bluuebunny/crossref_metadata_2025 huggingface dataset:
Admissions to a large tertiary care hospital and Omicron BA.1 and BA.2 SARS-CoV-2 PCR positivity: primary, contributing, or incidental COVID-19
Authors: Voor in ’t holt Anne F. , Haanappel Cynthia P. , Rahamat – Langendoen Janette , Molenkamp Richard , van Nood Els , van den Toorn Leon M. , Peeters Robin P. , van Rossum Annemarie M.C. , Severin Juliëtte A.
Published: April 2022

SARS-CoV-2 Omicron variants BA.1 and BA.2 seem to show reduced clinical severity. We classified 172 COVID-19 Omicron patient admissions. 66.2% of patients were admitted with primary or admission-contributing COVID-19. We therefore must be careful to base healthcare and public health decisions on the total number of hospitalized COVID-19 patients alone.
Interplay between mosaic chromosomal alterations and polygenic risk score increases risk of non-small cell lung cancer
Authors: Qin Na , Chen Congcong , Yang Liu , Liu Su , Xie Yuan , Xu Xianfeng , Zhou Jun , Dai Juncheng , Jin Guangfu , Ma Hongxia , Wang Cheng , Shen Hongbing , Hu Zhibin
Published: April 2022

We investigated autosomal mosaic chromosomal alterations (mCAs) in 10,248 non-small cell lung cancer (NSCLC) cases and 9,298 cancer-free controls of Chinese ancestry. Mosaic loss and copy-neutral loss of heterozygosity were associated with an increased risk of NSCLC, while mosaic gain was associated with a decreased risk of NSCLC, especially those spanning telomeres. The increased cell fraction of mCAs was also correlated with an increasing NSCLC risk in the affected individuals. Both multiplicative and additive interactions were observed between polygenic risk score (PRS) and the presence of mosaic loss, where carriers of mosaic loss events with cell fractions ≥5% among the high genetic risk group had the greatest risk for developing NSCLC. These findings suggest that mCA events may act as a new endogenous indicator for risk of NSCLC and have the potential to be jointly used with PRS to optimize risk stratification of NSCLC.
A year in the public life of COVID-19 and Vitamin D: Representation in UK news media and implications for health communications
Authors: Mavroeidi Alexandra , Innes Ryan , Miyake Esperanza , Pennington Diane
Published: April 2022

Objectives

To investigate how the relationship between vitamin D and COVID-19 has been presented in traditional media sources (UK newspapers) and assess the level of misinformation associated with this issue by comparing newspaper article content to the evidence-based guidelines.

Design

Qualitative study

Setting

Data were collected over the first year of the pandemic (February 2019-20), from the five most widely read UK based newspapers by searching the Nexis database using keywords “vitamin D” and “COVID”. An inductive thematic analysis was carried out on the data to identify themes and subthemes. Quality control of the coding was conducted on a sample of the dataset (20%). Data were also compared to the “ground truth” identified as the NICE report titled “COVID-19 rapid guideline: vitamin D” to explore the accuracy of media outputs.

Results

The four main themes identified were ‘association of vitamin D with COVID-19’, ‘politically informed views’, ‘vitamin D deficiency’ and ‘vitamin D sources’. When compared to the ground truth, most of the information from newspaper articles relating to the key findings was ‘correct’ for each of the findings, except for COVID-19 infection.

Conclusions

Although most of the information included in newspaper articles concerning the relationship of vitamin D with COVID-19 was ‘correct’, this study highlighted that there was still a notable amount of ‘incorrect’ information published. In the context of COVID-19, it is imperative that media outputs are accurate and inform the public and front-line health professionals as correct information is a key factor in disease prevention. Future research should focus on the accuracy of media outputs to further investigate health misinformation as an issue in traditional media and how that may affect public health. Attempts should be made to improve journalistic integrity through more rigorous and standardised regulations enforced across all media outlets so that public knowledge on current events is based on evidence rather than conjecture.

Summary boxes

Data sharing statement:

We are happy to share any data if/when asked.
The testing of the DAC algorithm for classifying Lymphoma Cell of Origin samples using HTG’s targeted gene expression system
Authors: Davies John R. , Care Matthew A. , Mell Tracey , Barrans Sharon , Burton Cathy , Westhead David R.
Published: April 2022

An implementation of the windows based DLBCL automatic classification (DAC) algorithm for determining cell of origin (COO) written in the R language and designed for use with the HTG EdgeSeq Reveal Software package is described. Classifications using the new implementation (DAC-R) were compared to the those using the original version (DAC-Win), the HTG DLBCL COO classifier, the HTG EdgeSeq Reveal DLBCL algorithm. Classifications made using HTG data were tested for concordance with those made using WG-DASL data for the same samples. To analyse small numbers of samples a background dataset was developed to allow for the reliable classification of individual cases. Classification accuracy was assessed using percentage of agreement of discrete classification groups and Pearson correlation of probability scores where appropriate. In the data tested it was seen that the correlation of probability scores for DAC-R and DAC-Win was 0.9985 or higher. Agreement with the HTG DLBCL COO classifier was 85.1% and agreement with the HTG EdgeSeq Reveal DLBCL algorithm was also high (Pearson correlation of GCB probabilities = 0.91). Agreement between classifications made using HTG and WG-DASL data was also high (83.7%). In summary, the R based algorithm of DAC successfully replicates the functionality of the original routine and produces comparable COO calls in data produced from the HTG Pan B-Cell Lymphoma Panel to the other methods listed.
The methodologies to assess the effects of non-pharmaceutical interventions during COVID-19: a systematic review
Authors: Banholzer Nicolas , Lison Adrian , Özcelik Dennis , Stadler Tanja , Feuerriegel Stefan , Vach Werner
Published: April 2022

Non-pharmaceutical interventions, such as school closures and stay-at-home orders, have been implemented around the world to control the spread of SARS-CoV-2. Their effects on health-related outcomes have been the subject of numerous empirical studies. However, these studies show fairly large variation among methodologies in use, reflecting the absence of an established methodological framework. On the one hand, variation in methodologies may be desirable to assess the robustness of results; on the other hand, a lack of common standards can impede comparability among studies. To establish a comprehensive overview over the methodologies in use, we conducted a systematic review of studies assessing the effects of non-pharmaceutical interventions on health-related outcomes between January 1, 2020 and January 12, 2021 (n=248). We identified substantial variation in methodologies with respect to study setting, outcome, intervention, methodological approach, and effect assessment. On this basis, we point to shortcomings of existing studies and make recommendations for the design of future studies.
Multi-faceted analysis of COVID-19 epidemic in the Republic of Korea considering Omicron variant: Mathematical modeling-based study
Authors: Ko Youngsuk , Mendoza Victoria May , Mendoza Renier , Seo Yubin , Lee Jacob , Lee Jonggul , Kwon Donghyok , Jung Eunok
Published: April 2022

Background

The most recent variant of concern, Omicron (B.1.1.529), has caused numerous cases worldwide including the Republic of Korea due to its fast transmission and reduced vaccine effectiveness.

Methods

A mathematical model considering age-structure, vaccine, antiviral treatment, and influx of the Omicron variant was developed. We estimated transmission rates among age groups using maximum likelihood estimation for the age-structured model. The impact of nonpharmaceutical interventions (in community and border), quantified by a parameter μin the force of infection, and vaccination were examined through a multi-faceted analysis. A theory-based endemic equilibrium study was performed to find the manageable number of cases according to Omicron-and healthcare-related factors.

Results

By fitting the model to the available data, the estimated values of μ ranged from 0.31 to 0.73, representing the intensity of nonpharmaceutical interventions such as social distancing level. If μ < 0.55 and 300,000 booster shots were administered daily from February 3, 2022, the number of severe cases was forecasted to exceed the severe bed capacity. Moreover, the number of daily cases is reduced as the timing of screening measures is delayed. If screening measure was intensified as early as November 24, 2021 and the number of overseas entrant cases was contained to 1 case per 10 days, simulations showed that the daily incidence by February 3, 2022 could have been reduced by 87%. Furthermore, we found that the incidence number in mid-December 2021 exceeded the theory-driven manageable number of daily cases.

Conclusion

Nonpharmaceutical interventions, vaccination, and antiviral therapy influence the spread of Omicron and number of severe cases in the Republic of Korea. Intensive and early screening measures during the emergence of a new variant is key in controlling the epidemic size. Using the endemic equilibrium of the model, a formula for the manageable daily cases depending on the severity rate and average length of hospital stay was derived so that the number of severe cases does not surpass the severe bed capacity.
Treatment group outcome variance difference after dropout as an indicator of missing-not-at-random bias in randomized clinical trials
Authors: Hazewinkel Audinga-Dea , Tilling Kate , Wade Kaitlin H. , Palmer Tom
Published: April 2022

Randomized controlled trials (RCTs) are considered the gold standard for assessing the causal effect of an exposure on an outcome, but are vulnerable to bias from missing data. When outcomes are missing not at random (MNAR), estimates from complete case analysis (CCA) will be biased. There is no statistical test for distinguishing between outcomes missing at random (MAR) and MNAR, and current strategies rely on comparing dropout proportions and covariate distributions, and using auxiliary information to assess the likelihood of dropout being associated with the outcome. We propose using the observed variance difference across treatment groups as a tool for assessing the risk of dropout being MNAR. In an RCT, at randomization, the distributions of all covariates should be equal in the populations randomized to the intervention and control arms. Under the assumption of homogeneous treatment effects, the variance of the outcome will also be equal in the two populations over the course of followup. We show that under MAR dropout, the observed outcome variances, conditional on the variables included in the model, are equal across groups, while MNAR dropout may result in unequal variances. Consequently, unequal observed conditional group variances are an indicator of MNAR dropout and possible bias of the estimated treatment effect. Heterogeneity of treatment effect affects the intervention group variance, and is another potential cause of observing different outcome variances. We show that, for longitudinal data, we can isolate the effect of MNAR outcome-dependent dropout by considering the variance difference at baseline in the same set of patients that are observed at final follow-up. We illustrate our method in simulation and in applications using individual-level patient data and summary data.
Public exams decrease anxiety and facilitate deeper conceptual thinking
Authors: Wiggins Benjamin , Lily Leah , Busch Carly , Landys Meta , Shlichta J. Gwen , Shi Tianhong , Ngwenyama Tandi
Published: April 2022

Assessment methods across post-secondary STEM education are traditionally constrained by logistics and likely contribute to the widespread inequities in STEM education outcomes. As part of attempts to improve and diversify the methods used in assessment, the authors have developed a flexible and low-tech style known as ‘public exams’ based in educational best practices. Public exams attempt to authentically involve students into the process of assessment through the use of pre-released portions of the exam. Using mixed-methods research techniques at a closely matched pair of institutions (a research-intensive university and a community college classroom), we observed signals of positive impact from the public exam on student learning experiences. Public exams appear to promote deeper thought, to direct students more efficiently to the core concepts in the discipline, and to decrease student anxiety around exams. The public exam experience does not show evidence for exacerbating gaps in exam outcomes for students from underrepresented backgrounds. This suggests that public exams are worth deeper investigation as an evidence-based and effective assessment style.
Familial risk of psychosis in obsessive-compulsive disorder: Impact on clinical characteristics, comorbidity and treatment response
Authors: Balachander Srinivas , Thatikonda Navya Spurthi , Kannampuzha Anand Jose , Bhattacharya Mahashweta , Sheth Sweta , Ramesh Vinutha , Alexander Alen Chandy , Moorthy Muthukumaran , Joseph Mino Susan , Selvaraj Sowmya , Ithal Dhruva , Sreeraj Vanteemar S , John John P , Venkatasubramanian Ganesan , Viswanath Biju , Reddy YC Janardhan , Jain Sanjeev ,   ADBS consortium
Published: April 2022

Background

Family studies in obsessive-compulsive disorder (OCD) indicate higher rates of psychosis among their first-degree relatives (FDRs). However, the etiological and clinical relationships between the two disorders remain unclear. We compared the clinical characteristics & pharmacological treatment response in patients diagnosed with OCD with a family history of psychosis (OCD-FHP), with a family history of OCD (OCD-FHO) and those with sporadic OCD (OCD-S).

Methods

A total of 226 patients who met DSM-IV criteria for OCD (OCD-FHP=59, OCD-FHO=112, OCD-S=55) were included for analysis. All patients were evaluated using the Mini International Neuropsychiatric Interview (MINI 6.0.0), Yale-Brown Obsessive-Compulsive Scale (YBOCS), and the Family Interview for Genetic Studies (FIGS). Treatment response was characterized over naturalistic follow-up.

Results

The three groups did not differ across any demographic or clinical variables other than treatment response. Patients in the OCD-FHP group were found to have received a greater number of trials with serotonin reuptake inhibitors (SRI) [F(2,223)=7.99, p<0.001], were more likely to have failed ≥ 2 trials of SRIs (χ2=8.45, p=0.014), and less likely to have attained remission (χ2=6.57, p=0.037)

Conclusions

We observed that having a relative with psychosis may predispose to treatment resistance in OCD. Further research on the influence of genetic liability to psychosis on treatment response in OCD may offer novel translational leads.
Persistent post-COVID-19 smell loss is associated with inflammatory infiltration and altered olfactory epithelial gene expression
Authors: Finlay John B. , Brann David H. , Abi-Hachem Ralph , Jang David W. , Oliva Allison D. , Ko Tiffany , Gupta Rupali , Wellford Sebastian A. , Moseman E. Ashley , Jang Sophie S. , Yan Carol H. , Matusnami Hiroaki , Tsukahara Tatsuya , Datta Sandeep Robert , Goldstein Bradley J.
Published: April 2022

Most human subjects infected by SARS-CoV-2 report an acute alteration in their sense of smell, and more than 25% of COVID patients report lasting olfactory dysfunction. While animal studies and human autopsy tissues have suggested mechanisms underlying acute loss of smell, the pathophysiology that underlies persistent smell loss remains unclear. Here we combine objective measurements of smell loss in patients suffering from post-acute sequelae of SARS-CoV-2 infection (PASC) with single cell sequencing and histology of the olfactory epithelium (OE). This approach reveals that the OE of patients with persistent smell loss harbors a diffuse infiltrate of T cells expressing interferon-gamma; gene expression in sustentacular cells appears to reflect a response to inflammatory signaling, which is accompanied by a reduction in the number of olfactory sensory neurons relative to support cells. These data identify a persistent epithelial inflammatory process associated with PASC, and suggests mechanisms through which this T cell-mediated inflammation alters the sense of smell.
fMetastatic potential in clonal melanoma cells is driven by a rare, early-invading subpopulation
Authors: Kaur Amanpreet , Cuenca Luciann , Kiani Karun , Busch Gianna T. , Fingerman Dylan , Dunagin Margaret C. , Li Jingxin , Dardani Ian , Sanford Eric M. , Pemberton Jordan , Goyal Yogesh , Weeraratna Ashani T. , Herlyn Meenhard , Raj Arjun
Published: April 2022

Metastasis occurs when tumor cells leave the primary tumor site and disseminate to distal organs. Even though most cells remain in the primary tumor, the circumstances by which a small fraction of them disseminate remain unclear. Here, we show that a rare, highly invasive subpopulation of melanoma cells can be detected within clonal cell lines due to non-genetic fluctuations in gene expression. The highly invasive phenotype was intrinsic to the cells, independent of their environment, and was marked by transiently high levels ofSEMA3Cexpression, as revealed by RNA-sequencing analysis. Furthermore, the invasive subpopulation drove the bulk dissemination of tumor cells to distal locations in a mouse model of melanoma. The transcription factorNKX2.2regulated the proportion of invasive cells in the melanoma 1205Lu cell line. Furthermore, an overall tradeoff between proliferation and invasion in single cells was observed. Our results suggest that phenotypes like metastasis may arise from intrinsic differences stemming from non-genetic fluctuations between single cells.
scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics
Authors: Li Qian
Published: April 2022

Despite the continued efforts to computationally dissect developmental processes using single-cell genomics, a batch-unaffected tool that is able to both infer and predict the underlying dynamics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accurate prediction of the cellular dynamics in diverse processes. For inference, scTour can efficiently and simultaneously estimate the developmental pseudotime, intronic read-independent vector field, and transcriptomic latent space under a single, integrated framework. For prediction, scTour can precisely reconstruct the underlying dynamics of unseen cellular states or an independent dataset agnostic to the model. Of note, both the inference and prediction are invariant to batch effects. scTour’s functionalities are successfully applied to a variety of biological processes from 17 datasets such as cell differentiation, reprogramming and zonation, providing a comprehensive infrastructure to investigate the cellular mechanisms underpinning development in an efficient manner.
The Effects of Vitamin E Analogues α-Tocopherol and γ-Tocotrienol on the Human Osteocyte Response to Ultra-high Molecular Weight Polyethylene Wear Particles
Authors: Ormsby Renee T , Hosaka Kunihiro , Evdokiou Andreas , Odysseos Andreani , Findlay David M , Solomon Lucian B. , Atkins Gerald J
Published: April 2022

Polyethylene (PE) liners are a common bearing surface of orthopaedic prostheses. Wear particles of ultra-high molecular weight PE (UHMWPE) contribute to periprosthetic osteolysis, a major cause of aseptic loosening. Vitamin E is added to some PE liners to prevent oxidative degradation. Osteocytes, an important cell type for controlling both bone mineralisation and bone resorption, have been shown to respond UHMWPE particles by upregulating pro-osteoclastogenic and osteocytic osteolysis. Here, we examined the effects of the vitamin E analogues α-tocopherol and γ-tocotrienol alone or in the context of UHMWPE particles on human osteocyte gene expression and mineralisation behaviour. Human osteoblasts differentiated to an osteocyte-like stage were exposed to UHMWPE wear particles in the presence or absence of either α-Tocopherol or γ-Tocotrienol. Both α-Tocopherol and γ-Tocotrienol induced antioxidant-related gene expression. UHMWPE particles independently upregulated antioxidant gene expression, suggesting an effect of wear particles on oxidative stress. Both vitamin E analogues strongly induced OPG mRNA expression and γ-Tocotrienol also inhibited RANKL mRNA expression, resulting in a significantly reduced RANKL:OPG mRNA ratio (p < 0.01) overall. UHMWPE particles reversed the suppressive effect of α-Tocopherol but not of γ-Tocotrienol on this pro-osteoclastogenic index. UHMWPE particles also upregulated osteocytic-osteolysis related gene expression. Vitamin E analogues alone or in combination with UHMWPE particles also resulted in upregulation of these genes. Consistent with this, both vitamin E analogues promoted calcium release from mineralised cultures of osteocyte-like cells. Our findings suggest that while vitamin E may suppress osteocyte support of osteoclastogenesis in the presence of UHMWPE particles, the antioxidant effect may induce osteocytic osteolysis, which could promote periprosthetic osteolysis. It will be important to conduct further studies of vitamin E to determine the long-term effects of its inclusion in prosthetic materials.
A deep reinforcement learning approach to reconstructing quaternary structures of protein dimers through self-learning
Authors: Soltanikazemi Elham , Roy Raj S. , Quadir Farhan , Cheng Jianlin
Published: April 2022

Predicted interchain residue-residue contacts can be used to build the quaternary structure of protein complexes from scratch. However, only a small number of methods have been developed to reconstruct protein quaternary structures using predicted interchain contacts. Here, we present an agent-based self-learning method based on deep reinforcement learning (DRLComplex) to build protein complex structures using interchain contacts as distance constraints. We rigorously tested the DRLComplex on two standard datasets of homodimeric and heterodimeric dimers (the CASP-CAPRI homodimer dataset and Std_32 heterodimer dataset) using both true and predicted contacts. Utilizing true contacts as input, the DRLComplex achieved a high average TM-score of 0.9895 and 0.9881 and a low average interface RMSD (I_RMSD) of 0.2197 and 0.92 on the two datasets, respectively. When predicted contacts are used, the method achieves the TM-score of 0.73 and 0.76 for homodimers and heterodimers respectively. The accuracy of reconstructed quaternary structures depends on the accuracy of contact predictions. Compared with other optimization methods of reconstructing quaternary structures from interchain contacts, DRLComplex performs similarly to an advanced gradient descent method and better than a Markov Chain Monte Carlo simulation method and a simulated annealing-based method. The source code of DRLComplex is available at:https://github.com/jianlin-cheng/DRLComplex
Gut microbiota composition correlates with disease severity in myelodysplastic syndrome
Authors: Riello Giovanna Barbosa Correia , Mendonça da Silva Priscila , da Silva Oliveira Francisca Andrea , Taiane Germano de Oliveira Roberta , da Silva Francisco Eliclecio Rodrigues , da Frota França Ivo Gabriel , Miyajima Fábio , Melo Vânia Maria Maciel , Pinheiro Ronald Feitosa , Macedo Danielle S.
Published: April 2022

The myelodysplastic syndrome (MDS) is a heterogeneous group of clonal disorders of hematopoietic progenitor cells related to ineffective hematopoiesis and an increased risk of transformation to acute myelogenous leukemia. MDS is divided into categories, namely lineage dysplasia (MDS-SLD), MDS with ring sideroblasts (MDS-RS), MDS with multilineage dysplasia (MDS-MLD), MDS with excess blasts (MDS-EB). The International Prognostic Classification System (IPSS) ranks the patients as very low, low, intermediate, high, and very high based on disease evolution and survival rates. Evidence points to toll-like receptor (TLR) abnormal signaling as an underlying mechanism of this disease, providing a link between MDS and immune dysfunction. Notably, microbial signals, such as lipopolysaccharide from gram-negative bacteria can activate or suppress TLRs. Therefore, we hypothesized that MDS patients present gut microbiota alterations associated with disease subtypes and prognosis. We sequenced the 16S rRNA gene from fecal samples of 30 MDS patients and 16 healthy elderly controls to test this hypothesis. We observed a negative correlation between Prevotella spp. and Akkermansia spp. in MDS patients compared with the control group. High-risk patients presented a significant increase in the genus Prevotella spp. in relation to the other risk categories. There was a significant reduction in the abundance of the genus Akkermansia spp. in high-risk patients compared with low- and intermediate-risk. There was a significant decrease in the genus Ruminococcus spp. in MDS-EB patients compared with controls. Our findings show a new association between gut dysbiosis and higher-risk MDS, with a predominance of gram-negative bacteria in the gut of these patients.
Gender Moderates the Mediating Pathway between Social Deprivation, Body Mass Index and Physical Activity
Authors: Maltagliati Silvio , Saoudi Ilyes , Sarrazin Philippe , Cullati Stéphane , Sieber Stefan , Chalabaev Aïna , Cheval Boris
Published: April 2022

Physical activity is unequally practiced across populations: relative to more privileged individuals, deprived people are less likely to be physically active. However, pathways underlying the association between deprivation and physical activity remain overlooked. Here, we examined whether the association between several indicators of deprivation (administrative area deprivation and self-reported individual material and social deprivation) and physical activity was mediated by body mass index (BMI). In addition, consistent with an intersectional perspective, we tested whether this mediating pathway was moderated by participants’ gender and we hypothesized that the mediating effect of BMI would be stronger among women, relative to men. We used two independent large-scale studies to test the proposed pathways cross-sectionally and prospectively. In a first sample composed of 5,723 British adults (Study 1), BMI partly mediated the cross-sectional association between administrative area deprivation and self-reported physical activity. Moreover, relative to men, the detrimental effect of deprivation on BMI was exacerbated among women, with BMI mediating 3.1% of the association between deprivation and physical activity among women (vs 1.5% among men). In a second sample composed of 8,358 European older adults (Study 2), our results confirmed the findings observed in Study 1: BMI partly mediated the prospective association between perceived material and social deprivation and self-reported physical activity. Moreover, compared to men, the effect of deprivation on BMI was more pronounced among women, with BMI respectively mediating 8.1% and 3.4% of the association between material and social deprivation and physical activity among women (vs 1.3% and 1.2% among men). These findings suggest that BMI partly explained the detrimental association between deprivation and physical activity, with this effect being stronger among women. Our study highlights the need to further consider how gender may shape the mechanisms behind the association between disadvantaged socio-economic circumstances and physical activity.
Confounder-adjusted MRI-based predictors of multiple sclerosis disability
Authors: Kim Yujin , Varosanec Mihael , Kosa Peter , Bielekova Bibiana
Published: April 2022

Introduction

Both aging and multiple sclerosis (MS) cause central nervous system (CNS) atrophy. Excess brain atrophy in MS has been interpreted as accelerated aging. Current paper tests an alternative hypothesis: MS causes CNS atrophy by mechanism(s) different from physiological aging. Thus, subtracting effects of physiological confounders on CNS structures would isolate MS-specific effects.

Methods

Standardized brain MRI and neurological examination were acquired prospectively in 649 participants enrolled in ClinicalTrials.gov Identifier: NCT00794352 protocol. CNS volumes were measured retrospectively, by automated Lesion-TOADS algorithm and by Spinal Cord Toolbox, in a blinded fashion. Physiological confounders identified in 80 healthy volunteers were regressed out by stepwise multiple linear regression. MS specificity of confounder-adjusted MRI features was assessed in non-MS cohort (n=160). MS patients were randomly split into training (n=277) and validation (n=132) cohorts. Gradient boosting machine (GBM) models were generated in MS training cohort from unadjusted and confounder-adjusted CNS volumes against four disability scales.

Results

Confounder adjustment highlighted MS-specific progressive loss of CNS white matter. GBM model performance decreased substantially from training to cross-validation, to independent validation cohorts, but all models predicted cognitive and physical disability with low p-values and effect sizes that outperforms published literature based on recent meta-analysis. Models built from confounder-adjusted MRI predictors outperformed models from unadjusted predictors in the validation cohort.

Conclusion

GBM models from confounder-adjusted volumetric MRI features reflect MS-specific CNS injury, and due to stronger correlation with clinical outcomes compared to brain atrophy these models should be explored in future MS clinical trials.

Highlights

Regressing out physiological confounders affecting volume of CNS structures in healthy volunteers, strengthened correlations between white matter volumes and disability outcomes in MS cohorts

Aggregating volumetric features into generalized boosting machine (GBM) models outperformed correlations of individual MRI biomarkers with clinical outcomes in MS

Developed more sensitive and reliable models that predict MS-associated disability

Independent validation cohorts show true model performances

Developed GBM models should be explored in future MS clinical trials
Pyochelin biotransformation byStaphylococcus aureusshapes bacterial competition withPseudomonas aeruginosain polymicrobial infections
Authors: Jenul C. , Keim K. , Jens J. , Zeiler M. J. , Schilcher K. , Schurr M. , Melander C. , Phelan V.V. , Horswill A.R.
Published: April 2022

Pseudomonas aeruginosaandStaphylococcus aureusare among the most frequently isolated bacterial species from polymicrobial infections of cystic fibrosis patients and chronic wounds. We applied mass spectrometry guided interaction studies to determine how chemical interaction shapes the fitness and community structure during co-infection of these two pathogens. We demonstrate thatS. aureusis equipped with an elegant mechanism to inactivate pyochelin via the yet uncharacterized methyltransferase Spm (staphylococcalpyochelinmethyltransferase). Methylation of pyochelin abolishes the siderophore activity of pyochelin and significantly lowers pyochelin-mediated intracellular ROS production inS. aureus. In a murine wound co-infection model, aS. aureusmutant unable to methylate pyochelin shows significantly lower fitness as compared to its parental strain. Thus, Spm mediated pyochelin methylation is a novel mechanism to increaseS. aureussurvival duringin vivocompetition withP. aeruginosa.
Organelle-selective click labeling coupled with flow cytometry allows high-throughput CRISPR screening of genes involved in phosphatidylcholine metabolism
Authors: Tsuchiya Masaki , Tachibana Nobuhiko , Nagao Kohjiro , Tamura Tomonori , Hamachi Itaru
Published: April 2022

Lipids comprise biomembranes and are involved in many crucial cell functions. While cellular lipid synthesis and transport appear to be governed by intricate protein networks, the whole scheme is insufficiently understood. Although functional genome-wide screening should contribute to deciphering the regulatory networks of lipid metabolism, technical challenges remain – especially for high-throughput readouts of lipid phenotypes. Here, we coupled organelle-selective click labeling of phosphatidylcholine (PC) with flow cytometry-based CRISPR screening technologies to convert organellar PC phenotypes into a simple fluorescence readout for genome-wide screening. This technique, named O-ClickFC, was successfully applied in genome-scale CRISPR-knockout screens to identify previously reported genes associated with PC synthesis (PCYT1A, ACACA), vesicular membrane trafficking (SEC23B, RAB5C), and non-vesicular transport (PITPNB, STARD7). Moreover, this work revealed previously uncharacterized roles of FLVCR1 as a new choline transporter; CHEK1 as a post-translational regulator of the PC-synthetic pathway, and TMEM30A as responsible for translocation of PC to the outside of the plasma membrane bilayer. These findings demonstrate the versatility of O-ClickFC as an unprecedented platform for genetic dissection of cellular lipid metabolism.
Neural instructive signals for associative cerebellar learning
Authors: Silva N. Tatiana , Ramírez-Buriticá Jorge , Pritchett Dominique L. , Carey Megan R.
Published: April 2022

Supervised learning depends on instructive signals that shape the output of neural circuits to support learned changes in behavior. Climbing fiber inputs to the cerebellar cortex represent one of the strongest candidates in the vertebrate brain for conveying neural instructive signals. However, recent studies have shown that Purkinje cell stimulation can also drive cerebellar learning, and the relative importance of these two neuron types in providing instructive signals for cerebellum-dependent behaviors remains unresolved. Here we used cell-type specific perturbations of climbing fibers, Purkinje cells, and other cerebellar circuit elements to systematically evaluate their contributions to delay eyeblink conditioning. Our findings reveal that while optogenetic stimulation of either climbing fibers or Purkinje cells are capable of driving learning under some conditions, even subtle reductions in climbing fiber signaling completely block learning to natural conditioning stimuli. We conclude that climbing fibers and corresponding Purkinje cell complex-spike events provide essential instructive signals for associative cerebellar learning.
A systems biology approach to disentangle the direct and indirect effects of global transcription factors on gene expression in Escherichia coli
Authors: Iyer Mahesh S. , Pal Ankita , Venkatesh K. V.
Published: April 2022

Delineating the pleiotropic effects of global transcriptional factors (TFs) is critical in understanding the system-wide regulatory response in a particular environment. Currently, with the availability of genome-wide TF binding and gene expression data for Escherichia coli, several gene targets can be assigned to the global TFs albeit inconsistently. Here, using a systematic integrated approach with emphasis on metabolism, we characterize and quantify the direct effects as well as the growth-rate mediated indirect effects of global TFs using deletion mutants of FNR, ArcA, and IHF regulators under glucose fermentative condition. Apart from the previous known metabolite-TF interactions, we predicted with high confidence several novel interactions arising from the allosteric effects of the intracellular metabolites. Our combined experimental and compendium level computational analyses revealed the co-expressed genes regulated by these TFs as well as the coordination of the direct and indirect target gene expressions in the context of the economy of intracellular metabolites. Besides, we extended our analysis to combinatorial deletions of these TFs to determine their cross-talk effects as well as conserved patterns of regulatory interactions. Overall, this study leverages the fundamentals of TF-driven regulation which could serve as a better template for deciphering mechanisms underlying complex phenotypes.
HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript
Authors: Vo Tam , Brownmiller Tayvia , Hall Katherine , Jones Tamara L. , Choudhari Sulbha , Grammatikakis Ioannis , Ludwig Katelyn R. , Caplen Natasha J.
Published: April 2022

In the presence of physiological monovalent cations, thousands of RNA G-rich sequences can form parallel G-quadruplexes (G4s) unless RNA-binding proteins inhibit, destabilize, or resolve the formation of such secondary RNA structures. Here, we have used a disease-relevant model system to investigate the biophysical properties of the RNA-binding protein HNRNPH1’s interaction with G-rich sequences. We demonstrate the importance of twoEWSR1-exon 8 G-rich regions in mediating the exclusion of this exon from the oncogenicEWS-FLI1transcripts expressed in a subset of Ewing sarcomas, using complementary analysis of tumor data, long-read sequencing, and minigene studies. We determined that HNRNPH1 binds theEWSR1-exon 8 G-rich sequences with low nM affinities irrespective of whether in a non-G4 or G4 state but exhibits different kinetics depending on RNA structure. Specifically, HNRNPH1 associates and dissociates from G4-folded RNA faster than the identical sequences in a non-G4 state. Importantly, we demonstrate using gel shift and spectroscopic assays that HNRNPH1, particularly the qRRM1-qRRM2 domains, destabilizes the G4s formed by theEWSR1-exon 8 G-rich sequences in a non-catalytic fashion. Our results indicate that HNRNPH1’s binding of G-rich sequences favors the accumulation of RNA in a non-G4 state and that this contributes to its regulation of RNA processing.
SirA inhibits the essential DnaA:DnaD interaction to block helicase recruitment during Bacillus subtilis sporulation
Authors: Winterhalter Charles , Stevens Daniel , Fenyk Stepan , Pelliciari Simone , Marchand Elie , Soultanas Panos , Ilangovan Aravindan , Murray Heath
Published: April 2022

Bidirectional DNA replication from a chromosome origin requires the asymmetric loading of two helicases, one for each replisome. Our understanding of the molecular mechanisms underpinning helicase loading at bacterial chromosome origins is incomplete. Here we report both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. Systematic characterization of the essential initiation protein DnaD revealed distinct protein interfaces required for homo-oligomerization, interaction with the master initiator protein DnaA, and interaction with the helicase co-loader protein DnaB. Informed by these properties of DnaD, we went on to find that the developmentally expressed repressor of DNA replication initiation, SirA, blocks the interaction between DnaD with DnaA, thereby inhibiting helicase recruitment to the origin during sporulation. These results advance our understanding of the mechanisms underpinning DNA replication initiation in B. subtilis, as well as guiding the search for essential cellular activities to target for antimicrobial drug design.
Homing pigeon (Columba livia) dominance hierarchies are stable over time and resistant to perturbation
Authors: Urquia-Samele Amaia A. , Portugal Steven J.
Published: April 2022

Dominance hierarchies are a social dynamic common in many species, which help balance the costs and benefits of social living. Which individuals in a group occupy high ranking positions is influenced by a multitude of different intrinsic and/or extrinsic factors. While homing pigeons (Columba livia) have been a model system for their navigational abilities and flight dynamics, less is known about their dominance hierarchies and general social behaviour when not in flight. Here we document the dominance hierarchies in two closed populations of homing pigeons, and investigate the physiological factors associated with dominance rank, including body size, metabolic rate, personality, and iridescent plumage % reflectance. Measurements of body size and resting metabolic rate all positively correlated with dominance rank in accordance with the performance model of energetic management. Iridescent plumage % reflectance was negatively correlated with rank, suggesting a potential cost of dominance. Attempts to alter hierarchy structure through manipulations of body mass and feather iridescence were ineffective which hierarchy dynamics remaining stable throughout the perturbations and across measurement sessions.
Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells
Authors: Pasquesi Giulia Irene Maria , Kelly Conor J. , Ordonez Andrea D. , Chuong Edward B.
Published: April 2022

Background

Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN- stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN.

Results

We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN.

Conclusion

Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function.
Synaptotagmin 9 modulates spontaneous neurotransmitter release in striatal neurons by regulating substance P secretion
Authors: Seibert Michael J. , Evans Chantell S. , Stanley Kevin S. , Wu Zhenyong , Chapman Edwin R.
Published: April 2022

Synaptotagmin 9 (SYT9) is a tandem C2-domain Ca2+ sensor for exocytosis in neuroendocrine cells; its function in neurons remains unclear. Here, we show that endogenous SYT9 does not trigger rapid synaptic vesicle exocytosis in cultured cortical, hippocampal, or striatal neurons; rather, synaptotagmin 1 (SYT1) fulfills this function. SYT9 is able to regulate evoked synaptic vesicle exocytosis, but only when massively over-expressed. In striatal neurons, loss of SYT9 reduced the rate of spontaneous miniature neurotransmitter release events (minis). To delve into the underlying mechanism, we localized SYT9 within these neurons and found that it is targeted to dense core vesicles, where it regulates the release of substance P (SP), a neuropeptide known to modulate mini frequency. Exogenous SP, but not other striatal peptide hormones, completely rescued the Syt9 KO mini phenotype. Biochemical experiments revealed that Ca2+-binding to the C2A domain of SYT9 triggers membrane fusion in vitro, and mutations that disrupt this activity abolished the ability of SYT9 to regulate both SP release and mini frequency in striatal neurons. We conclude that SYT9 indirectly regulates synaptic transmission in striatal neurons by controlling SP release.
Bone hierarchical structure: spatial variation across length scales
Authors: Wittig Nina K. , Birkedal Henrik
Published: April 2022

Bone is a complex hierarchical biomineralized material, which is special amongst biominerals because it is replete with cells, namely, osteocytes. While bone has been scrutinized for centuries, many questions remain open and new research hints that the ultrastructure of bone, encompassing both the bone matrix itself and the embedded cell network, is much more heterogeneous than hitherto realized. A number of these new findings have been made thanks to the enormous developments in X-ray imaging that have occurred in recent decades, and there is promise that they will also allow many of the remaining open questions to be addressed. X-ray absorption or phase imaging affords high three-dimensional (3D) resolution and allows traversing the length scales of bone all the way down to the fine details of the lacuno-canalicular network housing the osteocytes. Multimodal X-ray imaging provides combined information covering both the length scales defined by the size of the measured volume and tomographic resolution, as well as those probed by the signal that is measured. In X-ray diffraction computed tomography (XRD-CT), for example, diffraction signals can be reconstructed tomographically, which offers detailed information about the spatial variations in the crystallographic properties of the bone biomineral. Orientational information can be obtained by tensor tomography. The combination of both small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) tensor tomography gives information on the orientation of bone nanostructure and crystals, respectively. These new technical developments promise that great strides towards understanding bone structure can be expected in the near future. In this review, recent findings that have resulted from X-ray imaging are highlighted and speculation is given on what can be expected to follow.
A GH115 α-glucuronidase structure reveals dimerization-mediated substrate binding and a proton wire potentially important for catalysis
Authors: Wilkens Casper , Vuillemin Marlene , Pilgaard Bo , Polikarpov Igor , Morth Jens Preben
Published: April 2022

Xylan is a major constituent of plant cell walls and is a potential source of biomaterials, and the derived oligosaccharides have been shown to have prebiotic effects. Xylans can be highly substituted with different sugar moieties, which pose steric hindrance to the xylanases that catalyse the hydrolysis of the xylan backbone. One such substituent is α-D-glucuronic acid, which is linked to the O2′ position of the β-1,4 D-xylopyranoses composing the main chain of xylans. The xylan-specific α-glucuronidases from glycoside hydrolase family 115 (GH115) specifically catalyse the removal of α-D-glucuronic acid (GlcA) or methylated GlcA (MeGlcA). Here, the molecular basis by which the bacterial GH115 member wtsAgu115A interacts with the main chain of xylan and the indirect involvement of divalent ions in the formation of the Michaelis–Menten complex are described. A crystal structure at 2.65 Å resolution of wtsAgu115A originating from a metagenome from an anaerobic digester fed with wastewater treatment sludge was determined in complex with xylohexaose, and Asp303 was identified as the likely general acid. The residue acting as the general base could not be identified. However, a proton wire connecting the active site to the metal site was observed and hence a previous hypothesis suggesting a Grotthuss-like mechanism cannot be rejected. Only a single molecule was found in the asymmetric unit. However, wtsAgu115A forms a dimer with a symmetry-related molecule in the crystal lattice. The xylohexaose moieties of the xylohexaose are recognized by residues from both protomers, thus creating a xylohexaose recognition site at the dimer interface. The dimer was confirmed by analytical size-exclusion chromatography in solution. Kinetic analysis with aldouronic acids resulted in a Hill coefficient of greater than 2, suggesting cooperativity between the two binding sites. Three Ca2+ ions were identified in the wtsAgu115A structures. One Ca2+ ion is of particular interest as it is coordinated by the residues of the loops that also interact with the substrate. Activity studies showed that the presence of Mg2+ or Mn2+ resulted in a higher activity towards aldouronic acids, while the less restrictive coordination geometry of Ca2+ resulted in a decrease in activity.