bluuebunny/crossref_metadata_2025 huggingface dataset:
MODL-02. A novelCre-conditionalcMYC-driven MB Group 3 transgenic mouse model shows traceable leptomeningeal dissemination.
Authors: Morcavallo Alaide , Barker Karen , Kwok Colin , Boult Jessica K R , da Silva Patricia Benites Goncalves , Okonechnikov Konstantin , Zuckermann Marc , Gorrini Chiara , Jacques Thomas S , Robinson Simon P , Clifford Steven C , Weiss William A , Pfister Stefan M , Kawauchi Daisuke , Chesler Louis
Published: June 2022

Medulloblastoma (MB), the most common embryonal tumour of the Central Nervous System, occurs in the cerebellum. Treatment regimens involve surgery, craniospinal radiotherapy, and chemotherapy. The greatest mortality is associated with disseminated disease, almost exclusively found in the leptomeningeal space. Unfortunately, knowledge about the aetiology of MB spread is limited and the need for kinder and efficacious therapy remains an unmet goal. Of the four molecular classified MB groups, Group3 (Gr3) MB presents with a high frequency of metastasis at diagnosis, with the worst overall survival. Gr3 MB tumours are dominated by primitive progenitor-like cells and cMYC deregulation; often, p53 deficiency is observed at relapse. To dissect the biology of primary and metastatic Gr3 MB, we have developed a new germline genetically engineered mouse model (GEMM), harbouring cMYC amplification in a Tamoxifen-inducible p53 functional background (Trp53ERTAM strain). A novel LSL-cMYC-CopGFP-Luciferase transgene was integrated into the Rosa-26 locus of the mouse genome. Transgenic mice were crossed with a strain expressing Cre recombinase under the Blbp promoter targeting embryonic neural progenitors, and subsequently bred to Trp53ERTAM mice. As result, the cMYC overexpression was sufficient to generate tumours. Tumour penetrance was observed in all the expected tumour bearing genotypes, with increased aggressiveness in a non-functional p53 background. Bioluminescence imaging demonstrated tumour onset in the brain and dissemination along the spinal cord. CopGFP positive tumour cells were isolated from primary and metastatic tumours. Pathological interrogation confirmed that tumours present large cell/anaplastic (LCA) histology. Analysis of preliminary transcriptional profiling data proved that tumours cluster with human Gr3 MB. Ongoing methylation profiling and multi-omics approaches will inform on the tumour cells of origin and clonal divergence of primary tumour versus metastasis. In conclusion, we have successfully developed a novel immunocompetent mouse model of metastatic Gr3 MB with which we can investigate therapeutic vulnerabilities of MB.
MODL-08. Cellular yield and xenograft creation from probe washing after stereotactic biopsy of deep-seated CNS tumors in children
Authors: DeCuypere Michael , Xiao Sophie , Du Yuchen , Lam Sandi , Li Xiao-Nan
Published: June 2022

Intracranial tumors located in otherwise difficult-to-resect regions of the brain are routinely biopsied to obtain tissue diagnosis and guide clinical decision making. However, tissue yield from these stereotactic biopsy samples is limited and leaves little remaining for research purposes or tumor banking. Given the importance of molecular diagnostics and rise of targeted therapies, research into the genetic and immune landscape of these lesions is of paramount importance, especially for inoperable and deep-seated tumors. We sought to obtain viable cellular material from otherwise discarded biopsy probes without visible tumor sample within the probe. Cells were obtained from clinically challenging pediatric tumors of the brainstem, thalamus, and pineal region by washing biopsy probes in FBS media immediately after completion of a stereotactic biopsy. The wash was then filtered and re-suspended in media before evenly distributing in a 24 well plate for culture purposes. A total of 15 samples were collected from probe washes, including 6 diffuse midline gliomas of the brain stem, 7 supratentorial diffuse midline gliomas, and 2 tumors in the pineal region. Viable tumor cells were obtained from 9/15 samples, ranging from 500 to approximately 525,000 cells per sample wash (219,222 ± 181,951). Orthotopic implantation into matching locations was completed with 7 tumor samples. Formation of a patient-derived orthotopic xenograft was confirmed in one thalamic high-grade glioma (165,000 cells). Three of the five diffuse midline gliomas of the brainstem showed early signs of tumor formation (yielding >2 million cells) and will be validated. In conclusion, viable tumor cells can be collected from biopsy probe washes after stereotactic biopsy, without visible tumor within the probe. Tumor cells can be used for patient-derived orthotopic xenograft tumor formation, which allows for new avenues in the development of animal models of difficult to resect brain tumors.
MODL-09. Exploring the role of Magmas (mitochondria-associated protein involved in granulocyte-macrophage colony-stimulating factor signal transduction) inhibition as a potential therapeutic intervention in medulloblastoma
Authors: Hoerig Clay , Plant-Fox Ashley , Di Kaijun , Lepe Javi , Douglas Christopher , Lomeli Naomi , Das Bhaskar , Bota Daniela
Published: June 2022

BACKGROUND: Brain tumors are the second most common type of pediatric cancer and the leading cause of all cancer-related deaths in children. Medulloblastoma (MB) is the most common type of malignant pediatric brain tumor and has a five-year overall survival ranging from 40-75%, depending on the patient’s age and other prognostic features. There are various anti-cancer therapies against medulloblastoma, but the treatment of recurrent and refractory disease remains a challenge. As a result, the need for new and novel therapies remain a top priority. One area of interest in CNS tumors are targets within mitochondria. Magmas overexpression has been reported in multiple types of metabolically active tissue and cancer cells, including prostate cancer, pituitary adenoma, and glioma. Some new data suggest that specific subgroups of medulloblastoma may also overexpress Magmas. This ongoing study aims to examine whether Magmas inhibition by compound “BT9” could be beneficial in the treatment of medulloblastoma. METHODS: We continue to study the ability of a Magmas inhibitor (BT#9) as a therapeutic agent in stable medulloblastoma cell lines and patient-derived primary cultures by performing MTT assays, tunnel assays, flow cytometry, migration assays, and invasion assays. RESULTS: Similar to the adult GBM studies, Magmas inhibition by BT#9 had signiﬁcant cytotoxic eﬀects, causing both decreased cell proliferation, increased apoptosis, and blocked cell migration in medulloblastoma cell lines DAOY, D283, and D425. IC50s determined for each during different time points demonstrated an average range 2-5μM compared to the average range seen in adult glioblastoma cell cultures which could range up to 10 μM. These findings suggest that the inhibition of Magmas could potentially optimize clinical outcomes in recurrent/refractory medulloblastoma and warrants further investigation. Our future studies will include the determination of IC50s for primary cell cultures and in vitro testing with patient-derived xenograft models.
MODL-19. Exploiting DNA damage response inhibitors to enhance radiation efficacy in medulloblastoma models
Authors: Dholaria Hetal , Buck Jessica , Hii Hilary , Carline Brooke , Bryne Jacob , Kuchibhotla Mani , Lawler Jessica , Porter Gilbert , Whitehouse Jacqueline , Howlett Meegan , Gottardo Nick , Endersby Raelene
Published: June 2022

Despite treatment intensification, survival for certain high-risk subgroups of medulloblastoma (MB) such as p53 mutant SHH (SHHa) and MYC amplified Group 3 (Gr3) have remained dismal. Recently, the use of Carboplatin as radiosensitiser with craniospinal irradiation (CSI) has shown survival benefit in children with Gr3 MB. However, there is an ongoing need to discover newer, non-chemo radiosensitisers which have minimal toxicity and unequivocal benefit in high-risk MB. Radiation is a potent inducer of DNA damage in cancer cells. CHK1/2, ATR, and WEE1 kinases are critical regulators of the DNA damage response (DDR). We hypothesised that inhibition of these kinases may enhance radiation-induced cytotoxicity in MB. We utilised small-animal radiotherapy platform to deliver CSI to MB-tumour-bearing mice that closely mimic clinical settings. Here we demonstrate systematic preclinical evaluation of DDR inhibitors (DDRi) as radiosensitiser in MB models. In vitro treatment of Gr3 MB cell lines with either CHK1/2 inhibitor (CHKi, Prexasertib, AZD7762), ATR inhibitor (ATRi, AZD6738), or WEE1 inhibitor (WEE1i, AZD1775) along with radiation ceased post-radiation cell cycle arrest, prohibiting DNA repair, and increasing apoptosis. The combination also reduced the colony-forming ability of MB cells post-irradiation. In vivo, CSI and DDRi, each induced modest apoptosis in orthotopically-implanted high-risk MB mice. When these models were treated with CHKi+CSI, ATRi+CSI or WEE1i+CSI, the effect was cumulative. Importantly, addition of DDRi to CSI significantly prolonged the survival of MB-bearing mice compared to CSI alone. Here we also explored strategy of “vertical blockade” by simultaneous use of CHKi and WEE1i which when combined with CSI also prolonged survival in MB-bearing mice. Additionally, we evaluated various regimens to best deliver these novel agents with CSI, maximising effect and minimising toxicity. Our study opens up new realms of radiosensitisation with the use of DDRi in paediatric medulloblastoma and provides robust preclinical evidence for clinical translation.
EPEN-21. Developing a sensitive method for detection of minimal residual disease in ependymoma using metabolomic analysis of cerebrospinal fluid
Authors: Woodward Alison , Amugi Laudina , Patel Kishan , Kilpatrick Charlotte , Kim Dong-hyun , Dandapani Madhumita
Published: June 2022

INTRODUCTION: Ependymoma (EPN) is the second most common malignant paediatric brain tumour with poor survival and significant neuro-cognitive impairment from current treatments (surgery and radiotherapy). Relapse occurs in 50% of patients within 2 years, despite no evidence of tumour on MRI. This suggests that they have minimal residual disease (MRD) at the end of treatment. Developing an accurate MRD detection method could help select patients who would benefit from further continuation chemotherapy, thereby improving survival. There is also an unmet need for an accurate test to diagnose relapse early when the disease could be more treatable. METHODS: Pilot untargeted liquid chromatography-mass spectrometry (LC-MS) analysis was carried out in cerebrospinal fluid (CSF) samples from patients with ependymoma. CSF from patients in remission from leukemia were used as controls. RESULTS: Pilot data from analysis of CSF using LC-MS demonstrates that this is a feasible approach to characterise CSF metabolomic profile. Also, EPN CSF profile is significantly different from control CSF, with significant elevation of few key metabolites (Vitamin D derivatives and betaine) in EPN CSF compared to control CSF. Immunohistochemical analysis of EPN tumour tissue microarrays confirms the expression of betaine / one-carbon pathway enzymes such as methionine synthase and betaine—homocysteine S-methyltransferase. Further validation of CSF profile with tumour metabolomic profile and serial CSF sample profiling is currently underway. Subgroup-specific differences and targeted analysis to develop a panel of biomarkers is also being explored. CONCLUSION: Early results suggest that CSF-based metabolite profiling using LC-MS is feasible and could help detect minimal residual disease in ependymoma. Further validation is required to analyse subgroup-specific differences and correlate quantitative changes in metabolites with changing disease burden.
Documenting the Impact Potential of a Menthol Cigarette Ban at Point-of-Sale: A Photograph-Based Analysis of the Presence and Placement of Menthol Versus Regular Cigarette Packs on the Shelves of Tobacco Retail Outlets in New York City
Authors: Kirchner Thomas R , Guttentag Alexandra , Vantu Avigail , Silver Diana
Published: June 2022

Introduction

To investigate the absolute and proportionate number of menthol versus regular cigarette packs displayed on the shelves inside tobacco retail outlets (TROs) across New York City (NYC).

Aims and Methods

Photographic surveillance methods were used to capture the presence and proportionate amount of all visible cigarette packs on the shelves inside N = 160 TROs. Statistical analyses examined the absolute and proportionate number of menthol packs in each TRO as a function of NYC borough, the local TRO environment, population smoking rates derived from the NYC Community Health Survey, and other demographic indicators from the American Community Survey.

Results

The total number of cigarette packs on the shelves of each TRO and the proportion of menthol packs varied significantly across TROs, averaging about one-quarter of all packs displayed (M = 0.274; SD = .15). Modeling results indicate that the proportion of menthol packs displayed was significantly greater in areas with elevated population smoking rates (odds ratio [OR] = 1.03, CI: 1.01–1.06) and density of TROs per 1000 residents (OR = 1.23; CI: 1.01–1.49), although these associations varied in complex ways with the proportion living under the federal poverty level and the proportion under age 18 years residing within each zip-code.

Conclusions

Results of this study demonstrate the utility of photograph-based TRO audit methods for objective, reliable documentation of the presence and proportionate amount of menthol versus other cigarette pack types on TRO shelves and highlight the need to account for sources of variation between small areas when examining the TRO product landscape and evaluating the effectiveness of regulatory actions against menthol.

Implications

This study describes use of a “hands-free” surveillance technique that offers valuable advantages over traditional retailer surveillance techniques. Comprehensive photographic surveillance data collection allows for more objective measurements of, in this case, the retail outlet’s tobacco power wall, as multiple coders can review the same images and interrater reliability can be empirically tested. The results of this analysis highlight the need to account for local variation between small areas when examining TRO product landscapes and the effects of policy changes at the retailer level
Reloading DNA History in Rice Domestication
Authors: Izawa Takeshi
Published: June 2022

Although crop domestication is a prehistoric event, DNA (or genome) sequences of modern cultivars and the accession lines of wild relatives contain information regarding the history of crop domestication and the breeding process. Accordingly, with plentiful genomic data, many new findings have been obtained concerning the crop domestication process, for which various (some controversial) interpretations exist. Since approximately 20 years ago, dozens of quantitative trait genes (QTGs) related to the domestication process have been cloned from several crops including rice, a global staple food. However, the determination of how and when these QTGs were involved in rice domestication requires a precise understanding of the DNA code. In addition to the identification of domestication-related QTGs, large-scale rice genome analysis based on short-read Illumina data (but with shallow depth) including more than 1,000 rice cultivars and hundreds of wild rice (or Oryza rufipogon) lines, along with extensive genome analysis including more than 3,000 cultivars with sufficient Illumina data, has been reported. From these data, the genome-wide changes during rice domestication have been explained. However, these genome-wide changes were not interpreted based on QTG changes for domestication-related traits during rice domestication. In addition, a substantial gap remains between the archeological hypothesis based on ancient relics and findings from DNA variations among current cultivars. Thus, this review reconsiders the present status of rice domestication research from a biologist’s perspective.
Impact of protein supplementation on semen quality, fertility, andBMP1Rgene expression in sheep of Bangladesh
Authors: Khan Md. Kabirul Islam , Hossain Md. Iqbal , Momin Md. Moksedul
Published: June 2022

A study was carried out to know the impact of protein supplementation on fertility and expressions of the fertility gene BMP1R. Three International Organization for Standardization (ISO), isocaloric but different levels of protein supplement ration (11.70% crude protein [CP] for control/To, 12.99% CP for T1, and 13.86% CP for T2) were fed to three different groups of sheep. DNA was extracted from the whole blood sample for polymerase chain reaction (PCR) of the BMP1R fertility gene, and purified PCR products were sequenced by a Sanger sequencer. Sequence alignment, pair, and multi-alignment comparison of the BMP1R gene of the species were done with MEGA6. The semen volume (1.0 mL), sperm counts (4.2 × 107 million), and percentage of normal (94.3%) and viable sperm (3.7%) were higher in treatment 2 than in the other two groups. The semen volume (1.0 mL), sperm counts (4.2 × 107 million), and the percentage of normal (94.3%) and viable sperm (3.7%) were higher in treatment 2 than in the other two groups. Ewes treated with supplemented, protein concentrate reached the conception at an earlier age (treatment 1, 9.5 ± 0.16 mo and treatment 2, 10.3 ± 0.04 mo) than control (9.8 ± 0.15 mo). The lambing interval varied, from 198 to 202 d. Lamb’s birth weights in three treated groups were ranging from 1.2 to 1.39 kg. The designated sequences of BMP1R gene revealed 100% homology with the sequence of Kazakh sheep. The present study indicated that the influence of nutrition on reproductive performance and genomic study will be helpful for the genetic improvement of low-productive sheep.
Exporting the Luxembourg Rail Protocol to the Convention on International Interests in Mobile Equipment to Africa
Authors: Otabor-Olubor Iyare
Published: June 2022

This article recommends the Cape Town Convention on International Interests in Mobile Equipment and appeals to African countries to accede to the Luxembourg Protocol on Railway Rolling Stock (Rail Protocol). The discussion in this article focuses on the extent to which Article XXII of the Rail Protocol can be applied with respect to Africa. The article critically analyses the competence of the African Economic Community (AEC) and its sub-regional organizations to accede to the Cape Town Convention and Rail Protocol. The author provides a detailed argumentative analysis of the legal mandate of the AEC and the influence of African Union (AU) laws on the competence of the AEC’s sub-regional organizations to make declarations under the Cape Town Convention and Rail Protocol. The analysis confirms that competence to accede to the Convention and Rail Protocol resides with sovereign States in Africa and not with the AU, the AEC, the Organisation pour l’harmonisation en Afrique du Droit des Affaires, or any existing sub-regional organization in Africa.
An Objective and Easy-to-Use Glaucoma Functional Severity Staging System Based on Artificial Intelligence
Authors: Huang Xiaoqin , Saki Fatemeh , Wang Mengyu , Elze Tobias , Boland Michael V. , Pasquale Louis R. , Johnson Chris A. , Yousefi Siamak
Published: June 2022

Objective:

The objective of this study was to develop an objective and easy-to-use glaucoma staging system based on visual fields (VFs).

Subjects and Participants:

A total of 13,231 VFs from 8077 subjects were used to develop models and 8024 VFs from 4445 subjects were used to validate models.

Methods:

We developed an unsupervised machine learning model to identify clusters with similar VF values. We annotated the clusters based on their respective mean deviation (MD). We computed optimal MD thresholds that discriminate clusters with the highest accuracy based on Bayes minimum error principle. We evaluated the accuracy of the staging system and validated findings based on an independent validation dataset.

Results:

The unsupervised k-means algorithm discovered 4 clusters with 6784, 4034, 1541, and 872 VFs and average MDs of 0.0 dB (±1.4: SD), −4.8 dB (±1.9), −12.2 dB (±2.9), and −23.0 dB (±3.8), respectively. The supervised Bayes minimum error classifier identified optimal MD thresholds of −2.2, −8.0, and −17.3 dB for discriminating normal eyes and eyes at the early, moderate, and advanced stages of glaucoma. The accuracy of the glaucoma staging system was 94%, based on identified MD thresholds with respect to the initial k-means clusters.

Conclusions:

We discovered that 4 severity levels based on MD thresholds of −2.2, −8.0, and −17.3 dB, provides the optimal number of severity stages based on unsupervised and supervised machine learning. This glaucoma staging system is unbiased, objective, easy-to-use, and consistent, which makes it highly suitable for use in glaucoma research and for day-to-day clinical practice.
Mapping of Perfusion During Full-Thickness Blepharotomy Using Laser Speckle Contrast Imaging
Authors: Wiktorin Anna H. C. , Berggren Johanna V. , Malmsjö Malin , Lindstedt Sandra , Sheikh Rafi , Bohman Elin
Published: June 2022

Purpose:

The aim of this study was to monitor how the blood perfusion in human upper eyelids is affected during full-thickness blepharotomy.

Methods:

Seven eyelids in 5 patients with upper eyelid retraction due to Graves’ disease underwent full-thickness blepharotomy. Perfusion was measured using laser speckle contrast imaging in the eyelid margin and in the conjunctival pedicle.

Results:

Immediately following the procedure, a nonsignificant reduction in perfusion was observed in the skin of the pretarsal eyelid margin, being 66% of the initial value (p = n.s.). However, a statistically significant decrease in perfusion, to 53% of the initial value (p < 0.01), was seen in the central pedicle of the conjunctiva. There were no surgical complications such as infection, signs of ischemia, or bleeding.

Conclusions:

In this study, eyelid perfusion was mapped during full-thickness blepharotomy for the first time using laser speckle contrast imaging. The results showed that perfusion is sufficiently preserved during surgery, probably due to the rich vascular supply in the periocular region, which may explain the low risk of postoperative complications such as ischemia and infection.
Age-Related Changes in the Lacrimal Punctum Morphology in a Normal Population: Punctum Update (PUP) Study-Paper 1
Authors: Bothra Nandini , Saini Pragya , Ali Mohammad Javed
Published: June 2022

Purpose:

To define the clinical and optical coherence tomography (OCT) morphology of the lacrimal punctum and assess the age-related changes across 8 decades of life in a normal population.

Methods:

A total of 1310 high-magnification slit-lamp, Fourier-domain OCT (FD-OCT), and optical coherence tomography angiography (OCTA) images were obtained from 320 puncta of normal asymptomatic individuals representing the Indian population. The punctum and peri-punctal area were defined with the help of 2 rims (inner punctal rim and outer punctal rim ) and 3 zones (white zone [Wz], separation zone [Sz], and peri-punctal vascularity). FD-OCT images were used to measure the external punctal diameters and internal lacrimal punctal diameters and the reflectivity patterns of the 3 punctal layers. OCTA was used to assess the branching and extent of vascular networks.

Results:

The upper puncta were narrower and more circular than the lower puncta across the decades. The elevation of the punctal papilla began in the upper puncta in the fifth decade, involved the lower puncta in the sixth decade, and gradually became exaggerated by the eighth decade. A typical punctal narrowing in previously wide puncta began to appear in the sixth decade of life, peaks in the seventh decade, and reverses gradually and spontaneously by the end of the eighth decade of life. The third and fourth decades saw a narrowing of the Sz with prominent vascularity crossing the Sz to reach the Wz. The Sz became indistinct in the fifth and sixth decades of life. The FD-OCT showed gradual thickening and dominance of the fibrous layer from the fifth to eighth decade of life. The clinical vascularity in the peri-punctal region increases from the third decade onwards, with vascular networks becoming increasingly dense, intricate, and branched as the age progresses.

Conclusion:

The present study defined and characterized the involutional changes in a normal population’s first–eighth decades of life. Significant morphological changes were noticed across the different age groups with several clinical implications.
Immunogenicity and Safety of SARS-CoV-2 Vaccination in Patients With Rheumatic Diseases: A Systematic Review and Meta-analysis
Authors: Sood Akhil , Tran Minh , Murthy Vijaya , Gonzalez Emilio
Published: June 2022

Background

Patients with rheumatic disease (RD) are at increased risk for COVID-19 infection. Large clinical trials have demonstrated efficacy and safety of SARS-CoV-2 vaccine. However, patients with RD are typically excluded from these trials.

Objective

The aim of this study was to conduct a systematic review and meta-analysis examining the immunogenicity and safety of SARS-CoV-2 vaccination in patients with RD.

Methods

We systematically searched PubMed/MEDLINE and Scopus to identify observational studies that examined the immunogenicity and safety of SARS-CoV-2 vaccination in RD patients. Information on disease, immunosuppressant, vaccine type, and proportion of patients with serologic response was obtained from each study.

Results

There were 25 eligible studies. The pooled rate of seroconversion was 0.79 (95% confidence interval [CI], 0.72–0.86). Compared with control subjects, the odds of seroconversion were significantly lower (odds ratio, 0.11; 95% CI, 0.05–0.24). Users of rituximab showed the lowest rate of seroconversion (0.39; 95% CI, 0.29–0.51) followed by mycophenolate (0.56; 95% CI, 0.40–71). On the other hand, users of interleukin 17 (0.94; 95% CI, 0.78–0.98) and tumor necrosis factor inhibitors (0.94; 95% CI, 0.84–0.98) showed high seroconversion rate. Regarding safety of COVID-19 vaccine, approximately 2% of patients reported severe adverse events and 7% reported diseases flares following the first or second dose.

Conclusion

Vaccination against SARS-CoV-2 appears to be safe. Most RD patients developed humoral immune response following vaccination. However, the odds of seroconversion were significantly lower in RD patients compared with controls. This is likely driven by certain immunosuppressants including rituximab and mycophenolate. Future studies need to identify strategies to improve vaccine response in these patients.
One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants
Authors: Walker Jo , Grubaugh Nathan D. , Gonsalves Gregg , Pitzer Virginia , Rizvi Zain
Published: June 2022

Background

Over one million COVID-19 deaths have been recorded in the United States. Sustained global SARS-CoV-2 transmission has led to the emergence of new variants with increased transmissibility, virulence, and/or immune evasion. The specific burden of mortality from each variant over the course of the U.S. COVID-19 epidemic remains unclear.

Methods

We constructed an epidemiologic model using data reported by the CDC on COVID-19 mortality and circulating variant proportions to estimate the number of recorded COVID-19 deaths attributable to each SARS-CoV-2 variant in the U.S. We conducted sensitivity analysis to account for parameter uncertainty.

Findings

Of the 1,003,419 COVID-19 deaths recorded as of May 12, 2022, we estimate that 460,124 (46%) were attributable to WHO-designated variants. By U.S. Census Region, the South recorded the most variant deaths per capita (median estimate 158 per 100,000), while the Northeast recorded the fewest (111 per 100,000). Over 40 percent of national COVID-19 deaths were estimated to be caused by the combination of Alpha (median estimate 39,548 deaths), Delta (273,801), and Omicron (117,560).

Interpretation

SARS-CoV-2 variants that have emerged around the world have imposed a significant mortality burden in the U.S. In addition to national public health strategies, greater efforts are needed to lower the risk of new variants emerging, including through global COVID-19 vaccination, treatment, and outbreak mitigation.
Improving the quality of in-patient neonatal routine data as a pre-requisite for monitoring and improving quality of care at scale: A multi-site retrospective cohort study in Kenyan hospitals
Authors: Tuti Timothy , Aluvaala Jalemba , Chelangat Daisy , Mbevi George , Wainaina John , Mumelo Livingstone , Wairoto Kefa , Mochache Dolphine , Irimu Grace , Maina Michuki , English Mike
Published: June 2022

Objectives

The objectives of this study were to (1) determine if membership of a clinical information network (CIN) was associated with an improvement in the quality of documentation of in-patient neonatal care provided over time, and (2) characterise accuracy of prescribing for basic treatments provided to neonatal in-patients if data are adequate.

Design and Settings

This was a retrospective cohort study involving all children aged ≤28 days admitted to New-Born Units (NBUs) between January 2018 and December 2021 in 20 government hospitals with an interquartile range of annual NBU inpatient admissions between 550 and 1640 in Kenya. These hospitals participated in routine audit and feedback processes on quality of documentation and care over the study period.

Outcomes

The study’s outcomes were the number of patients as a proportion of all eligible patients with (1) complete domain-specific documentation scores, and (2) accurate domain-specific treatment prescription scores at admission.

Findings

80060 NBU admissions were eligible for inclusion. Upon joining the CIN, documentation scores in the monitoring (vital signs), other physical examination and bedside testing, discharge information, and maternal history domains demonstrated a statistically significant month-to-month relative improvement in number of patients with complete documentation of 7.6%, 2.9%, 2.4%, and 2.0% respectively. There was also statistically significant month-to-month improvement in prescribing accuracy after joining the CIN of 2.8% and 1.4% for feeds and fluids but not for Antibiotic prescriptions. Findings suggest that much of the variation observed is due to hospital-level factors.

Conclusions

It is possible to introduce tools that capture important clinical data at least 80% of the time in routine African hospital settings but analyses of such data will need to account for missingness using appropriate statistical techniques. These data allow trends in performance to be explored and could support better impact evaluation, performance benchmarking, exploration of links between health system inputs and outcomes and scrutiny of variation in quality and outcomes of hospital care.
Sleep Duration, Quality, and Risk of Peripheral Artery Disease: Multinational Cohort and Mendelian Randomization Studies
Authors: Yuan Shuai , Levin Michael G. , Titova Olga E , Chen Jie , Sun Yuhao ,   VA Million Veteran Program, Åkesson Agneta , Li Xue , Damrauer Scott M. , Larsson Susanna C.
Published: June 2022

Background

Sleep duration and quality has been associated with cardiovascular disease, however the effect of sleep on peripheral artery disease (PAD) specifically remains unestablished. We conducted cohort, case-control, and Mendelian randomization (MR) analyses to assess the associations of sleep duration and quality with PAD risk.

Methods

Sleep traits were assessed for associations with incident PAD using cohort analysis among 53,416 Swedish adults. Replicated was sought in a case-control study of 28,123 PAD cases and 128,459 controls from the VA Million Veteran Program (MVP) and a cohort study of 452,028 individuals from the UK Biobank study (UKB). Two-sample Mendelian randomization (MR) was used for casual inference-based analyses of sleep-related traits and PAD (31,307 PAD cases 211,753 controls).

Results

Observational analyses demonstrated a U-shaped association between sleep duration and PAD risk. In Swedish adults, incident PAD risk was higher in those with short sleep (<5 hours; hazard ratio (HR), 1.74; 95% confidence interval (CI) 1.31-2.31) or long sleep (≥8 hours; HR 1.24; 95% CI 1.08-1.43), compared to individuals with a sleep duration of 7 to <8 hours/night. This finding was supported by case-control analysis in MVP and cohort analysis in UKB. Observational analysis also revealed positive associations between poor sleep quality (HR, 1.81; 95% CI 1.13-2.90) and daytime napping (HR, 1.32; 95% CI 1.18-1.49) with PAD. MR analysis supported an inverse association between sleep duration (odds ratio per hour increase, 0.79, 95% CI, 0.55, 0.89) and PAD, and an association between short sleep and increased PAD (odds ratio, 1.20, 95% CI, 1.04-1.38). MR also found an association between insomnia with PAD (OR, 1.10; 95% CI 1,05-1.15) and a reverse association of PAD on shorter sleep (OR, 1.05; 95% CI 1.01-1.10).

Conclusions

Maintenance of healthy sleep habits, especially avoiding habitual short sleep, may prevent PAD.
A high confidencePhyscomitrium patensplasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution
Authors: Gombos Sven , Miras Manuel , Howe Vicky , Xi Lin , Pottier Mathieu , Kazemein Jasemi Neda S. , Schladt Moritz , Ejike Jona , Neumann Ulla , Hänsch Sebastian , Kuttig Franziska , Zhang Zhaoxia , Dickmanns Marcel , Xu Peng , Stefan Torsten , Baumeister Wolfgang , Frommer Wolf B. , Simon Rüdiger , Schulze Waltraud X.
Published: June 2022

Cells of multicellular organisms exchange nutrients, building blocks and information. In animals, this happens via gap junctions, in plants via plasmodesmata (PD). PD have striking properties, translocating a large range of molecules from ions, to metabolites, RNA and proteins up to 40 kDa. PD are hard to characterize due to being deeply embedded into cell walls and the presence of several membranes. While previous studies of protein composition of PD from angiosperms identified large lists of proteins, few were validated. Here, we developed a PD scoring approach in conjunction with systematic localization on a large scale to define a high-confidence PD proteome ofPhyscomitrium patens. This high confidence PD proteome comprises nearly 300 proteins, which together with thebona fidePD proteins from literature, are made available in the public PDDB database. Conservation of localization across plant species strengthens the reliability of plant PD proteomes and provides a basis for exploring the evolution of this important organelle. In particular, theP. patensPD proteome was highly enriched in cell wall modifying proteins. Callose-degrading glycolyl hydrolase family 17 (GHL17) proteins are presented as an abundant PD protein family with representatives across an evolutionary scale. Exclusively members of the alpha-clade of the GHL17 family are shown to be PD localized and their orthologs occur only in plant species which have developed PD. Members of the EXORDIUM-family and xyloglucan transglycosylases are additional cell-wall located proteins highly abundant in theP. patensPD proteome also showing evolutionary diversification of PD localized family members from other clade members.
Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping combined with genome sequence analysis
Authors: N’Guessan Arnaud , Kailasam Senthilkumar , Mostefai Fatima , Poujol Raphael , Grenier Jean-Christophe , Contini Paola , De Palma Raffaele , Haber Carsten , Stadler Volker , Bourque Guillaume , Hussin Julie G. , Shapiro B. Jesse , Fritz Jörg H. , Piccirillo Ciriaco A.
Published: June 2022

A deeper understanding of the molecular determinants that drive humoral responses to coronaviruses, and in particular severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is critical for improving and developing diagnostics, therapies and vaccines. Moreover, viral mutations can change key antigens in a manner that alters the ability of the immune system to detect and clear infections. In this study, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses of asymptomatic or recovered COVID-19-positive patients relative to COVID-19-negative patients. We made use of a novel high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses to rapidly identify B cell epitopes recognized by distinct antibody isotypes in patients’ blood sera. Using our integrated computational pipeline, we then evaluated the fine immunological properties of detected SARS-CoV-2 epitopes and relate them to their evolutionary and structural properties. While some epitopes are common across all CoVs, others are private to specific hCoVs. We also highlight the existence of hotspots of pre-existing immunity and identify a subset of cross-reactive epitopes that contributes to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves and SARS-CoV-2 variants, which have important implications for genomic surveillance and vaccine design. Lastly, we show that mutations in Spike and Nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts.
Characterization of entry pathways, species-specific ACE2 residues determining entry, and antibody neutralization evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 variants
Authors: Neerukonda Sabari Nath , Wang Richard , Vassell Russell , Baha Haseebullah , Lusvarghi Sabrina , Liu Shufeng , Wang Tony , Weiss Carol D. , Wang Wei
Published: June 2022

The SARS-CoV-2 Omicron variants were first detected in November 2021, and several Omicron lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) have since rapidly emerged. Studies characterizing the mechanisms of Omicron variant infection and sensitivity to neutralizing antibodies induced upon vaccination are ongoing by several groups. In the present study, we used pseudoviruses to show that the transmembrane serine protease 2 (TMPRSS2) enhances infection of BA.1, BA.1.1, BA.2, and BA.3 Omicron variants to lesser extent compared to ancestral D614G. We further show that Omicron variants have higher sensitivity to inhibition by soluble angiotensin converting enzyme 2 (ACE2) and the endosomal inhibitor chloroquine compared to D614G. The Omicron variants also more efficiently used ACE2 receptors from nine out of ten animal species tested, and unlike the D614G variant, used mouse ACE2 due to the Q493R and Q498R spike substitutions. Finally, neutralization of the Omicron variants by antibodies induced by three doses of Pfizer/BNT162b2 mRNA vaccine was 7-8-fold less potent than the D614G, and the Omicron variants still evade neutralization more efficiently.
Precise and stable edge orientation signaling by human first-order tactile neurons
Authors: Sukumar Vaishnavi , Johansson Roland S. , Pruszynski J. Andrew
Published: June 2022

Fast-adapting type 1 (FA-1) and slow-adapting type 1 (SA-1) first-order neurons in the human tactile system have distal axons that branch in the skin and form many transduction sites, yielding receptive fields with many highly sensitive zones or ‘subfields’. We previously demonstrated that this arrangement allows FA-1 and SA-1 neurons to signal the geometric features of touched objects, specifically the orientation of raised edges scanned with the fingertips. Here we show that such signaling operates for fine edge orientation differences (5-20°) and is stable across a broad range of scanning speeds (15-180 mm/s); that is, under conditions relevant for real-world hand use. We found that both FA-1 and SA-1 neurons weakly signal fine edge orientation differences via the intensity of their spiking responses and only when considering a single scanning speed. Both neuron types showed much stronger edge orientation signaling in the sequential structure of the evoked spike trains and FA-1 neurons performed better than SA-1 neurons. Represented in the spatial domain, the sequential structure was strikingly invariant across scanning speeds, especially those naturally used in tactile spatial discrimination tasks. This speed invariance suggests that neurons’ responses are structured via sequential stimulation of their subfields and thus links this capacity to their terminal organization in the skin. Indeed, the spatial precision of elicited action potentials rationally matched spatial acuity of subfield arrangements, which typically corresponds to the dimension of individual fingertip ridges.

Significance Statement

The distal axons of human first-order tactile neurons branch and innervate many mechanosensitive end organs in the skin. For those neurons terminating in end organs associated with fingerprint ridges (Meissner and Merkel), this branching results in cutaneous receptive fields with multiple subfields spread across several ridges. Consequently, when a fingertip scans the surface of an object, the spatial coincidence between a neuron’s subfields and the tactile stimulus defines the sequential structure of the evoked spike train (i.e., the presence of action potential bursts and the gaps between them). Here we show that, for surfaces composed of oriented edges, this sequential structure signals information about edge orientation differences at the limit of what people can feel and that the spatial precision of the structuring is maintained across a broad range of speeds relevant for real-world hand use. We submit that, to be of human relevance, models of higher order tactile processing must consider the impact of multifocal receptive fields in the periphery. For example, the speed invariance of tactile fine-form/texture perception may arise simply because the same subsets of peripheral subfields in the population of first-order tactile neurons are stimulated together regardless of speed.
Roles of RodZ and Class A PBP1b in the Assembly and Regulation of the Peripheral Peptidoglycan Elongasome in Ovoid-Shaped Cells ofStreptococcus pneumoniaeD39
Authors: Lamanna Melissa M. , Manzoor Irfan , Joseph Merrin , Ye Ziyun A. , Benedet Mattia , Zanardi Alessia , Ren Zhongqing , Wang Xindan , Massidda Orietta , Tsui Ho-Ching T. , Winkler Malcolm E.
Published: June 2022

RodZ of rod-shaped bacteria functions to link MreB filaments to the Rod peptidoglycan (PG) synthase complex that moves circumferentially perpendicular to the long cell axis, creating hoop-like sidewall PG. Ovoid-shaped bacteria, such asStreptococcus pneumoniae(pneumococcus;Spn) that lack MreB, use a different modality for peripheral PG elongation that emanates from the midcell of dividing cells. Yet,S. pneumoniaeencodes a RodZ homolog similar to RodZ in rod-shaped bacteria. We show here that the helix-turn-helix and transmembrane domains of RodZ(Spn) are essential for growth at 37°C. ΔrodZmutations are suppressed by Δpbp1a,mpgA(Y488D), and ΔkhpAmutations that suppress ΔmreC, but not ΔcozE. Consistent with a role in PG elongation, RodZ(Spn) co-localizes with MreC and aPBP1a throughout the cell cycle and forms complexes and interacts with PG elongasome proteins and regulators. Depletion of RodZ(Spn) results in aberrantly shaped, non-growing cells and mislocalization of elongasome proteins MreC, PBP2b, and RodA. Moreover, Tn-seq reveals that RodZ(Spn), but not MreCD(Spn), displays a specific synthetic-viable genetic relationship with aPBP1b, whose function is unknown. We conclude that RodZ(Spn) acts as a scaffolding protein required for elongasome assembly and function and that aPBP1b, like aPBP1a, plays a role in elongasome regulation and possibly peripheral PG synthesis.

Graphical Summary
Recording large-scale, cellular-resolution neuronal activity from freely-moving mice
Authors: Das Aniruddha , Holden Sarah , Borovicka Julie , Icardi Jacob , Patel Davina , Patel Rushik , Raber Jacob , Dana Hod
Published: June 2022

Current methods for recording large-scale neuronal activity from behaving mice with single-cell resolution require either fixing the mouse head under a microscope or attachment of a recording device to the animal’s skull. Both of these options significantly affect the animal behavior and hence also the recorded brain activity patterns. Here, we introduce a new method to acquire snapshots of single-cell cortical activity maps from freely-moving mice using a calcium sensor called CaMPARI. CaMPARI has a unique property of irreversibly changing its color from green to red inside active neurons when illuminated with 400nm light. We capitalize on this property to demonstrate cortex-wide activity recording without any head fixation or attachment of a miniaturized device to the mouse’s head. Multiple cortical regions were recorded while the mouse was performing a battery of behavioral and cognitive tests. We identified task-dependent activity patterns across motor and somatosensory cortices, with significant differences across sub-regions of the motor cortex. This new CaMPARI-based recording method expands the capabilities of recording neuronal activity from freely-moving and behaving mice under minimally-restrictive experimental conditions and provides large-scale volumetric data that are not accessible otherwise.
Accurate pan-cancer tumor purity estimation from gene expression data
Authors: Revkov Egor , Kulshrestha Tanmay , Sung Ken Wing-Kin , Jacobsen Skanderup Anders
Published: June 2022

Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion of cancer cells in a sample) can both confound integrative analysis and enable studies of tumor heterogeneity. Here we developed PUREE, which uses a weakly supervised learning approach to infer tumor purity from a tumor gene expression profile. PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. PUREE predicted purity with high accuracy across distinct solid tumor types and generalized to tumor samples from unseen tumor types and cohorts. Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. In a comprehensive benchmark, PUREE outperformed existing transcriptome-based purity estimation approaches. Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data.