bluuebunny/crossref_metadata_2025 huggingface dataset:
Hair loss in females and thromboembolism in males are significantly enriched in post-acute sequelae of COVID (PASC) relative to recent medical history
Authors: Akama-Garren Elliot , Anand Praveen , Cristea-Platon Tudor , Lenehan Patrick , Lindemer Emily , Bade Sairam , Liukasemsarn Saran , O’Horo John C. , Hurt Ryan T. , Williams Amy W. , Gores Gregory J. , Badley Andrew D. , Awasthi Samir , Soundararajan Venky
Published: January 2021

After one year of the COVID-19 pandemic, over 130 million individuals worldwide have been infected with the novel coronavirus, yet the post-acute sequelae of COVID-19 (PASC), also referred to as the ‘long COVID’ syndrome, remains mostly uncharacterized. We leveraged machine-augmented curation of the physician notes from electronic health records (EHRs) across the multi-state Mayo Clinic health system to retrospectively contrast the occurrence of symptoms and diseases in COVID-19 patients in the post-COVID period relative to the pre-COVID period (n=6,413). Through comparison of the frequency of 10,039 signs and symptoms before and after diagnosis, we identified an increase in hypertensive chronic kidney disease (OR 47.3, 95% CI 23.9-93.6, p=3.50×10−9), thromboembolism (OR 3.84, 95% CI 3.22-4.57, p=1.18×10−4), and hair loss (OR 2.44, 95% CI 2.15-2.76, p=8.46×10−3) in COVID-19 patients three to six months after diagnosis. The sequelae associated with long COVID were notably different among male vs female patients and patients above vs under 55 years old, with the hair loss enrichment found primarily in females and the thromboembolism enrichment in males. These findings compel targeted investigations into what may be persistent dermatologic, cardiovascular, and coagulopathic phenotypes following SARS-CoV-2 infection.
Modelling COVID -19 transmission in a hemodialysis centre using simulation generated contacts matrices
Authors: Tofighi Mohammadali , Asgary Ali , Merchant Asad A. , Shafiee Mohammad Ali , Najafabadi Mahdi M. , Nadri Nazanin , Aarabi Mehdi , Heffernan Jane , Wu Jianhong
Published: January 2021

The COVID-19 pandemic has been particularly threatening to the patients with end-stage kidney disease (ESKD) on intermittent hemodialysis and their care providers. Hemodialysis patients who receive life-sustaining medical therapy in healthcare settings, face unique challenges as they need to be at a dialysis unit three or more times a week, where they are confined to specific settings and tended to by dialysis nurses and staff with physical interaction and in close proximity. Despite the importance and critical situation of the dialysis units, modelling studies of the SARS-CoV-2 spread in these settings are very limited. In this paper, we have used a combination of discrete event and agent-based simulation models, to study the operations of a typical large dialysis unit and generate contact matrices to examine outbreak scenarios. We present the details of the contact matrix generation process and demonstrate how the simulation calculates a micro-scale contact matrix comprising the number and duration of contacts at a micro-scale time step. We have used the contacts matrix in an agent-based model to predict disease transmission under different scenarios. The results show that micro-simulation can be used to estimate contact matrices, which can be used effectively for disease modelling in dialysis and similar settings.
Morphological changes after cranial fractionated photon radiotherapy: localized loss of white matter and grey matter volume with increasing dose
Authors: Nagtegaal SHJ , David S , van Grinsven EE , van Zandvoort MJE , Seravalli E , Snijders TJ , Philippens MEP , Verhoeff JJC
Published: January 2021

Purpose

Numerous brain MR imaging studies have been performed to understand radiation-induced cognitive decline. However, many of them focus on a single region of interest, e.g. cerebral cortex or hippocampus. In this study, we use deformation-based morphometry (DBM) and voxel-based morphometry (VBM) to measure the morphological changes in patients receiving fractionated photon RT, and relate these to the dose. Additionally, we study tissue specific volume changes in white matter (WM), grey matter (GM), cerebrospinal fluid and total intracranial volume (TIV).

Methods and Materials

From our database, we selected 28 patients with MRI of high quality available at baseline and 1 year after RT. Scans were rigidly registered to each other, and to the planning CT and dose file. We used DBM to study non-tissue-specific volumetric changes, and VBM to study volume loss in grey matter. Observed changes were then related to the applied radiation dose (EQD2). Additionally, brain tissue was segmented into WM, GM and cerebrospinal fluid, and changes in these volumes and TIV were tested.

Results

Performing DBM resulted in clusters of dose-dependent volume loss 1 year after RT seen throughout the brain. Both WM and GM were affected; within the latter both cerebral cortex and subcortical nuclei show volume loss. Volume loss rates ranging from 5.3 to 15.3%/30 Gy were seen in the cerebral cortical regions in which more than 40% of voxels were affected. In VBM, similar loss rates were seen in the cortex and nuclei. The total volume of WM and GM significantly decreased with rates of 5.8% and 2.1%, while TIV remained unchanged as expected.

Conclusions

Radiotherapy is associated with dose-dependent intracranial morphological changes throughout the entire brain. Therefore, we will consider to revise sparing of organs at risk based on future cognitive and neurofunctional data.
OPTIMIZING COVID-19 VACCINE USAGE
Authors: Jara Carlos Poblete , Velloso Lício A. , de Araújo Eliana Pereira
Published: January 2021

As the worldwide vaccination, it is imperative to minimize vaccine wastage by effectively using all doses available. Vaccine wastage can occur at multiple points during the vaccination process, but it is mainly because the device dead space and the filling process technique. However, there are no studies discussing the waste volume effect of COVID-19 vaccines in clinical practice. There is an increasing COVID-19 vaccine demand that we estimate up to several billion dual doses. The objective of this study was to assess the number of 0.3mL doses obtained from a multiple-dose vial using 1ml and 3ml syringes with different type of needles replicating the first COVID-19 vaccination protocol.

Our results suggest that it is possible to obtain six or seven doses from each vial instead five. We provide evidence to optimize between 20% and 40% additional vaccine doses per vial if the current 5-dose vials are used, making scarce supplies go further.

It is our duty, as researchers, to ensure the efficacy and efficiency of the worldwide COVID-19 vaccination process. However, if standard syringes-needles and technique are used, there may not be sufficient volume to draw extra doses from a single vial.
Brain activity is contingent on neuropsychological function in an fMRI study of Verbal Working Memory in Amyotrophic Lateral Sclerosis
Authors: Kobeleva Xenia , Machts Judith , Veit Maria , Vielhaber Stefan , Petri Susanne , Schoenfeld Mircea Ariel
Published: January 2021

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that causes progressive degeneration of neurons in motor and non-motor regions, affecting multiple cognitive domains. To contribute to the growing research field that employs structural and functional neuroimaging to investigate the effect of ALS on different working memory components, we conducted a functional magnetic resonance imaging (fMRI) study exploring the localization and intensity of alterations in neural activity. Being the first study to specifically address verbal working memory via fMRI in the context of ALS, we employed the verbal n-back task with 0-back and 2-back conditions. Despite ALS patients showing unimpaired accuracies (p = 0.724) and reaction times (p = 0.0785), there was significantly increased brain activity of frontotemporal and parietal regions in the 2-back minus 0-back contrast in patients compared to controls using nonparametric statistics with 5000 permutations and a T-threshold of 2.5. This increased brain activity during working memory performance was largely associated with better neuropsychological function within the ALS group, suggesting a compensatory effect. This study therefore adds to the current knowledge on neural correlates of working memory in ALS and contributes to a more nuanced understanding of hyperactivity during cognitive processes in fMRI studies of ALS.
Edoxaban versus warfarin on stroke risk in patients with atrial fibrillation: a territory-wide cohort study
Authors: Kong Dicken , Zhou Jiandong , Lee Sharen , Kit Leung Keith Sai , Liu Tong , Sawant Abhishek C , Corbelli John , Wai Abraham KC , Chang Carlin , Zhang Qingpeng , Tse Gary
Published: January 2021

Background

In this territory-wide, observational, propensity score-matched cohort study, we evaluate the development of transient ischaemic attack and ischaemic stroke (TIA/Ischaemic stroke) in patients with AF treated with edoxaban or warfarin.

Methods

This was an observational, territory-wide cohort study of patients between January 1st, 2016 and December 31st, 2019, in Hong Kong. The inclusion were patients with i) atrial fibrillation, and ii) edoxaban or warfarin prescription. 1:2 propensity score matching was performed between edoxaban and warfarin users. Univariate Cox regression identifies significant risk predictors of the primary, secondary and safety outcomes. Hazard ratios (HRs) with corresponding 95% confidence interval [CI] and p values were reported.

Results

This cohort included 3464 patients (54.18% males, median baseline age: 72 years old, IQR: 63-80, max: 100 years old), 664 (19.17%) with edoxaban use and 2800 (80.83%) with warfarin use. After a median follow-up of 606 days (IQR: 306-1044, max: 1520 days), 91(incidence rate: 2.62%) developed TIA/ischaemic stroke: 1.51% (10/664) in the edoxaban group and 2.89% (81/2800) in the warfarin group. Edoxaban was associated with a lower risk of TIA or ischemic stroke when compared to warfarin.

Conclusions

Edoxaban use was associated with a lower risk of TIA or ischemic stroke after propensity score matching for demographics, comorbidities and medication use.
Comparative effects of sodium glucose cotransporter 2 (SGLT2) inhibitors and dipeptidyl peptidase-4 (DPP4) inhibitors on new-onset atrial fibrillation and stroke outcomes
Authors: Lee Sharen , Zhou Jiandong , Chang Carlin , Liu Tong , Chang Dong , Wong Wing Tak , Leung Keith SK , Wai Abraham KC , Yung Cheung Bernard Man , Tse Gary , Zhang Qingpeng
Published: January 2021

Background

SGLT2I and DPP4I are medications prescribed for type 2 diabetes mellitus patients. However, there are few population-based studies comparing their effects on incident atrial fibrillation or ischemic stroke.

Methods

This was a territory-wide cohort study of type 2 diabetes mellitus patients prescribed SGLT2I or DPP4I between January 1st, 2015 to December 31st, 2019 in Hong Kong. Patients with both DPP4I and SGLT2I use and patients with drug discontinuation were excluded. Patients with prior AF or stroke were excluded for the respective analysis. 1:2 propensity-score matching was conducted for demographics, past comorbidities and medications using nearest-neighbor matching method. Cox models were used to identify significant predictors for new onset heart failure (HF) or myocardial infarction (MI), cardiovascular and all-cause mortality.

Results

The AF-free cohort included 49108 patients (mean age: 66.48 years old [SD: 12.89], 55.32% males) and the stroke-free cohort included 49563 patients (27244 males [54.96%], mean baseline age: 66.7 years old [SD: 12.97, max: 104.6 years old]). After propensity score matching, SGLT2i use was associated with a lower risk of new onset AF (HR: 0.43[0.28, 0.66]), cardiovascular mortality (HR: 0.79[0.58, 1.09]) and all-cause mortality (HR: 0.69[0.60, 0.79]) in the AF-free cohort. It was also associated with a lower risk of new onset stroke (0.46[0.33, 0.64]), cardiovascular mortality (HR: 0.74[0.55, 1.00]) and all-cause mortality (HR: 0.64[0.56, 0.74]) in the stroke-free cohort.

Conclusions

The novelty of our work si that SGLT2 inhibitors are protective against atrial fibrillation and stroke development for the first time. These findings should be validated in other cohorts.
Angiotensin converting enzyme inhibitors and risk of lung cancer: a population-based cohort study
Authors: Hung Joshua Kai Fung , Zhou Jiandong , Lee Sharen , Xia Yunlong , Liu Ying , Zhang Yuhui , Wong Wing Tak , Li Guangling , Liu Tong , Yung Cheung Bernard Man , Kei Wong Ian Chi , Zhang Qingpeng , Tse Gary
Published: January 2021

Objectives

To determine whether the use of angiotensin converting enzyme inhibitors (ACEIs) was associated with a higher risk of lung cancer when compared to use of angiotensin receptor blockers (ARBs).

Study Design

Population-based cohort study.

Setting

Public hospitals under the Hospital Authority in Hong Kong, P.R. China.

Methods

Patients admitted to public hospitals and first prescribed with ACEI and/or ARB between 1 January 2001 and 31 December 2018 were analyzed. The last follow-up date was 31 August 2020, or death, whichever was earlier.

Outcomes

The primary outcome was the incidence of lung cancer. Logistic regression was used to calculate odds ratio [ORs] with 95% confidence intervals associated with the use of ACEIs compared to ARBs. Incidence and odds ratios were estimated for temporal analysis of incident cancer risk associated with time since the first prescription of ACEI or ARB.

Results

In the unmatched cohort, 56,697 patients and 357,011 patients were included the ARB and ACEI cohorts, with lung cancer incidence of 2.16% and 1.29%, respectively. Using 1:3 matching for ARB to ACEI users, the incidences were 2.32% and 1.29%. ACEI use was associated with increased risks of lung cancer both before (hazard ratio: 1.30 [1.21-1.40], P<0.0001) and after (1.40 [1.29-1.51], P<0.0001) matching. There was a dose-dependent relationship between ACEI exposure and lung cancer risk.

Conclusions

ACEI use was associated with increased risk of lung cancer compared with ARB use at all time points. Additionally, incidence risk increases with the duration of exposure.
A novel computational approach to reconstruct SARS-CoV-2 infection dynamics through the inference of unsampled sources of infection
Authors: Perera Deshan , Perks Ben , Potemkin Michael , Gordon Paul , Gill John , van Marle Guido , Long Quan
Published: January 2021

Infectious diseases such as the COVID19 pandemic cemented the importance of disease tracking. The role of asymptomatic, undiagnosed individuals in driving infection has become evident. Their unaccountability results in ineffective prevention. We developed a pipeline using genomic data to accurately predict a population’s transmission network complete with the inference of unsampled sources. The system utilises Bayesian phylogenetics to capture evolutionary and infection dynamics of SARS-CoV-2. It identified the effectiveness of preventive measures in Canada’s Atlantic bubble and mobile populations such as New York State. Its robustness extends to the prediction of cross-species disease transmission as we inferred SARS-CoV-2 transmission from humans to lions and tigers in New York City’s Bronx Zoo. The proposed method’s ability to generate such complete transmission networks, provides a more detailed insight into the transmission dynamics within a population. This potential frontline tool will be of direct help in “the battle to bend the curve”.
Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality
Authors: Silva Julio , Lucas Carolina , Sundaram Maria , Israelow Benjamin , Wong Patrick , Klein Jon , Tokuyama Maria , Lu Peiwen , Venkataraman Arvind , Liu Feimei , Mao Tianyang , Oh Ji Eun , Park Annsea , Casanovas-Massana Arnau , Vogels Chantal B. F. , Muenker M. Catherine , Zell Joseph , Fournier John B. , Campbell Melissa , Chiorazzi Michael , Fuentes Edwin Ruiz , Petrone Mary E , Kalinich Chaney C. , Ott Isabel M. , Watkins Annie , Moore Adam J. , Nakahata Maura ,   Yale IMPACT Team, Grubaugh Nathan D. , Farhadian Shelli , Cruz Charles Dela , Ko Albert I. , Schulz Wade L. , Ring Aaron , Ma Shuangge , Omer Saad , Wyllie Anne L , Iwasaki Akiko
Published: January 2021

While several clinical and immunological parameters correlate with disease severity and mortality in SARS-CoV-2 infection, work remains in identifying unifying correlates of coronavirus disease 2019 (COVID-19) that can be used to guide clinical practice. Here, we examine saliva and nasopharyngeal (NP) viral load over time and correlate them with patient demographics, and cellular and immune profiling. We found that saliva viral load was significantly higher in those with COVID-19 risk factors; that it correlated with increasing levels of disease severity and showed a superior ability over nasopharyngeal viral load as a predictor of mortality over time (AUC=0.90). A comprehensive analysis of immune factors and cell subsets revealed strong predictors of high and low saliva viral load, which were associated with increased disease severity or better overall outcomes, respectively. Saliva viral load was positively associated with many known COVID-19 inflammatory markers such as IL-6, IL-18, IL-10, and CXCL10, as well as type 1 immune response cytokines. Higher saliva viral loads strongly correlated with the progressive depletion of platelets, lymphocytes, and effector T cell subsets including circulating follicular CD4 T cells (cTfh). Anti-spike (S) and anti-receptor binding domain (RBD) IgG levels were negatively correlated with saliva viral load showing a strong temporal association that could help distinguish severity and mortality in COVID-19. Finally, patients with fatal COVID-19 exhibited higher viral loads, which correlated with the depletion of cTfh cells, and lower production of anti-RBD and anti-S IgG levels. Together these results demonstrated that viral load – as measured by saliva but not nasopharyngeal — is a dynamic unifying correlate of disease presentation, severity, and mortality over time.
Tumor-Antagonizing Fibroblasts Secrete Prolargin as Tumor Suppressor in Hepatocellular Carcinoma
Authors: Chiavarina Barbara , Ronca Roberto , Otaka Yukihiro , Sutton Roger Bryan , Rezzola Sara , Yokobori Takehiko , Chiodelli Paola , Souche Regis , Maraver Antonio , Faa Gavino , Oyama Tetsunari , Gofflot Stephanie , Bellahcène Akeila , Detry Olivier , Delvenne Philippe , Castronovo Vincent , Nishiyama Masahiko , Turtoi Andrei
Published: January 2021

Systemic treatment of hepatocellular carcinoma (HCC) targets the tumor microenvironment (TME) by combining immunotherapy with angiogenesis inhibitors. Cancer-associated fibroblasts (CAF) are important components of the TME, however their targeting in clinics remains challenging. To this end, the existence of tumor supressing CAF and their poor characterisation is a major conundrum. Starting from proteomics and single cell analysis, we outline CAF heterogeneity in HCC and describe a subtype of CAF that express a novel tumor-related protein prolargin. Upon secretion prolargin is deposited in the TME where its levels positively correlate with patient outcome (HR=0.37; p=0.01).In vivo, tumors with lower prolargin expression display faster progression (5-fold; p=0.01) and stronger angiogenesis. Mechanistically, aggressive HCC cells degrade prolargin using matrix metalloprotease 3 (MMP3). We show that prolargin binds and inhibits several growth factors, key to tumor progression. Inhibiting prolargin degradation combined with sorafenib, demonstrated superior tumor control compared to sorafenib treatment alone. In conclusion, prolargin-expressing CAF have tumor-antagonizing properties. Stabilizing prolargin tumoral levels should be considered for systemic therapy of HCC, involving CAF in existing TME targeting.
Amino acids targeted based metabolomics study in non-segmental Vitiligo: a pilot study
Authors: Marzabani Rezvan , Rezadoost Hassan , Chopanian Peyman , Mozafari Nikoo , Jafari Mohieddin , Mirzaie Mehdi , Karimi Mehrdad
Published: January 2021

Introduction

Vitiligo is an asymptomatic disorder that results from the loss of pigments (melanin), causing skin or mucosal depigmentation and impairs beauty.

Objective

Due to the complexity of the pathogenesis of this disease and various theories including self-safety theory, oxidative stress, neurological theory and internal defects of melanocytes behind it, and finally, the vast role of amino acids in body metabolism and various activities of the body, amino acids targeted based metabolomics was set up to follow any fluctuation inside this disease.

Methodology

The study of amino acid profiles in plasma of people with non-segmental vitiligo using a liquid chromatography equipped with fluorescent detector was performed to find remarkable biomarkers for the diagnosis and evaluation of disease severity of patients with vitiligo. Twenty-two amino acids derivatized witho-phthalaldehyde (OPA) and fluorylmethyloxycarbonyl chloride (FMOC), were precisely determined. Next, the concentrations of these twenty-two amino acids and their corresponding molar ratios were calculated in 37 patients (including 18 females and 19 males) and corresponding 34 healthy individuals (18 females and 16 males). Using R programing, the data were completely analyzed between the two groups of patients and healthy to find suitable and reliable biomarkers.

Results

Interestingly, comparing the two groups, in the patient group, tyrosine, cysteine, the ratio of tyrosine to lysine and the ratio of cysteine to ornithine were increased while, arginine, lysine, ornithine and glycine ratios to cysteine have been decreased. These amino acids were selected for identification of patients with accuracy of detection of approximately 0.95 using the assessment of logistic regression.

Conclusion

These results indicate a disruption of the production of melanin, increased immune activity and oxidative stress, which are also involved in the effects of vitiligo. Therefore, these amino acids can be used as biomarker for the evaluation of risk, prevention of complications in individuals at risk and monitoring of treatment process.
Multi-Spatial Scale Dynamic Interactions between Functional Sources Reveal Sex-Specific Changes in Schizophrenia
Authors: Iraji A. , Faghiri A. , Fu Z. , Rachakonda S. , Kochunov P. , Belger A. , Ford J.M. , McEwen S. , Mathalon D.H. , Mueller B.A. , Pearlson G.D. , Potkin S.G. , Preda A. , Turner J.A. , van Erp T.G.M. , Calhoun V.D.
Published: January 2021

We introduce an extension of independent component analysis (ICA), called multiscale ICA (msICA), and design an approach to capture dynamic functional source interactions within and between multiple spatial scales. msICA estimates functional sources at multiple spatial scales without imposing direct constraints on the size of functional sources, overcomes the limitation of using fixed anatomical locations, and eliminates the need for model-order selection in ICA analysis. We leveraged this approach to study sex-specific and -common connectivity patterns in schizophrenia.

Results show dynamic reconfiguration and interaction within and between multi-spatial scales. Sex-specific differences occur (1) within the subcortical domain, (2) between the somatomotor and cerebellum domains, and (3) between the temporal domain and several others, including the subcortical, visual, and default mode domains. Most of the sex-specific differences belong to between-spatial scale functional interactions and are associated with a dynamic state with strong functional interactions between the visual, somatomotor, and temporal domains and their anticorrelation patterns with the rest of the brain. We observed significant correlations between multi-spatial scale functional interactions and symptom scores, highlighting the importance of multiscale analyses to identify potential biomarkers for schizophrenia. As such, we recommend such analyses as an important option for future functional connectivity studies.
A relative-motion method for parsing spatio-temporal behaviour of dyads using GPS relocation data
Authors: Vissat Ludovica Luisa , Blackburn Jason K. , Getz Wayne M.
Published: January 2021

In this paper, we introduce a novel method for classifying and computing the frequencies of movement modes of intra and interspecific dyads, focusing in particular on distance-mediated approach, retreat, following and side by side movement modes.

Besides distance, the method includes factors such as sex, age, time of day, or season that cause frequencies of movement modes to deviate from random.

We demonstrate and validate our method using both simulated and empirical data. Our simulated data were obtained from a relative-motion, biased random-walk (RM-BRW) model with attraction and repulsion circumferences. Our empirical data were GPS relocation time series collected from African elephants in Etosha National Park, Namibia. The simulated data were primarily used to validate our method while the empirical data analysis were used to illustrate the types of behavioral assessment that our methodology reveals.

Our methodology facilitates automated, observer-bias-free analysis of the locomotive interactions of dyads using GPS relocation data, which is becoming increasingly ubiquitous as telemetry and related technologies improve. Our method should open up a whole new vista of behavioral-interaction type analyses to movement and behavioral ecologists.
Rapid fabrication of hydrogel micropatterns by projection stereolithography for studying self-organized developmental patterning
Authors: Zhu Ye , Sazer Daniel , Miller Jordan , Warmflash Aryeh
Published: January 2021

Self-organized patterning of mammalian embryonic stem cells on micropatterned surfaces has previously been established as an in vitro platform for early mammalian developmental studies, complimentary toin vivostudies. Traditional micropatterning methods, such as micro-contact printing (μCP), involve relatively complicated fabrication procedures, which restricts widespread adoption by biologists. Here, we demonstrate a rapid method of micropatterning by printing hydrogel micro-features onto a glass-bottomed culture vessel. The micro-features are printed using a projection stereolithography bioprinter yielding hydrogel structures that geometrically restrict the attachment of cells or protein. Compared to traditional, physical photomasks, a digitally tunable virtual photomask is used in the projector to generate blue light patterns that enable rapid iteration with minimal cost and effort. We show that a protocol that makes use of this method together with LN521 coating creates a surface suitable for human embryonic stem cell (hESC) attachment and growth with minimal non-specific adhesion. We further demonstrate that self-patterning of hESCs following previously published gastrulation and ectodermal induction protocols achieves results comparable with those obtained with commercially available plates (CYTOO).
Milk losses linked to udder health treatments at dairy farms with automatic milking systems
Authors: Adriaens Ines , Van Den Brulle Igor , Aernouts Ben
Published: January 2021

Milk losses caused by intramammary infections (IMI) have a massive impact on farm profitability and sustainability. In this study, we analyzed milk losses from 4 553 treated IMI cases at 41 AMS dairy farms. Milk losses were estimated based on the difference between the expected and the true production. To estimate the unperturbed lactation curve, we applied an iterative procedure using the Wood model and a variance-dependent threshold on the milk yield residuals. We calculated milk losses both in a fixed window around the first treatment day of each IMI case and in the perturbations corresponding to this day, at cow level as well as at quarter level. In a fixed time window of day -5 to 30 around the first treatment, the absolute median milk losses per case were 101.5 kg, highly dependent on the parity and the lactation stage with absolute milk losses highest in multiparous cows and at peak lactation. Relative milk losses expressed in percentage were highest on the treatment day, and full recovery was often not reached within 30 days from treatment onset. In 62% of the cases, we found a perturbation in milk yield at cow level at the time of treatment. On average, perturbations started 8.7 days before the first treatment and median absolute milk losses increased to 128 kg milk per perturbation. Mastitis is not expected to have equal effects on the four quarters so this study additionally investigated losses in the individual udder quarters. We used a data-based method leveraging milk yield and electrical conductivity to project the presumably infected quarter and compared losses with the average of presumably non-infected quarters. Median absolute losses in a fixed 36-day window around treatment varied between 50.2 kg for front and 59.3 kg for hind infected quarters compared to respectively 24.7 and 26.3 kg for the median losses in the non-infected quarters. Also here, these losses depended on lactation stage and parity. Expressed proportionally to expected yield, the relative median milk losses in infected quarters on the treatment day were 20% higher in infected quarters with a higher variability and slower recovery. In 86% of the treated IMI cases, at least one perturbation was found at the quarter level. This analysis confirms the high impact of IMI on milk production, and the large variation between quarter losses illustrates the potential of quarter analysis for on-farm monitoring at farms with an automated milking system.

Highlights

Milk losses were estimated for treated cases of intramammary infections

Milk losses were highly variable across cases with a median of 101 kg

We found large differences between infected and non-infected quarters

Quantification of milk losses can be the basis for better udder health management
Magnetic tweezers meets AFM: ultra-stable protein dynamics across the force spectrum
Authors: Alonso-Caballero Alvaro , Tapia-Rojo Rafael , Badilla Carmen L. , Fernandez Julio M.
Published: January 2021

Proteins that operate under force—cell adhesion, mechanosensing—exhibit a wide range of mechanostabilities. Single-molecule magnetic tweezers has enabled the exploration of the dynamics under force of these proteins with subpiconewton resolution and unbeatable stability in the 0.1-120 pN range. However, proteins featuring a high mechanostability (>120 pN) have remained elusive with this technique and have been addressed with Atomic Force Microscopy (AFM), which can reach higher forces but displays less stability and resolution. Herein, we develop a magnetic tweezers approach that can apply AFM-like mechanical loads while maintaining its hallmark resolution and stability in a range of forces that spans from 1 to 500 pN. We demonstrate our approach by exploring the folding and unfolding dynamics of the highly mechanostable adhesive protein FimA from the Gram-positive pathogenActinomyces oris. FimA unfolds at loads >300 pN, while its folding occurs at forces <15 pN, producing a large dissipation of energy that could be crucial for the shock absorption of mechanical challenges during host invasion. Our novel magnetic tweezers approach entails an all-in-one force spectroscopy technique for protein dynamics studies across a broad spectrum of physiologically-relevant forces and timescales.
Single Cell RNA-seq and Mass Cytometry Reveals a Novel and a Targetable Population of Macrophages in Idiopathic Pulmonary Fibrosis
Authors: Ayaub EA , Poli S , Ng J , Adams T , Schupp J , Quesada-Arias L , Poli F , Cosme C , Robertson M , Martinez-Manzano J , Liang X , Villalba J , Lederer J , Chu SG , Raby BA , Washko G , Coarfa C , Perrella MA , El-Chemaly S , Kaminski N , Rosas IO
Published: January 2021

In this study, we leveraged a combination of single cell RNAseq, cytometry by time of flight (CyTOF), and flow cytometry to study the biology of a unique macrophage population in pulmonary fibrosis. Using the profiling data from 312,928 cells derived from 32 idiopathic pulmonary fibrosis (IPF), 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we identified an expanded population of macrophages in IPF that have a unique transcriptional profile associated with pro-fibrotic signature. These macrophages attain a hybrid transitional state between alveolar and interstitial macrophages, are enriched with biological processes of pro-fibrotic immune cells, and express novel surface markers and genes that have not been previously reported. We then applied single cell CyTOF to simultaneously measure 37 markers to precisely phenotype the uniquely expanded macrophage subset in IPF lungs. The SPADE algorithm independently identified an expanded macrophage cluster, and validated CD84 and CD36 as novel surface markers that highly label this cluster. Using a separate validation cohort, we confirmed an increase in CD84++CD36++macrophage population in IPF compared to control and COPD lungs by flow cytometry. Further, using the signature from the IPF-specific macrophages and the LINCS drug database, we predicted small molecules that could reverse the signature of IPF-specific macrophages, and validated two molecules, CRT and Cucur, using THP-1 derived human macrophages and precision-cut lung slices (PCLS) from IPF patients. Utilizing a multi-dimensional translational approach, our work identified a novel and targetable population of macrophages found in end-stage pulmonary fibrosis.

One Sentence Summary

Single cell RNAseq, CyTOF, and flow cytometry reveal the presence of an aberrant macrophage population in pulmonary fibrosis
Lipid distributions and transleaflet cholesterol migration near heterogeneous surfaces in asymmetric bilayers
Authors: Cino Elio A. , Borbuliak Mariia , Hu Shangnong , Tieleman D. Peter
Published: January 2021

Specific and nonspecific protein-lipid interactions in cell membranes have important roles in an abundance of biological functions. We have used coarse-grained (CG) molecular dynamics (MD) simulations to assess lipid distributions and cholesterol flipping dynamics around surfaces in a model asymmetric plasma membrane containing one of six structurally distinct entities: aquaporin-1 (AQP1), the bacterial β-barrel outer membrane proteins OmpF and OmpX, KcsA potassium channel, WALP23 peptide, and a carbon nanotube (CNT). Our findings revealed varied lipid partitioning and cholesterol flipping times around the different solutes, and putative cholesterol binding sites in AQP1 and KcsA. The results suggest that protein-lipid interactions can be highly variable, and that surface-dependant lipid profiles are effectively manifested in CG simulations with the Martini force field.
Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells
Authors: Domanskyi Sergii , Hakansson Alex , Meng Michelle , Pham Benjamin K , Graff Zivin Joshua S. , Piermarocchi Carlo , Paternostro Giovanni , Ferrara Napoleone
Published: January 2021

VEGF inhibitor drugs have been successful, especially in ophthalmology, but not all patients respond to them. Combinations of drugs are likely to be needed for more effective therapies of angiogenesis-related diseases. In this paper we describe naturally occurring combinations of receptors in endothelial cells that might help to understand how cells communicate and to identify targets for drug combinations. We also develop and share a new software tool called DECNEO to identify them.

Single-cell gene expression data are used to identify a set of co-expressed endothelial cell receptors, conserved among species (mice and humans) and enriched, within a network, of connections to up-regulated genes. This set includes several receptors previously shown to play a role in angiogenesis. Multiple statistical tests from large datasets, including an independent validation set, support the reproducibility, evolutionary conservation and role in angiogenesis of these naturally occurring combinations of receptors. We also show tissue-specific combinations and, in the case of choroid endothelial cells, consistency with both well-established and recent experimental findings, presented in a separate paper.

The results and methods presented here advance the understanding of signaling to endothelial cells. The methods are generally applicable to the decoding of intercellular combinations of signals.
SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses
Authors: Wang Li , Fan Xiaoyu , Bonenfant Gaston , Cui Dan , Hossain Jaber , Jiang Nannan , Larson Gloria , Currier Michael , Liddell Jimma , Wilson Malania , Tamin Azaibi , Harcourt Jennifer , Ciomperlik-Patton Jessica , Pang Hong , Dybdahl-Sissoko Naomi , Campagnoli Ray , Shi Pei-Yong , Barnes John , Thornburg Natalie J. , Wentworth David E. , Zhou Bin
Published: January 2021

Coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses is inevitable as the COVID-19 pandemic continues. This study aimed to evaluate cell lines commonly used in virus diagnosis and isolation for their susceptibility to SARS-CoV-2. While multiple kidney cell lines from monkeys were susceptible and permissive to SARS-CoV-2, many cell types derived from human, dog, mink, cat, mouse, or chicken were not. Analysis of MDCK cells, which are most commonly used for surveillance and study of influenza viruses, demonstrated that they were insusceptible to SARS-CoV-2 and that the cellular barrier to productive infection was due to low expression level of the angiotensin converting enzyme 2 (ACE2) receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by over-expression of canine ACE2 in trans. Moreover, SARS-CoV-2 cell tropism did not appear to be affected by a D614G mutation in the spike protein.
Indole-3-glycerolphosphate synthase, a branchpoint for the biosynthesis of tryptophan, indole, and benzoxazinoids in maize
Authors: Richter Annett , Powell Adrian F. , Mirzaei Mahdieh , Wang Lucy J. , Movahed Navid , Miller Julia K. , Piñeros Miguel A. , Jander Georg
Published: January 2021

The maize (Zea mays) genome encodes three indole-3-glycerolphosphate synthase enzymes (IGPS1, 2, and 3) catalyzing the conversion of 1-(2-carboxyphenylamino)-l-deoxyribulose-5-phosphate to indole-3-glycerolphosphate. Three further maize enzymes (BX1, benzoxazinoneless 1; TSA, tryptophan synthase α subunit; and IGL, indole glycerolphosphate lyase) convert indole-3-glycerolphosphate to indole, which is released as a volatile defense signaling compound and also serves as a precursor for the biosynthesis of tryptophan and defense-related benzoxazinoids. Phylogenetic analyses showed that IGPS2 is similar to enzymes found in both monocots and dicots, whereas maize IGPS1 and IGPS3 are in monocot-specific clades. Fusions of yellow fluorescent protein (YFP) with maize IGPS enzymes and indole-3-glycerolphosphate lyases were all localized in chloroplasts. In bimolecular fluorescence complementation assays, IGPS1 interacted strongly with BX1 and IGL, IGPS2 interacted primarily with TSA, and IGPS3 interacted equally with all three indole-3-glycerolphosphate lyases. WhereasIGPS1andIGPS3expression was induced by insect feeding,IGPS2expression was not. Transposon insertions inIGPS1andIGPS3reduced the abundance of both benzoxazinoids and free indole.Spodoptera exigua(beet armyworm) larvae show improved growth onigps1mutant maize plants. Together, these results suggest that IGPS1 and IGPS3 function mainly in the biosynthesis of defensive metabolites, whereas IGPS2 may be involved in the biosynthesis of tryptophan. This metabolic channeling is similar, though less exclusive than that proposed for the three maize indole-3-glycerolphosphate lyases.
Distinct roles and actions of PDI family enzymes in catalysis of nascent-chain disulfide formation
Authors: Hirayama Chihiro , Machida Kodai , Noi Kentaro , Murakawa Tadayoshi , Okumura Masaki , Ogura Teru , Imataka Hiroaki , Inaba Kenji
Published: January 2021

The mammalian endoplasmic reticulum (ER) harbors more than 20 members of the protein disulfide isomerase (PDI) family that act to maintain proteostasis. Herein, we developed anin vitrosystem for directly monitoring PDI- or ERp46-catalyzed disulfide bond formation in ribosome-associated nascent chains (RNC) of human serum albumin. The results indicated that ERp46 more efficiently introduced disulfide bonds into nascent chains with short segments exposed outside the ribosome exit site than PDI. Single-molecule analysis by high-speed atomic force microscopy further revealed that PDI binds nascent chains persistently, forming a stable face-to-face homodimer, whereas ERp46 binds for a shorter time in monomeric form, indicating their different mechanisms for substrate recognition and disulfide bond introduction. Similarly to ERp46, a PDI mutant with an occluded substrate-binding pocket displayed shorter-time RNC binding and higher efficiency in disulfide introduction than wild-type PDI. Altogether, ERp46 serves as a more potent disulfide introducer especially during the early stages of translation, whereas PDI can catalyze disulfide formation in RNC when longer nascent chains emerge out from ribosome.
Mutagenesis Mapping of RNA Structures within the Foot-and-Mouth Disease Virus Genome Reveals Functional Elements Localised in the Polymerase (3Dpol) Encoding Region
Authors: Lasecka-Dykes Lidia , Tulloch Fiona , Simmonds Peter , Luke Garry A. , Ribeca Paolo , Gold Sarah , Knowles Nick J. , Wright Caroline F. , Wadsworth Jemma , Azhar Mehreen , King Donald P. , Tuthill Tobias J. , Jackson Terry , Ryan Martin D.
Published: January 2021

RNA structure plays a crucial role in the replication of positive sense RNA viruses and can form functional elements within the untranslated regions (UTRs) and the protein coding sequences (or open reading frames (ORFs)). While RNA structures in the UTRs of several picornaviruses have been functionally characterised, the roles of putative RNA structures predicted for the ORF remain largely undefined. Here we have undertaken a bioinformatic analysis of the foot-and-mouth disease virus (FMDV) genome and predicted the existence of 53 evolutionarily conserved RNA structures within the ORF. Forty-five (45) of these structures were located in the regions encoding the non-structural proteins (nsps). To investigate if the structures in the regions encoding the nsps are required for FMDV replication we used a mutagenesis method, CDLR mapping, where sequential coding segments were shuffled to minimise RNA secondary structures while preserving protein coding, native dinucleotide frequencies and codon usage. To examine the impact of these changes on replicative fitness, mutated sequences were inserted into an FMDV sub-genomic replicon. We found that three of the RNA structures, all at the 3’ termini of the FMDV ORF, were critical for replicon replication. Contrastingly, disruption of the other 42 conserved RNA structures that lie within the regions encoding the nsps had no effect on replicon replication, suggesting that these structures are not required for initiating translation or replication of viral RNA. Conserved RNA structures that are not essential for virus replication could provide ideal targets for the rational attenuation of a wide range of FMDV strains.

Importance

Some RNA structures formed by the genomes of RNA viruses are critical for viral replication. Our study shows that of 45 conserved RNA structures located within the regions of the foot-and-mouth disease virus (FMDV) genome that encode the non-structural proteins, only three are essential for replication of an FMDV sub-genomic replicon. Replicons replication is dependent on RNA translation and synthesis; thus, our results suggest that the three RNA structures are critical for either initiation of viral RNA translation and/or viral RNA synthesis. Although further studies are required to identify if the remaining 42 RNA structures have other roles in virus replication, they may provide targets for the rational large-scale attenuation of a wide range of FMDV strains. FMDV causes a highly contagious disease posing a constant threat to global livestock industries. Such weakened FMDV strains could be investigated as live-attenuated vaccines or could enhance biosecurity of conventional inactivated vaccine production.
Molecular epidemiology of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire (UK) 2008-2018
Authors: Lipworth Samuel , Vihta Karina-Doris , Chau Kevin , Barker Leanne , George Sophie , Kavanagh James , Davies Timothy , Vaughan Alison , Andersson Monique , Jeffery Katie , Oakley Sarah , Morgan Marcus , Hopkins Susan , Peto Timothy E. A. , Crook Derrick W. , Walker Ann Sarah , Stoesser Nicole
Published: January 2021

The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however the causes of this are unclear and effective interventions are therefore hard to design. In this study we sequenced 3468 sequential, unselected isolates over a decade in Oxfordshire, UK. We demonstrate that the observed increases in E. coli incidence were not driven by clonal expansion; instead, four major sequence types (STs) continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp. most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types; consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs). Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs, and suggests that no single specific pathogen genetic factors are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks.