bluuebunny/crossref_metadata_2025 huggingface dataset:
Palliative care in the treatment of women with breast cancer: a scoping review protocol
Authors: Velasco-Yanez Romel Jonathan , Fernandes Ana Fátima Carvalho , Mattos Samuel Miranda , Moreira Thereza Maria Magalhães , Castro Régia Christina Moura Barbosa , Lopes-Junior Luís Carlos
Published: March 2022

Introduction: Palliative care is an approach that improves patients' quality of life and their families when they face problems inherent to a life-threatening illness. In the current scenario where breast cancer ranks first among the most common types of cancer in women, research has revealed little control by these patients over the symptoms of the disease and its treatment, resulting in poor quality of life, which should be the focus of attention of palliative care. Thus, the purpose of this study is to map and synthesize the available evidence on palliative care in treating breast cancer women.
Methods: This scoping review protocol was elaborated following the methodological recommendations proposed by the Joanna Briggs Institute (JBI) and the PRISMA Extension for Scoping Reviews (PRISMA-ScR) checklist. All study designs, experimental studies, observational studies, qualitative studies, mixed studies, and reviews reporting the palliative care for breast cancer women, will be considered. The following electronic databases will be searched: MEDLINE (via PubMed), Embase, Cochrane Library, Web of Science, Scopus, JBI Evidence Synthesis, Epistemonikos, CINAHL (via EBSCO), LILACS, and the electronic repository SciELO. In addition, The British Library, Google Scholar, Preprints for Health Sciences [medRXiv], Open Grey, Who Library Database, ProQuest Global Dissertations and Theses, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform will be searched. No language or date restriction will be applied in the search strategy. Two investigators will independently select studies and perform data extraction and critical appraisal using the using JBI design-specific tolos. A narrative synthesis of the evidence will be carried out and will be grouped and presented in tables and graphic models. Also, a similarity analysis will be performed using IRaMuTeQ software version 0.7 alpha 2, leading to textual categories and themes.
Expected Results: The findings of this review will help to identify the gaps for the design of future primary research on women with breast cancer in palliative care. Ultimately, will position care services, managers, and health professionals in the knowledge of the phenomenon, so that they can implement the best evidence-based palliative care practices and improve the quality of care provided to breast cancer patients.
Open Science Framework Registration: osf.io/5bwq7
Development and clinimetric testing of the Unified Drug-Induced Movement Disorders Scale (UDIMS)
Authors: Sachdev Perminder S , Mohan Adith , Cheah Su Lynn , Takacs Anna , Lo Jessica W , Koncz Rebecca , Crawford John D
Published: March 2022

Objective: Several movement disorders develop secondary to the use of psychotropic drugs, for which multiple symptom rating scales are in common use. We planned to develop the Unified Drug-Induced Movement Scale (UDIMS) to assess the severity and impact of drug-induced dyskinesia, tremor, drug-induced parkinsonism, akathisia, dystonia and myoclonus with a single instrument.

Methods: Based on a literature review, consultation and pilot work, a 12-item instrument was developed, with each item rated on a 0-4 scale. The clinimetric properties of UDIMS were examined in 53 psychiatric patients on psychotropic medications, using established ratings scales for validation. The factor structure of the scale was examined, and the movement disorder correlates of distress and disability were determined.

Results: The instrument has good inter-rater reliability. Its correspondence with three other scales - Abnormal Involuntary Movements Scale, Simpson-Angus Scale and Prince Henry Hospital Akathisia Scale - for the relevant items was high. A principal components analysis yielded four factors, considered to represent tremor, parkinsonism, akathisia and dyskinesia. Overall movement-disorder related disability was related to parkinsonism and dyskinesia, while distress to all four components.

Conclusions: UDIMS is a reliable and valid scale to quantify a range of drug-induced movement disorders (DIMDs), that obviates the need for the use of multiple rating scales. Its widespread use by both clinicians and researchers, and further refinement based on this, will help promote the detection and treatment of drug-induced movement disorders, thereby reducing both distress and disability.
Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity
Authors: Garcia Sarahi L , Nuy Julia K , Mehrshad Maliheh , Hampel Justyna J , Sedano-Nuñez Vicente T , Buck Moritz , Divne Anna-Maria , Lindström Eva S , Petras Daniel , Hawkes Jeffrey , Bertilsson Stefan
Published: March 2022

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and fundamental for planetary processes and ecosystem functioning. While the link between microbial community composition and heterotrophic utilization of DOM has been recognized, the full diversity of organic compounds, their bioavailability, degradability and specific influences on the diversity and function of heterotrophs are still not clear. Here we experimentally investigate heterotrophic bacteria in thirty-three freshwater model communities. We identified 34 different heterotrophs growing in ambient lake DOM with taxonomic affiliations matching abundant freshwater bacterioplankton. We further describe 25 different heterotrophs growing in the phycosphere of M. Aeruginosa and 6 heterotrophs growing on the DOM produced by M. Aeruginosa with taxonomic affiliation in accord to phycosphere heterotrophs. In our experiment we observed that heterotrophs that live in the phycosphere remove more dissolved organic carbon than abundant freshwater heterotrophs. Moreover, phycosphere heterotrophs have bigger genomes than abundant lake bacteria. Altogether of the 4224 chemical features that were resolved by LC-MS, only 1229 were seen in all three treatments. None of the common/shared compounds were removed across all the model communities, suggesting contrasting niches of the studied taxa. Altogether our study highlights how each model community, with its unique taxonomic assemblages and organotroph functioning is upkept by the chemodiversity of DOM.
Quantifying formations of Neutravidin clusters on biotinylated mixed silane Self-Assembled Monolayers
Authors: Ghosh Ushnik
Published: March 2022

Towards the goal of developing bio-chip / lab-on-a-chip substrates capable of performing highly specific bio-chemical reactions, Neutravidin binding to mixed Biotinylated Silane Self-Assembled Monolayers were studied using Confocal Fluorescence Light Microscopy. Non-specific bindings, specifically the formations of Neutravidin clusters, were quantified. Several experiments were conducted to determine the concentrations of Neutravidin necessary to not saturate surface binding to Biotinylated Self-Assembled Monolayers, determine the effectiveness of using FBS blocking buffers to reduce non-specific binding, optimize the repeatability of Neutravidin binding to Biotinlyated mixed Self-Assembled Monolayers with Silane-PEG-Biotin compositions ranging from 0 to 15%, and quantify background Neutravidin bindings and the corresponding formations of Neutravidin clusters to Self-Assembled Monolayers as Silane-PEG-Biotin percent compositions increase from 0 to 15%. The Neutravidin, Silane-PEG-Biotin, and Silane mPEG concentrations and ratios needed to develop homogeneous Neutravidin films, without the formations of clusters, on the Self-Assembled Monolayers have been determined.
Environmental Conditions and Vigilance Behaviour in the Smooth-coated Otter, Lutrogale perspicillata
Authors: Travell Nathan Paul , Fernandez Katrina
Published: March 2022

Vigilance is an ecologically important behaviour that acts as a defence mechanism against threats such as predators, competitors, and environmental pressures. Being vigilant can place energetic constraints on an individual, as conducting other behaviours such as grooming can be limited. The smooth-coated otter is a vulnerable species, and understanding baseline behaviour, such as vigilance, and stressor effects can be a crucial step in implementing any conservation strategies. However, literature on this charismatic species is relatively sparse, with the majority of research covering prey items, habitat use and extent of occurrence. Using camera trap footage along with historical climate datasets, the current study assessed various aspects of vigilance behaviour of the smooth-coated otter. These aspects include how long individuals dedicated to being vigilant, what they prioritised being vigilant over, and how intense their vigilance efforts were. Variables that are expected to change with global climate change such as temperature, and to an extent, air pressure, were associated with increases in vigilance duration. Wind speeds, which are also expected to be affected by climate change, along with increasing numbers of conspecifics, were linked to increased intensity possibly highlighting that increasing ambient movement results in more frequent head rotations. When vigilance is ineffectual however, such during periods of higher rainfall, cloud cover or at night, intensity decreases, and gazing towards conspecifics increases - possibly to reaffirm where safety lies when threats cannot be adequately monitored.
A Machine Learning Framework to Predict Subcellular Morphology of Endothelial Cells for Digital Twin Generation
Authors: Contreras Miguel , Hafenstine Rex W , Bachman William , Long David S
Published: March 2022

Gaining insight into different cell behaviors is key to better understanding different pathologies. These behaviors may be explained in part through close observation of 3D cell morphology. Therefore, the objective of this research was to develop a machine learning (ML) framework that can predict 3D subcellular morphological variation of endothelial cells (ECs) to generate digital twins. ECs were cultured and their membrane, nucleus, and focal adhesion (FA) sites were stained and imaged with confocal microscopy. The multicellular confocal z stacks were segmented resulting in a total of 60 single-cell stacks. Fifty randomly picked cells were augmented 20-fold to train the ML framework, and the remaining 10 were used for an independent test of prediction accuracy. The ML framework was based on an open-source conditional generative adversarial network (cGAN), which was expanded to make 3D predictions using membrane only as input to predict nucleus and FA morphology. After training the framework, the results on the independent test showed an average prediction accuracy of ~87% for nucleus and ~70% for FA sites. The predictions were used to build a digital twin of each EC and compared to their respective ground truth, showing an average ~79% global accuracy and ~84% accuracy in FA-Nucleus distribution. The results presented show the effectiveness of the developed ML framework to generate digital twins of ECs using limited amount of data. These digital twins can be used to couple EC morphology with different behaviors. The ML framework can be potentially expanded to predict morphology of other subcellular structures as well as to study other types of cells.
The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply
Authors: Durand Mickaël , Brehaut Virginie , Clément Gilles , Kelemen Zsolt , Macé Julien , Feil Regina , Duville Garry , Launay-Avon Alexandra , Roux Christine Paysant-Le , Lunn John E. , Roudier François , Krapp Anne
Published: March 2022

Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Ongoing work has identified several transcriptional regulators of nitrate signaling, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN 7 (NLP7), but additional regulators likely remain to be identified. Here, we characterized Arabidopsis NLP2 as a master upstream transcriptional regulator of early nitrate responses that interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, a DNA binding motif, and some target genes with NLP7. Additional genetic, genomic and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multi-tiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production.

One-sentence summary

NLP2 and NLP7 orchestrate plant responses to nitrate supply and control nitrate- dependent regulation of carbon and energy metabolism.
On the Design of a PID Bio-controller with Set Point Weighting and Filtered Derivative Action
Authors: Alexis Emmanouil , Cardelli Luca , Papachristodoulou Antonis
Published: March 2022

Effective and robust regulation of biomolecular processes is crucial for designing reliable synthetic bio-devices functioning in uncertain and constantly changing biological environments. Proportional-Integral-Derivative (PID) controllers are undeniably the most common way of implementing feedback control in modern technological applications. Here, we introduce a highly tunable PID bio-controller with set point weighting and filtered derivative action presented as a chemical reaction network with mass action kinetics. To demonstrate its effectiveness, we apply our PID scheme on a simple biological process of two mutually activated species, one of which is assumed to be the output of interest. To highlight its performance advantages we compare it to PI regulation using numerical simulations in both the deterministic and stochastic setting.
Longitudinal changes of white matter hyperintensities in sporadic small vessel disease: a systematic review and meta-analysis
Authors: Jochems Angela CC , Arteaga Carmen , Chappell Francesca M , Ritakari Tuula , Hooley Monique , Doubal Fergus N , Muñoz Maniega Susana , Wardlaw Joanna M
Published: March 2022

Background and objectives

White matter hyperintensities (WMH) are frequent imaging features of small vessel disease (SVD) and related to poor clinical outcomes. WMH progression over time is well described, but regression was also noted recently, although the frequency and associated factors are unknown. This systematic review and meta-analysis aims to assess longitudinal intra-individual WMH volume changes in sporadic SVD.

Methods

Following PRISMA guidelines we searched EMBASE and MEDLINE for papers up to 28 January 2022 on WMH volume changes using MRI on ≥2 time-points in adults with sporadic SVD. We classified populations (healthy/community-dwelling, stroke, cognitive, other vascular risk factors, depression) based on study characteristics. We performed random-effects meta-analyses with Knapp-Hartung adjustment to determine mean WMH volume change (change in mL, % of intracranial volume [%ICV], or mL/year), 95%CI and prediction intervals (PI, limits of increase and decrease) using unadjusted data. Risk of Bias Assessment tool for Non-randomised Studies (RoBANS) was used to assess risk of bias.

Results

Forty papers, 10,932 participants, met the inclusion criteria. Mean WMH volume increased over time by: 1.74 mL (95% CI 1.23, 2.26; PI -1.24, 4.73 mL; 27 papers, N=7411, mean time interval 2.7 years, SD=1.65); 0.25%ICV (95% CI 0.14, 0.36; PI -0.06, 0.56; 6 papers, N=1071, mean time interval 3.5 years, SD =1.54); or 0.61 mL/year (95% CI 0.37, 0.85; PI -0.25, 1.46; 7 papers, N=2450). Additionally, 13 papers specifically mentioned and/or provided data on WMH regression, which occurred in asymptomatic, stroke, and cognitive presentations of SVD.

Discussion

Net mean WMH volume increases over time mask wide-ranging change (e.g. mean increase of 1¾mL ranging from 1¼mL decrease to 4¾ml increase), with regression documented explicitly in up to 1/3 of participants. More knowledge on underlying mechanisms, associated factors and clinical correlates is needed, as WMH regression could be an important intervention target.
Association between tobacco exposure, blood pressure, and arterial stiffness in South African adults and children
Authors: Nembulu Betty , Kolkenbeck-Ruh Andrea , Gafane-Matemane Lebo , Kruger Ruan , Breet Yolandi , Ware Lisa Jayne
Published: March 2022

Introduction: Sociodemographic factors, health status and health behaviour have all been associated with arterial stiffness. We examined the association between tobacco use or exposure and pulse wave velocity (PWV, a marker of arterial stiffness) in black South African adults and children against a background of other known risk factors.
Methods: Two datasets were used: African-PREDICT (A-P; n=587 apparently healthy black adult men and women, 20-30 years) and Birth-to-Twenty-Plus (Bt20; n=95 black adult women, 28-68 years and n=47 black children, 4-10 years). A cotinine value >10 ng/ml in urine (Bt20) or serum (A-P) was considered as tobacco exposed and carotid-femoral PWV was measured using the SphygmoCor XCEL device. Regression analysis included cotinine and other known risk factors.
Results: One third of adults (32%) and almost half of all children (45%) were tobacco exposed with the prevalence of elevated blood pressure (BP) approximately twice as high as their non-exposed counterparts (adults, p=0.014; children, p=0.017). Cotinine was the only variable that significantly associated positively with PWV in both adults and children in univariate analysis (p<0.05), but only MAP remained significant for adults in multivariate analysis (p=0.001).
Conclusions: In this sample, tobacco exposure was adversely associated with vascular health in adults and children. BP was higher in the tobacco exposed adults and children compared to their non-exposed counterparts. These findings suggest tobacco cessation programs for adults should include screening for blood pressure and consider the impact of tobacco exposure on child vascular health.
Predictors of unfavourable treatment outcome in patients diagnosed with drug-resistant tuberculosis in the Torres Strait / Papua New Guinea border region
Authors: Foster J’Belle , Mendez Diana , Marais Ben J. , Peniyamina Dunstan , McBryde Emma S.
Published: March 2022

Drug-resistant tuberculosis (DR-TB) is an ongoing challenge in the Torres Strait Islands (TSI) / Papua New Guinea (PNG) border region. Treatment success rates have historically been poor for patients diagnosed with DR-TB, leading to increased transmission. This study aimed to identify variables associated with unfavourable outcome in patients diagnosed with DR-TB to inform programmatic improvements.

A retrospective study of all DR-TB cases who presented to Australian health facilities in the Torres Strait between 1 March 2000 and 31 March 2020 was performed. This time period covers four distinct TB programmatic approaches which reflect Australian and Queensland Government decisions on TB management in this remote region. Univariate and multivariate predictors of unfavourable outcome were analysed. Unfavourable outcome was defined as lost to follow up, treatment failure and death. Successful outcome was defined as cure and treatment completion.

In total, 133 patients with resistance to at least one TB drug were identified. The vast majority (123/133; 92%) of DR-TB patients had pulmonary involvement; and of these, 41% (50/123) had both pulmonary and extrapulmonary TB. Unfavourable outcomes were observed in 29% (39/133) of patients. Patients living with human immunodeficiency virus, renal disease or diabetes (4/133; 4/133; 3/133) had an increased frequency of unfavourable outcome (p<0.05), but the numbers were small. Among all 133 DR-TB patients, 41% had a low lymphocyte count, which was significantly associated with unfavourable outcome (p<0.05). We noted a 50% increase in successful outcomes achieved in the 2016 - 2020 programmatic period, compared to earlier periods (OR 5.3, 95% Confidence Interval [1.3, 20.4]). Being a close contact of a known TB case was associated with improved outcome.

While DR-TB treatment outcomes have improved over time, enhanced surveillance for DR-TB, better cross border collaboration and consistent diagnosis and management of comorbidities and other risk factors should further improve patient care and outcomes.
Vaccine effectiveness of two and three doses of BNT162b2 and CoronaVac against COVID-19 in Hong Kong
Authors: McMenamin Martina E. , Nealon Joshua , Lin Yun , Wong Jessica Y. , Cheung Justin K. , Lau Eric H. Y. , Wu Peng , Leung Gabriel M. , Cowling Benjamin J.
Published: March 2022

Background

Hong Kong maintained extremely low circulation of SARS-CoV-2 until a major community epidemic of Omicron BA.2 starting in January 2022. Both mRNA BNT162b2 (BioNTech/Fosun Pharma) and inactivated CoronaVac (Sinovac) vaccines are widely available, however coverage has remained low in older adults. Vaccine effectiveness in this predominantly infection-naïve population is unknown.

Methods

We used individual-level case data on mild/moderate, severe/fatal and fatal hospitalized COVID-19 from December 31, 2021 to March 8, 2022, along with census information and coverage data of BNT162b2 and CoronaVac. We used a negative binomial model, adjusting for age and calendar day to estimate vaccine effectiveness of one, two and three dose schedules of both vaccines, and relative effectiveness by number of doses and vaccine type.

Findings

A total of 12.7 million vaccine doses were administered in Hong Kong’s 7.3 million population, and we analyzed data from confirmed cases with mild/moderate (N=5,474), severe/fatal (N=5,294) and fatal (N=4,093) COVID-19. Two doses of either vaccine protected against severe disease and death, with higher effectiveness among adults ≥60 years with BNT162b2 (VE: 88.2%, 95% confidence interval, CI: 84.4%, 91.1%) compared to CoronaVac (VE: 74.1%, 95% CI: 67.8%, 79.2%). Three doses of either vaccine offered very high levels of protection against severe outcomes (VE: 98.1%, 95% CI: 97.1%, 98.8%).

Interpretation

Third doses of either BNT162b2 or CoronaVac provide substantial additional protection against severe COVID-19 and should be prioritized, particularly in older adults who received CoronaVac primary schedules. Longer follow-up is needed to assess persistence of different vaccine platforms and schedules.

Funding

COVID-19 Vaccines Evaluation Program, Chinese Center for Disease Control and Prevention
People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses
Authors: Lapointe Hope R. , Mwimanzi Francis , Cheung Peter K. , Sang Yurou , Yaseen Fatima , Umviligihozo Gisele , Kalikawe Rebecca , Speckmaier Sarah , Moran-Garcia Nadia , Datwani Sneha , Duncan Maggie C. , Agafitei Olga , Ennis Siobhan , Young Landon , Ali Hesham , Ganase Bruce , Omondi F. Harrison , Dong Winnie , Toy Junine , Sereda Paul , Burns Laura , Costiniuk Cecilia T. , Cooper Curtis , Anis Aslam H. , Leung Victor , Holmes Daniel , DeMarco Mari L. , Simons Janet , Hedgcock Malcolm , Prystajecky Natalie , Lowe Christopher F. , Pantophlet Ralph , Romney Marc G. , Barrios Rolando , Guillemi Silvia , Brumme Chanson J. , Montaner Julio S.G. , Hull Mark , Harris Marianne , Niikura Masahiro , Brockman Mark A. , Brumme Zabrina L.
Published: March 2022

Background

Longer-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose.

Methods

We measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls.

Results

Though humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though anti-Omicron responses were consistently weaker than against wild-type.

Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses.

Conclusion

PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after two- and three-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.
Jupytope: Computational extraction of structural properties of viral epitopes
Authors: Rashid Shamima , Ann Ng Teng , Keong Kwoh Chee
Published: March 2022

Epitope residues located on viral surface proteins are of immense interest in immunology and related applications such as vaccine development, disease diagnosis and drug design. Most tools rely on sequence based statistical comparisons, such as information entropy of residue positions in aligned columns to infer location and properties of epitope sites. To facilitate cross-structural comparisons of epitopes on viral surface proteins, a python-based extraction tool implemented with Jupyter notebook is presented (Jupytope). Given a viral antigen structure of interest, a list of known epitope sites and a reference structure, the corresponding epitope structural properties can quickly be obtained. The tool integrates biopython modules for commonly used software such as NACCESS, DSSP as well as residue depth and outputs a list of structure derived properties such as dihedral angles, solvent accessibility, residue depth and secondary structure that can be saved in several convenient data formats. To ensure correct spatial alignment, Jupytope takes a list of given epitope sites and their corresponding reference structure and aligns them before extracting the desired properties. Examples are demonstrated for epitopes of Influenza and SARS-CoV2 viral strains. The extracted properties assist detection of two Influenza subtypes and show potential in distinguishing between four major clades of SARS-CoV2, as compared with randomized labels. The tool will facilitate analytical and predictive works on viral epitopes through the extracted structural information.

Key Messages

Jupytope combines existing 3D-structural software to extract the properties of viral epitopes into a convenient text or csv file format

The structural properties serve as parameters or features that quantitatively capture viral epitopes

Association of structural properties to viral subtypes (for Influenza) or clades (SARS-CoV2) is demonstrated with a simple XGBoost model

Structure datasets mapped to SARS-CoV2 WHO clades and Pango lineages, as well as chain annotations are available for download
Decoding functional high-density lipoprotein particle surfaceome interactions
Authors: Frey Kathrin , Goetze Sandra , Rohrer Lucia , von Eckardstein Arnold , Wollscheid Bernd
Published: March 2022

High-density lipoprotein (HDL) is a mixture of complex particles mediating reverse cholesterol transport in the human body and several cytoprotective activities. Despite its relevance for human health, many aspects of HDL-mediated lipid trafficking and cellular signaling remain elusive at the molecular level. During HDL's journey throughout the body, its function is mediated through interactions with cell surface receptors on different cell types. Using four different cellular model systems HDL is interacting with, we comparatively analyzed their surfaceomes to define the HDL receptome. Surfaceome analysis of EA.hy926, HEPG2, foam cells, and human aortic endothelial cells (HAEC) revealed the main currently known HDL-receptor scavenger receptor B1 (SCRB1), as well as 154 shared cell surface receptors representing potential HDL interaction receptor candidates. Since vascular endothelial growth factor A (VEGF-A) was recently found as a regulatory factor of transendothelial transport of HDL, we next analyzed the VEGF modulated surfaceome of HAEC using auto-CSC technology. VEGF-A treatment led to a remodeling of the surfaceome of HAEC cells including the previously reported higher surfaceome abundance of SCRB1 upon treatment. 165 additional receptors were found on HAEC upon VEGF-A treatment representing SCRB1 co-regulated receptors potentially involved in HDL function. Using HATRIC-based ligand receptor capturing (HATRIC-LRC) technology on human endothelial cells, we specifically aimed for the identification of other bona fide (co-)receptors of HDL beyond SCRB1. HATRIC-LRC enabled, next to SCRB1, the identification of the receptor tyrosine-protein kinase Mer (MERTK), which we show is directly contributing to endothelial HDL binding and uptake. Subsequent proximity ligation assays (PLA) demonstrate furthermore the spatial vicinity of MERTK and SCRB1 on the endothelial cell surface. The data shown provide direct evidence for a complex and dynamic HDL receptome and that receptor nanoscale organization may influence functional HDL binding and uptake.
Persistent acetylation of histone H3 lysine 56 compromises the activity of DNA replication origins
Authors: Tremblay Roch , Mehrjoo Yosra , Simoneau Antoine , McQuaid Mary E. , Nislow Corey , Giaever Guri , Wurtele Hugo
Published: March 2022

InSaccharomyces cerevisiae, newly synthesized histone H3 are acetylated on lysine 56 (H3 K56ac) by the Rtt109 acetyltransferase prior to their deposition on nascent DNA behind replication forks. Two deacetylases of the sirtuin family, Hst3 and Hst4, remove H3 K56ac from chromatin following S phase.hst3Δhst4Δ cells present constitutive H3 K56ac, which sensitizes cells to replicative stress via mechanisms that remain unclear. We performed a screen to identify genes that influence cell fitness upon nicotinamide (NAM)-induced inhibition of sirtuins. The screen revealed thatDBF4heterozygosity causes NAM sensitivity.DBF4andCDC7encode subunits of the Dbf4-dependent kinase, which activates origins of DNA replication. We show that i) cells harboring thedbf4-1orcdc7-4hypomorphic alleles are sensitive to NAM, ii) Rif1, an inhibitor of Cdc7-dependent activation of origins, causes DNA damage and replication defects in NAM-treated cells andhst3Δhst4Δ mutants, and iii)cdc7-4 hst3Δhst4Δ cells display synthetic temperature sensitivity associated with delayed initiation of DNA replication. Such replication defects are not due to activation of the intra-S phase checkpoint but require Rtt109-dependent H3 K56ac. Overall, these results suggest that persistent H3 K56ac sensitizes cells to replicative stress in part by negatively influencing replication origin activity.
Light-sheet mesoscopy with the Mesolens provides fast sub-cellular resolution imaging throughout large tissue volumes.
Authors: Battistella Eliana , Schniete Jan , Wesencraft Katrina , Quintana Juan , McConnell Gail
Published: March 2022

Rapid imaging of large biological tissue specimens such as ultrathick sections of mouse brain cannot easily be performed with a standard microscope. Optical mesoscopy offers a solution, but thus far imaging has been too slow to be useful for routine use. We have developed two different illuminators for light-sheet mesoscopy with the Mesolens and we demonstrate their use in high-speed optical mesoscale imaging of large tissue specimens. The first light-sheet approach uses Gaussian optics and is straightforward to implement. It provides excellent lateral resolution and high-speed imaging, but the axial resolution is poor. The second light-sheet is a more complex Airy light-sheet that provides sub-cellular resolution in three dimensions that is comparable in quality to point-scanning confocal mesoscopy, but the light-sheet method of illuminating the specimen reduces the imaging time by a factor of 14. This creates new possibilities for high-content, higher-throughput optical bioimaging at the mesoscale.
Multi-omics analyses of MEN1 missense mutations identify disruption of menin-MLL and menin-JunD interactions as critical requirements for molecular pathogenicity
Authors: Dreijerink Koen M.A. , Ozyerli-Goknar Ezgi , Koidl Stefanie , van der Lelij Ewoud J. , van den Heuvel Priscilla , Kooijman Jeffrey J. , Biniossek Martin L , Rodenburg Kees W. , Nizamuddin Sheikh , Timmers H.Th.Marc
Published: March 2022

Loss-of-function mutations of the multiple endocrine neoplasia type 1 (MEN1) gene are causal to the MEN1 tumor syndrome, but they are also commonly found in sporadic pancreatic neuroendocrine tumors and other types of cancers. The MEN1 gene product, menin, is involved in transcriptional and chromatin regulation, most prominently as an integral component of KMT2A/MLL1 and KMT2B/MLL2 containing COMPASS-like histone H3K4 methyltransferase complexes. In a mutually exclusive fashion, menin also interacts with the JunD subunit of the AP-1 and ATF/CREB transcription factors. After in silico screening of 253 disease-related MEN1 missense mutations, we selected a set of nine menin mutations in surface-exposed residues. The protein interactomes of these mutants were assessed by quantitative mass spectrometry, which indicated that seven of the nine mutants disrupt interactions with both MLL1/2 and JunD complexes. Interestingly, we identified three missense mutations, R52G, E255K and E359K, which predominantly reduce the interaction with MLL1 compared to JunD. This observation was supported by a pronounced loss of binding of the R52G, E255K and E359K mutant proteins at unique MLL1 genomic binding sites with less effect on unique JunD sites. These findings support the general importance of the menin-MLL1 and menin-JunD interactions in MEN1 gene-associated pathogenic conditions.
A ubiquitin-independent proteasome pathway controls the CARD8 inflammasome
Authors: Hsiao Jeffrey C. , Neugroschl Atara R. , Chui Ashley J. , Taabazuing Cornelius Y. , Griswold Andrew R. , Wang Qinghui , Huang Hsin-Che , Orth-He Elizabeth L. , Ball Daniel P. , Hiotis Giorgos , Bachovchin Daniel A.
Published: March 2022

CARD8 is a pattern-recognition receptor that forms a caspase-1-activating inflammasome. CARD8 undergoes autoproteolysis, generating an N-terminal (NT) fragment with a disordered region and a ZU5 domain and a C-terminal (CT) fragment with UPA and CARD domains. DPP8 and DPP9 (DPP8/9) inhibitors, including Val-boroPro (VbP), accelerate the degradation of the NT fragment via a poorly characterized proteasome-mediated pathway, thereby releasing the inflammatory CT fragment from autoinhibition. Here, we show that the core 20S proteasome, which degrades disordered and misfolded proteins independent of ubiquitin, controls CARD8 activation. In unstressed cells, the 20S proteasome degrades just the NT disordered region, leaving behind the folded ZU5, UPA, and CARD domains to act as an inhibitor of inflammasome assembly. In VbP-stressed cells, the 20S proteasome degrades the entire NT fragment, perhaps due to ZU5 domain unfolding, freeing the CT fragment from autoinhibition. Overall, this work shows that the susceptibility of the CARD8 NT to 20S proteasome-mediated degradation controls inflammasome activation.
Repeat sequences limit the effectiveness of LGT and favoured the evolution of meiotic sex in early eukaryotes
Authors: Colnaghi Marco , Lane Nick , Pomiankowski Andrew
Published: March 2022

The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, whilst limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.
Intranasal Nanoemulsion Adjuvanted S-2P Vaccine Demonstrates Protection in Hamsters and Induces Systemic, Cell-Mediated and Mucosal Immunity in Mice
Authors: Ganesan Shyamala , Acosta Hugo , Brigolin Chris , Orange Kallista , Trabbic Kevin , Chen Charles , Lien Chia-En , Lin Yi-Jiun , Lin Meei-Yun , Chuang Ya-Shan , Fattom Ali , Bitko Vira
Published: March 2022

With the rapid progress made in the development of vaccines to fight the SARS-CoV-2 pandemic, almost >90% of vaccine candidates under development and a 100% of the licensed vaccines are delivered intramuscularly (IM). While these vaccines are highly efficacious against COVID-19 disease, their efficacy against SARS-CoV-2 infection of upper respiratory tract and transmission is at best temporary. Development of safe and efficacious vaccines that are able to induce robust mucosal and systemic immune responses are needed to control new variants. In this study, we have used our nanoemulsion adjuvant (NE01) to intranasally (IN) deliver stabilized spike protein (S-2P) to induce immunogenicity in mouse and hamster models. Data presented demonstrate the induction of robust immunity in mice resulting in 100% seroconversion and protection against SARS-CoV-2 in a hamster challenge model. There was a significant induction of mucosal immune responses as demonstrated by IgA- and IgG-producing memory B cells in the lungs of animals that received intranasal immunizations compared to an alum adjuvanted intramuscular vaccine. The efficacy of the S-2P/NE01 vaccine was also demonstrated in an intranasal hamster challenge model with SARS-CoV-2 and conferred significant protection against weight loss, lung pathology, and viral clearance from both upper and lower respiratory tract. Our findings demonstrate that intranasal NE01-adjuvanted vaccine promotes protective immunity against SARS-CoV-2 infection and disease through activation of three arms of immune system: humoral, cellular, and mucosal, suggesting that an intranasal SARS-CoV-2 vaccine may play a role in addressing a unique public health problem and unmet medical need.
Detection of Fortunate Molecules Induce PArticle Resolution Shift (PAR-shift) towards Single-molecule Limit in SMLM: A Technique for Resolving Molecular Clusters in Cellular System
Authors: Aravinth S , Joshi Prakash , Mondal Partha P.
Published: March 2022

Molecules capable of emitting a large number of photons (also known as fortunate molecules) are crucial for achieving resolution close to a single molecule limit (the actual size of a single molecule). We propose a long-exposure single molecule localization microscopy (leSMLM) technique that enables detection of fortunate molecules, which is based on the fact that detecting a relatively small subset of molecules with large photon emission increases its localization . Fortunate molecules have the ability to emit a large burst of photons over a prolonged time (> average triplet-state lifetime). So, a long exposure time allows the time window necessary to detect these elite molecules. The technique involves the detection of fortunate molecules to generate enough statistics for a quality reconstruction of the target protein distribution in a cellular system. Studies show a significant PArticle Resolution Shift (PAR-shift) of about 6 nm and 11 nm towards Single-molecule-limit (away from diffraction-limit) for an exposure time window of 60 ms and 90 ms, respectively. In addition, a significant decrease in the fraction of fortunate molecules (single molecules with small localization precision) is observed. Specifically, 8.33% and 3.43% molecules are found to emit in 30 − 60 ms and 60 − 90 ms, respectively, when compared to SMLM. The long exposure has enabled better visualization of Dendra2HA molecular cluster, with sub-clusters within a large cluster. Thus, the proposed technique (leSMLM) facilitates a better study of cluster formation in fixed samples. Overall, the method enables better spatial resolution at the cost of relatively poor temporal resolution.
Structure-forming CAG/CTG repeats interfere with gap repair to cause repeat expansions and chromosome breaks
Authors: Polleys Erica Jean , Del Priore Isabella , Mejia Marjorie de la Rosa , Haber James E. , Freudenreich Catherine H
Published: March 2022

Expanded CAG/CTG repeats are sites of DNA damage, leading to changes in repeat length. To determine how ssDNA gap filling affects repeat instability, we inserted (CAG)70 or (CTG)70 repeats into a single-strand annealing (SSA) assay system such that resection and filling in the ssDNA gap would occur across the repeat tract. After resection, when the CTG sequence was the single-stranded template for fill-in synthesis, repeat contractions were elevated and the ssDNA created a fragile site that led to large deletions involving flanking homologous sequences. In contrast, resection was inhibited when CTG was on the resected strand, resulting in repeat expansions. Deleting Rad9, the ortholog of 53BP1, rescued repeat instability and lost viability by increasing resection and fill-in speed. Deletion of Rad51 increased CTG contractions and decreased survival, implicating Rad51 in protecting ssDNA during gap filling. Taken together, DNA sequence within a single-stranded gap determines repair kinetics, fragility, and repeat instability.
Modeling the effect of cooperativity in ternary complex formation and targeted protein degradation mediated by heterobifunctional degraders
Authors: Park Daniel , Izaguirre Jesus , Coffey Rory , Xu Huafeng
Published: March 2022

Chemically induced proximity between certain endogenous enzymes and a protein of interest (POI) inside cells may cause post-translational modifications to the POI with biological consequences and potential therapeutic effects. Heterobifunctional (HBF) molecules that bind with one functional part to a target POI and with the other to an E3 ligase induce the formation of a target-HBF-E3 ternary complex, which can lead to ubiquitination and proteasomal degradation of the POI. Targeted protein degra-dation (TPD) by HBFs offers a promising approach to modulating disease-associated proteins, especially those that are intractable using other therapeutic approaches, such as enzymatic inhibition. The three-way interactions among the HBF, the target POI, and the ligase—including the protein-protein interaction (PPI) between the POI and the ligase—contribute to the stability of the ternary complex, manifested as positive or negative binding cooperativity in its formation. How such cooperativity affects HBF-mediated degradation is an open question. In this work, we develop a pharmaco-dynamic model that describes the kinetics of the key reactions in the TPD process, and we use this model to investigate the role of cooperativity in the ternary complex formation and in the target POI degradation. Our model predicts that, under certain conditions, increasing cooperativity may diminish degradation, implying an optimal range of cooperativity values for efficient degradation. We also develop a statistical inference model for determining cooperativity in intracellular ternary complex formation from cellular assay data, and demonstrate it by quantifying the change in cooperativity due to site-directed mutagenesis at the POI-ligase interface of the SMARCA2-ACBI1-VHL ternary complex. Our pharmacodynamic model provides a quantitative framework to dissect the complex HBF-mediated TPD process and may inform the rational design of effective HBF degraders.
Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2
Authors: Fang Zhenhao , Peng Lei , Lin Qianqian , Zhou Liqun , Yang Luojia , Feng Yanzhi , Ren Ping , Renauer Paul A. , Park Jonathan J. , Zhou Xiaoyu , Wilen Craig B. , Chen Sidi
Published: March 2022

The Omicron sub-lineage BA.2 of SARS-CoV-2 has recently become dominant across many areas in the world in the on-going waves of COVID-19. Compared to the ancestral/wild-type (WT) virus, Omicron lineage variants, both BA.1 and BA.2, contain high number of mutations, especially in the spike protein, causing significant immune escape that leads to substantial reduction of vaccine and antibody efficacy. Because of this antigenic drift, BA.2 exhibited differential resistance profile to monoclonal antibodies than BA.1. Thus, it is important to understand whether the immunity elicited by currently available vaccines are effective against the BA.2 subvariant. We directly tested the heterotypic vaccination responses against Omicron BA.2, using vaccinated serum from animals receiving WT- and variant-specific mRNA vaccine in lipid nanoparticle (LNP) formulations. Omicron BA.1 and BA.2 antigen showed similar reactivity to serum antibodies elicited by two doses of WT, B.1.351 and B.1.617 LNP-mRNAs. Neutralizing antibody titers of B.1.351 and B.1.617 LNP-mRNA were ~2-fold higher than that of WT LNP-mRNA. Both homologous boosting with WT LNP-mRNA and heterologous boosting with BA.1 LNP-mRNA substantially increased waning immunity of WT vaccinated mice against both BA.1 and BA.2 subvariants. The BA.1 LNP-mRNA booster was ~3-fold more efficient than WT LNP-mRNA at elevating neutralizing antibody titers of BA.2. Together, these data provided a direct preclinical evaluation of WT and variant-specific LNP-mRNAs in standard two-dose and as boosters against BA.1 and BA.2 subvariants.
Increased Circulating miR-155 identifies a subtype of preeclamptic patients
Authors: Wang Zhiyin , Duan Honglei , Wang Yuan , Liu Dan , Cao Chenrui , Dai Yimin , Zhao Guangfeng , Gu Ning , Zhou Yan , Zheng Mingming , Hu Yali
Published: March 2022

Preeclampsia is a heterogeneous disorder which affect maternal and fetal outcomes. The current classifications of preeclampsia such as “early-“ and “late-” types, and “mild” and “severe” forms, are too imprecise to delineate the pathophysiology of preeclampsia. Here we reported that roughly one third of preeclampsia patients had high expression of maternal serum miR-155 in the case-control study and longitudinal study. The maternal serum miR-155 increased as early as 11-13+6 weeks of gestation. The patients with high serum miR-155 had severer clinical symptoms such as higher blood pressure and urine protein, and more adverse maternal and fetal outcomes. Moreover, these patients could be clustered as one group according to clinical manifestation by t-distributed stochastic neighbor embedding analysis. Therefore, these data suggest that preeclamptic patients with high maternal serum miR-155 could be viewed as a subtype of preeclampsia.