular difference. In this study, we used large-scale immunofluorescence images and image-level subcellular locations to develop a deep-learning-based pipeline that could accurately recognize protein localizations in single cells. The pipeline consisted of two deep learning models, i.e. an image-based model and a cell-based model. The former used a multi-instance learning framework to comprehensively model protein distribution in multiple cells in each image, and could give both image-level and cell-level predictions. The latter firstly used clustering and heuristics algorithms to assign pseudo-labels of subcellular locations to the segmented cell images, and then used the pseudo-labels to train a classification model. Finally, the image-based model was fused with the cell-based model at the decision level to obtain the final ensemble model for single-cell prediction. Our experimental results showed that the ensemble model could achieve higher accuracy and robustness on independent test sets than state-of-the-art methods.
Understanding the Experience of Discussing Race and Racism During Clinical Supervision for Black Music Therapy Students
Authors: Imeri Janae Phaedra , Jones Jennifer D 
Published: December 2022

Abstract
The experiences of Black music therapy students discussing race and racism in clinical supervision were explored in this study. Participants included 5 Black music therapy students with at least one semester of supervised fieldwork. Recruitment occurred through varied methods utilizing professional networks and snowballing. Data included written survey responses and individual interviews. Utilizing a thematic analysis approach, researchers reviewed that each participant’s dataset generated preliminary codes. Next, researchers grouped codes and compared groupings across datasets. Researchers reached an agreement on 7 themes. Theme 1 addressed the immense vulnerability it takes for Black students to discuss race in and out of supervision. Theme 2 described defensive behaviors from white supervisors, staff members, and peers in response to discussing race. Theme 3 revealed the significance of validating that racism happens to Black students. Theme 4 noted the power supervisors wield over Black students, the privilege white supervisors possess, instances of racism from supervisors, and retaliation from supervisors in response to conversations of race. Theme 5 uncovered a pattern of white supervisors “acknowledging” their privilege and not acting on this self-discovery. Theme 6 examined participants’ feeling like an outsider and supporting themselves in their education. Theme 7 addressed exasperation due to an unchanging oppressive system. Findings connect to the emerging literature on culturally responsive supervision, provide new insights into the supervision of Black music therapy students, and identify the need for change.
Lived Experience Perspectives on Ableism Within and Beyond Music Therapists’ Professional Identities
Authors: Shaw Carolyn , Churchill Victoria , Curtain Sarah , Davies Allison , Davis Brede , Kalenderidis Zoë , Hunt Emily Langlois , McKenzie Benjamin , Murray Megan , Thompson Grace Anne 
Published: December 2022

Abstract
The 10 authors contributing to this reflective essay are comprised of music therapy practitioners, academics, and students with lived experience of disability, neurodivergence, or/and chronic physical and mental health conditions. We will discuss the impact of ableism in our music therapy work, both for participants and for music therapists. Beyond outright discrimination of people with disability, ableism is typically linked to an agenda to normalize and cure. In contrast, music therapists working from a position of post-ableist music therapy seek to collaboratively provide conditions and musical experiences that are less disabling and restrictive through addressing barriers and facilitating connections. We will discuss how including post-ableist perspectives might also create safer spaces for music therapists with lived experience of disability, neurodivergence, and/or chronic physical and mental health conditions. In this critical commentary, we wish to move from a deficit understanding of therapists with lived experience that is often implicit in codes of ethics and standards of practice, to one that celebrates the richness and knowledge that our experience brings. To embed post-ableist perspectives into our profession at all levels, we will discuss the implications for student training and supervision when accessibility is centered in practicum and classroom learning activities. In conclusion, we aim to make apparent the fact that therapists can and do come in all forms and with all backgrounds and that recognizing health diversity in our profession benefits us all.
Clinical Effectiveness of SARS-CoV-2 Booster Vaccine Against Omicron Infection in Residents and Staff of Long-term Care Facilities: A Prospective Cohort Study (VIVALDI)
Authors: Stirrup Oliver , Shrotri Madhumita , Adams Natalie L , Krutikov Maria , Nacer-Laidi Hadjer , Azmi Borscha , Palmer Tom , Fuller Christopher , Irwin-Singer Aidan , Baynton Verity , Tut Gokhan , Moss Paul , Hayward Andrew , Copas Andrew , Shallcross Laura 
Published: December 2022

Abstract

Background
Successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated the effectiveness of booster vaccination against infections, hospitalizations, and deaths among LTCF residents and staff in England.

Methods
We included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12, 2021–March 31, 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalization and death at 0–13, 14–48, 49–83, 84–111, 112–139, and 140+ days after dose 3 of SARS-CoV-2 vaccination compared with 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity, and local SARS-CoV-2 incidence.

Results
A total of 14 175 residents and 19 793 staff were included. In residents without prior SARS-CoV-2 infection, infection risk was reduced 0–111 days after the first booster, but no protection was apparent after 112 days. Additional protection following booster vaccination waned but was still present at 140+ days for COVID-associated hospitalization (adjusted hazard ratio [aHR], 0.20; 95% CI, 0.06–0.63) and death (aHR, 0.50; 95% CI, 0.20–1.27). Most residents (64.4%) had received primary course vaccine of AstraZeneca, but this did not impact pre- or postbooster risk. Staff showed a similar pattern of waning booster effectiveness against infection, with few hospitalizations and no deaths.

Conclusions
Our findings suggest that booster vaccination provided sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 4 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.
An expanding ring of the hypercompact H ii region W 49 N:A2
Authors: Miyawaki Ryosuke , Hayashi Masahiko , Hasegawa Tetsuo 
Published: December 2022

Abstract
We present 250 GHz continuum and H29α line data toward W 49 N:A2, a hypercompact H ii region ionized by an O9 star. The data obtained with ALMA at a resolution of ∼0${_{.}^{\prime\prime}}$05 (600 au) confirmed the presence of an ionized ring with a radius of ∼700 au inclined by ∼50° (0° for pole-on). It has a width of ∼1000 au and is relatively flat with a scale height of less than several hundred au. The tilted ring, or the apparent ellipse, has a prominent velocity difference between its NW and SE ridges along the minor axis, suggesting that it is expanding in the equatorial plane at a velocity of 13.2 km s−1. The ring also shows a hint of rotation at 2.7 km s−1, which is significantly (2.5 σ) smaller than the Kepler velocity of 5.2 km s−1 at its radius around the 20 M⊙ star. This can be interpreted as that the ring gas has been transported from the radius of ∼170 au by conserving its original specific angular momentum that it had there. The ionized ring may thus be a remnant of the accretion disk that fed the O9 star, the radiation or magnetic activities of which became so strong that the disk accretion was reversed due to the intense thermal or magneto-hydrodynamic pressure around the star. The data has revealed a rare example of how a massive star terminates its accretion at the end of its formation, transforming a hypercompact H ii region into an ultracompact H ii region.
The Heterogeneous Cellular States of Glioblastoma Stem Cells Revealed by Single-Cell Analysis
Authors: Yan Haoteng , Zhu Jiali , Ping Yanyan , Yan Min , Liao Gaoming , Yuan Huating , Zhou Yao , Xiang Fengyu , Pang Bo , Xu Jinyuan , Pang Lin 
Published: December 2022

AbstractGlioblastoma stem cells (GSCs) contributed to the progression, treatment resistance, and relapse of glioblastoma (GBM). However, current researches on GSCs were performed usually outside the human tumor microenvironment, ignoring the importance of the cellular states of primary GSCs. In this study, we leveraged single-cell transcriptome sequencing data of 6 independent GBM cohorts from public databases, and combined lineage and stemness features to identify primary GSCs. We dissected the cell states of GSCs and correlated them with the clinical outcomes of patients. As a result, we constructed a cellular hierarchy where GSCs resided at the center. In addition, we identified and characterized 2 different and recurrent GSCs subpopulations: proliferative GSCs (pGSCs) and quiescent GSCs (qGSCs). The pGSCs showed high cell cycle activity, indicating rapid cell division, while qGSCs showed a quiescent state. Then we traced the processes of tumor development by pseudo-time analysis and tumor phylogeny, and found that GSCs accumulated throughout the whole tumor development period. During the process, pGSCs mainly contributed to the early stage and qGSCs were enriched in the later stage. Finally, we constructed an 8-gene prognostic signature reflecting pGSCs activity and found that patients whose tumors were enriched for the pGSC signature had poor clinical outcomes. Our study highlights the primary GSCs heterogeneity and its correlation to tumor development and clinical outcomes, providing the potential targets for GBM treatment.
Acute Endothelial Allograft Rejection After Inoculation With the Novel Messenger RNA SARS-CoV-2 Vaccines
Authors: Zeidenweber Dorian A. , Aldave Anthony J. , Fung Simon S. M. 
Published: December 2022

Purpose:
The aim of this study was to report 3 cases of corneal endothelial allograft rejection shortly after immunization with SARS-CoV-2 messenger RNA (mRNA) vaccines and to describe the clinical course, management, and outcomes.

Methods:
This is a retrospective case series.

Results:
Three patients presented with corneal endothelial rejection 3 weeks after the second dose of a SARS-CoV-2 mRNA vaccine: a 25-year-old woman's 8-month status post-Descemet stripping endothelial keratoplasty for a failed penetrating keratoplasty (PK) (Pfizer-BioNTech COVID-19 vaccine), a 70-year-old man's 4-year status post-PK (Pfizer-BioNTech COVID-19 vaccine), and a 45-year-old woman's 8-month status post-PK (Moderna COVID-19 vaccine). Each of the patients was on a maintenance dose of prednisolone acetate twice daily, which was increased to 4 times daily before the first dose of Pfizer-BioNTech COVID-19 vaccine in the 25-year-old woman. At the time of diagnosis of endothelial rejection, prednisolone acetate was increased to every 1–2 hours for each patient, with resolution of the rejection in the PK recipients but progression to endothelial failure in the Descemet stripping endothelial keratoplasty recipient.

Conclusions:
Our report provides further evidence of a potential association between mRNA vaccines and corneal allograft rejection. Contrary to prior reports, corneal endothelial rejection associated with COVID-19 vaccines may be sufficiently severe to result in irreversible graft failure despite steroid prophylaxis.
Nontuberculous Mycobacterial Isolates Among Cancer Patients: A Single-Center 5-Year Experience
Authors: Addisu Anteneh , Alok Akankcha , Binkam Mounika , Chughtai Muhammad A. , Gutierrez Louisè L. , Greene John N. 
Published: December 2022

Background
Nontuberculous mycobacteria (NTM) are widely distributed in natural environments and are increasing causes of disease with significant morbidity and mortality in immunocompromised patients. We present a 5-year experience of NTM isolates at the Moffitt Cancer Center in Tampa, Fla.

Methods
We conducted a single-center, retrospective study of NTM isolates from January 2011 to February 2016. Records were searched to identify patients with NTM. Specimens included bronchial lavage, swabs, blood/body fluids, and tissue. Basic demographics of patients, clinical attributes, sites of isolation, and concomitant neoplasia were compared.

Results
There were a total of 196 isolates of NTM; 92 of 196 isolates (47%) were Mycobacterium avium complex (MAC). Mycobacterium abscessus, Mycobacterium gordonae, and Mycobacterium fortuitum accounted for 28%, 11%, and 7% of the top 4 isolates, respectively. There was no difference in types of NTM isolated based on the type of underlying neoplasm. Eleven percent of the respiratory isolates were from patients whose biopsy was negative for malignancy on workup of lung nodule. Skin/wound isolates accounted for 13%, and blood/serologic isolates accounted for 7%. Average age of patients was 68 (SD, 11) years; 92% were US born.

Conclusions
Nontuberculous mycobacteria isolated in our study were likely to be MAC and isolated from the respiratory tract; however, we did not find significant association between types of NTM and a given neoplasm. Mycobacterium abscessus was the next most frequent isolate from both respiratory and nonrespiratory specimens. More than 10% of isolates were from surgically excised pulmonary nodules that were benign. Improved NTM testing and scoring algorithms could reduce the need for surgical excision of pulmonary nodules.
New compartment model for COVID-19
Authors: Odagaki Takashi 
Published: December 2022

ABSTRACTPopulation is separated into five compartments for COVID-19; susceptible individuals (S), pre-symptomatic patients (P), asymptomatic patients (A), quarantined patients (Q) and recovered and/or dead patients (R). The time evolution of each compartment is described by a set of ordinary differential equations. Numerical solution to the set of differential equations shows that quarantining pre-symptomatic and asymptomatic patients is effective in controlling the pandemic. It is also shown that the ratio of non-symptomatic patients to the daily confirmed new cases can be as large as 20 and that the fraction of untraceable cases in new cases can be as large as 80%, depending on the policies for social distancing and PCR test.
Disease-modifying effects of Vincamine supplementation inDrosophilaand human cell models of Parkinson’s disease
Authors: Sanz Francisco José , Solana-Manrique Cristina , Paricio Nuria 
Published: December 2022

ABSTRACTParkinson’s disease (PD) is an incurable neurodegenerative disorder caused by the selective loss of dopaminergic neurons in thesubstantia nigra pars compacta. Current therapies are only symptomatic, and are not able to stop or delay its progression. In order to search new and more effective therapies, our group carried out a high-throughput screening assay, identifying several candidate compounds able to suppress motor defects inDJ-1βmutant flies (aDrosophilamodel of familial PD) and to reduce oxidative stress (OS)-induced lethality inDJ-1-deficient SH-SY5Y human cells. One of them was vincamine (VIN), a natural alkaloid obtained from the leaves ofVinca minor. Our results showed that VIN is able to suppress PD-related phenotypes in bothDrosophilaand human cell PD models. Specifically, VIN reduced OS levels in PD model flies. Besides, VIN diminished OS-induced lethality by decreasing apoptosis, increased mitochondrial viability and reduced OS levels inDJ-1-deficient human cells. In addition, we have demonstrated that VIN is able to exert its beneficial role, at least partially, by the inhibition of voltage-gated Na+channels. Therefore, we propose that these channels might be a promising target in the search for new compounds to treat PD, and that VIN constitutes a potential therapeutic treatment for the disease.
MYC directly transactivates CR2/CD21, the receptor of the Epstein-Barr virus, and enhances the viral infection of Burkitt lymphoma cells
Authors: Molina Ester , Garcia-Gutierrez Lucia , Junco Vanessa , Perez-Olivares Mercedes , de Yébenes Virginia G. , Blanco Rosa , Quevedo Laura , Acosta Juan C , Marín Ana V. , Ulgiati Daniela , Merino Ramon , Varela Ignacio , Regueiro José R. , de Alborán Ignacio Moreno , Ramiro Almudena , León Javier 
Published: December 2022

AbstractThe molecular hallmark of Burkitt lymphoma (BL) is a chromosomal translocation that results in deregulated expression ofMYConcogene. This translocation is present in virtually all BL. MYC is an oncogenic transcription factor deregulated in about half of total human tumors, by translocation or other mechanisms. Transcriptomic studies reveal more than 1000 genes regulated by MYC but a much smaller fraction of these genes is directly activated by MYC. All the endemic BL and many sporadic BL cells are associated to the Epstein-Barr virus (EBV) infection. The currently accepted mechanism for the MYC and BL association is that EBV is the causing agent inducing MYC translocation. Complement receptor 2 or CR2 (also called CD21) is a membrane protein that serves as EBV receptor in lymphoid cells. Here we show that CR2 is a direct MYC target gene. This conclusion is based on several evidences. First, MYC downregulation is linked toCR2downregulation both in proliferating and in arrested cells. Second, MYC binds humanCR2promoter and this binding depends on E-box elements. Third, MYC activatesCR2promoter in an E-box dependent manner. Four, MYC activatesCR2transcription in the absence of protein synthesis. Importantly, MYC also inducesCR2expression in mouse primary B cells. Thus, CR2 is abona fideMYC direct target gene. Moreover, higher MYC expression levels in Burkitt lymphoma-derived cells result in a more efficient EBV infection. We propose an alternative mechanism compatible with the correlation between EBV infection and MYC translocation observed in endemic BL, i.e., that deregulated MYC in BL cells occurs first and favors the EBV infection.