bluuebunny/crossref_metadata_2025 huggingface dataset:
MAXIMUM LIKELIHOOD ESTIMATION OF THE NUMBER OF NUCLEOTIDE SUBSTITUTIONS FROM RESTRICTION SITES DATA
Authors: Nei Masatoshi , Tajima Fumio
Published: January 2021

A simple method of the maximum likelihood estimation of the number of nucleotide substitutions is presented for the case where restriction sites data from many different restriction enzymes are available. An iteration method, based on nucleotide counting, is also developed. This method is simpler than the maximum likelihood method but gives the same estimate. A formula for computing the variance of a maximum likelihood estimate is also presented.
O-GlcNAcAtlas: A database of experimentally identified O-GlcNAc sites and proteins
Authors: Ma Junfeng , Li Yaoxiang , Hou Chunyan , Wu Ci
Published: January 2021

O-linked β-N-acetylglucosamine (O-GlcNAc) is a post-translational modification (i.e., O-GlcNAcylation) on the serine/threonine residues of proteins. As a unique intracellular monosaccharide modification, protein O-GlcNAcylation plays important roles in almost all biochemical processes examined. Aberrant O-GlcNAcylation underlies the etiologies of a number of chronic diseases. With the tremendous improvement of techniques, thousands of proteins along with their O-GlcNAc sites have been reported. However, until now, there are few databases dedicated to accommodate the rapid accumulation of such information. Thus, O-GlcNAcAtlas is created to integrate all experimentally identified O-GlcNAc sites and proteins. O-GlcNAcAtlas consists of two datasets (Dataset-I and Dataset-II, for unambiguously identified sites and ambiguously identified sites, respectively), representing a total number of 4571 O-GlcNAc modified proteins from all species studied from 1984 to 31 Dec 2019. For each protein, comprehensive information (including species, sample type, gene symbol, modified peptides and/or modification sites, site mapping methods and literature references) is provided. To solve the heterogeneity among the data collected from different sources, the sequence identity of these reported O-GlcNAc peptides are mapped to the UniProtKB protein entries. To our knowledge, O-GlcNAcAtlas is a highly comprehensive and rigorously curated database encapsulating all O-GlcNAc sites and proteins identified in the past 35 years. We expect that O-GlcNAcAtlas will be a useful resource to facilitate O-GlcNAc studies and computational analyses of protein O-GlcNAcylation. The public version of the web interface to the O-GlcNAcAtlas can be found at http://oglcnac.org/.
Sub-Saharan African information potential to unveil adaptations to infectious disease
Authors: Pedro Nicole , Pinto Ricardo J , Cavadas Bruno , Pereira Luisa
Published: January 2021

Sub-Saharan Africa is the most promising region of the world to conduct high-throughput studies to unveil adaptations to infectious diseases due to several reasons, namely, the longest evolving time-depth in the Homo sapiens phylogenetic tree (at least two-third older than any other worldwide region); the continuous burden of infectious diseases (still number one in health/life threat); and the coexistence of populations practising diverse subsistence modes (nomadic or seminomadic hunter-gatherers and agropastoralists, and sedentary agriculturalists, small urban and megacity groups). In this review, we will present the most up-to-date results that shed light on three main hypotheses related with this adaptation. One is the hypothesis of coevolution between host and pathogen, given enough time for the establishment of this highly dynamic relationship. The second hypothesis enunciates that the agricultural transition was responsible for the increase of the infectious disease burden, due to the huge expansion of the sedentary human population and the cohabitation with domesticates as main reservoirs of pathogens. The third hypothesis states that the boosting of our immune system against pathogens by past selection may have resulted in maladaptation of the developed hygienic societies, leading to an increase of allergic, inflammatory and autoimmune disorders. Further work will enlighten the biological mechanisms behind these main adaptations, which can be insightful for translation into diagnosis, prognosis and treatment interventions.
Occupational exposure to respirable crystalline silica and risk of autoimmune rheumatic diseases: a nationwide cohort study
Authors: Boudigaard Signe Hjuler , Schlünssen Vivi , Vestergaard Jesper Medom , Søndergaard Klaus , Torén Kjell , Peters Susan , Kromhout Hans , Kolstad Henrik A
Published: January 2021

Background

Exposure to respirable crystalline silica is suggested to increase the risk of autoimmune rheumatic diseases. We examined the association between respirable crystalline silica exposure and systemic sclerosis, rheumatoid arthritis, systemic lupus erythematosus and small vessel vasculitis.

Methods

In a cohort study of the total Danish working population, we included 1 541 505 male and 1 470 769 female workers followed since entering the labour market 1979–2015. Each worker was annually assigned a level of respirable crystalline silica exposure estimated with a quantitative job exposure matrix. We identified cases of autoimmune rheumatic diseases in a national patient register and examined sex-specific exposure-response relations by cumulative exposure and other exposure metrics.

Results

We identified 4673 male and 12 268 female cases. Adjusted for age and calendar year, men exposed to high levels of respirable crystalline silica compared with non-exposed showed increased incidence rate ratio (IRR) for the four diseases combined of 1.53 [95% confidence interval (CI): 1.39–1.69], for systemic sclerosis of 1.62 (1.08–2.44) and rheumatoid arthritis of 1.57 (1.41–1.75). The overall risk increased with increasing cumulative exposure attained since entering the workforce [IRR: 1.07 (1.05–1.09) per 50 µg/m3-years]. Female workers were less exposed to respirable crystalline silica, but showed comparable risk patterns with overall increased risk with increasing cumulative exposure [IRR: 1.04 (0.99–1.10) per 50 µg/m3-years].

Conclusions

This study shows an exposure-dependent association between occupational exposure to respirable crystalline silica and autoimmune rheumatic diseases and thus suggests causal effects, most evident for systemic sclerosis and rheumatoid arthritis.
Moving toward a sociotechnical systems approach to continuous health information technology design: the path forward for improving electronic health record usability and reducing clinician burnout
Authors: Carayon Pascale , Salwei Megan E
Published: January 2021

Based on our analysis of descriptions provided by four EHR vendors on their EHR usability efforts, we provide three recommendations aimed at improving the usability of health information technology and reducing clinician burnout. First, EHR vendors need to dedicate increased attention to the design of the entire sociotechnical (work) system, including the EHR technology and its usability as well as the interactions of the technology with other system elements. Second, EHR vendors need to deepen and broaden their understanding of the work of clinicians and care teams by using diverse and mixed method. Third, in collaboration with health care organizations, EHR vendors should engage in cycles of continuous design and learning in order to improve the usability of health IT.
Ambulatory physicians’ electronic health record self-efficacy
Authors: Hellems Martha Ann
Published: January 2021

Ambulatory providers were administered an EHR skills self-assessment survey to assess their confidence in learning about and using the electronic health record (EHR). Seventy-one providers participated. Only 35% of respondents felt that they had strong EHR skills, 92% felt confident that they could learn new skills, and 90% felt they could improve with practice. Forty-five percent of faculty physicians felt confident that they could use the EHR in a time-efficient manner and 52% felt could keep up with advances but 16% felt apprehensive about using the EHR. Ninety-four percent of faculty would welcome opportunities to learn more. These results suggest that most providers view using the EHR as a clinical skill they can master with training and practice and that physicians may be engaged by EHR training programs that focus on the use of the EHR as a clinical skill. This work has informed new training programs at our institution.
Spatiotemporal variations in fine-scale habitat use of the world’s second largest population of humpback dolphins
Authors: Liu Mingming , Lin Mingli , Dong Lijun , Zhang Peijun , Li Songhai
Published: January 2021

We assessed habitat use by the population of Indo-Pacific humpback dolphin, Sousa chinensis, in the waters off Zhanjiang, China, by performing boat-based surveys between 2013 and 2018. In total, we gathered 253 sightings of humpback dolphins. To assess habitat use of humpback dolphins within the study area, we measured two spatial metrics at each sighting site: WDT (tide-calibrated water-depth) and DS (distance to the nearest shore). Results showed that dolphins mainly were observed in shallow (WDT: 8.46 ± 5.13 m, mean ± SD) and inshore (DS: 2.17 ± 2.14 km) waters. Their preference of inhabiting shallow waters was more apparent during the wet season (April–September) than during the dry season (October–March); however, they were encountered in waters much closer to shore during the dry season than the wet season. By weighting survey effort, our sighting density maps further confirmed that humpback dolphins changed their habitat use between wet and dry seasons. Such spatiotemporal variations in dolphin habitat use might be associated with spatiotemporal movements of their prey. Our findings provide insights into variations in fine-scale habitat use of inshore apex predators, and also assist to designate proper conservation measures for these vulnerable animals.
3D mapping of the Crab Nebula with SITELLE – I. Deconvolution and kinematic reconstruction
Authors: Martin T , Milisavljevic D , Drissen L
Published: January 2021

We present a hyperspectral cube of the Crab Nebula obtained with the imaging Fourier transform spectrometer SITELLE on the Canada–France–Hawaii telescope. We describe our techniques used to deconvolve the 310 000 individual spectra ($R = 9\, 600$) containing Hα, [N ii] λλ6548, 6583, and [S ii] λλ6716, 6731 emission lines and create a detailed 3D reconstruction of the supernova (SN) remnant (SNR) assuming uniform global expansion. We find that the general boundaries of the 3D volume occupied by the Crab are not strictly ellipsoidal as commonly assumed, and instead appear to follow a ‘heart-shaped’ distribution that is symmetrical about the plane of the pulsar wind torus. Conspicuous restrictions in the bulk distribution of gas consistent with constrained expansion coincide with positions of the dark bays and east–west band of He-rich filaments, which may be associated with interaction with a pre-existing circumstellar disc. The distribution of filaments follows an intricate honeycomb-like arrangement with straight and rounded boundaries at large and small scales that are anticorrelated with distance from the centre of expansion. The distribution is not unlike the large-scale rings observed in SNRs 3C 58 and Cassiopeia A, where it has been attributed to turbulent mixing processes that encouraged outwardly expanding plumes of radioactive 56Ni-rich ejecta. These characteristics reflect critical details of the original SN of 1054 CE and its progenitor star, and may favour a low-energy explosion of an iron-core progenitor. We demonstrate that our main findings are robust despite regions of non-homologous expansion driven by acceleration of material by the pulsar wind nebula.
Power spectrum multipole expansion for H i intensity mapping experiments: unbiased parameter estimation
Authors: Soares Paula S , Cunnington Steven , Pourtsidou Alkistis , Blake Chris
Published: January 2021

We assess the performance of the multipole expansion formalism in the case of single-dish H i intensity mapping, including instrumental and foreground removal effects. This formalism is used to provide Markov chain Monte Carlo forecasts for a range of H i and cosmological parameters, including redshift space distortions and the Alcock–Paczynski effect. We first determine the range of validity of our power spectrum modelling by fitting to simulation data, concentrating on the monopole, quadrupole, and hexadecapole contributions. We then show that foreground subtraction effects can lead to severe biases in the determination of cosmological parameters, in particular the parameters relating to the transverse Baryon Acoustic Oscillations (BAO) rescaling, the growth rate, and the H i bias (α⊥, $\overline{T}_\rm{H{\small I}}f\sigma _8$, and $\overline{T}_{\mathrm {H}\,{\small I}}b_{\mathrm {H}\,{\small I}}\sigma _8$, respectively). We attempt to account for these biases by constructing a two-parameter foreground modelling prescription, and find that our prescription leads to unbiased parameter estimation at the expense of increasing the estimated uncertainties on cosmological parameters. In addition, we confirm that instrumental and foreground removal effects significantly impact the theoretical covariance matrix, and cause the covariance between different multipoles to become non-negligible. Finally, we show the effect of including higher order multipoles in our analysis, and how these can be used to investigate the presence of instrumental and systematic effects in H i intensity mapping data.
A heme•DNAzyme activated by hydrogen peroxide catalytically oxidizes thioethers by direct oxygen atom transfer rather than by a Compound I-like intermediate
Authors: Shumayrikh Nisreen M , Warren Jeffrey J , Bennet Andrew J , Sen Dipankar
Published: January 2021

Hemin [Fe(III)-protoporphyrin IX] is known to bind tightly to single-stranded DNA and RNA molecules that fold into G-quadruplexes (GQ). Such complexes are strongly activated for oxidative catalysis. These heme•DNAzymes and ribozymes have found broad utility in bioanalytical and medicinal chemistry and have also been shown to occur within living cells. However, how a GQ is able to activate hemin is poorly understood. Herein, we report fast kinetic measurements (using stopped-flow UV–vis spectrophotometry) to identify the H2O2-generated activated heme species within a heme•DNAzyme that is active for the oxidation of a thioether substrate, dibenzothiophene (DBT). Singular value decomposition and global fitting analysis was used to analyze the kinetic data, with the results being consistent with the heme•DNAzyme's DBT oxidation being catalyzed by the initial Fe(III)heme–H2O2 complex. Such a complex has been predicted computationally to be a powerful oxidant for thioether substrates. In the heme•DNAzyme, the DNA GQ enhances both the kinetics of formation of the active intermediate as well as the oxidation step of DBT by the active intermediate. We show, using both stopped flow spectrophotometry and EPR measurements, that a classic Compound I is not observable during the catalytic cycle for thioether sulfoxidation.
Characterization of Electronic Cigarette Warning Statements Portrayed in YouTube Videos
Authors: Jones Dina M , Guy Mignonne C , Soule Eric , Sakuma Kari-Lyn K , Pokhrel Pallav , Orloff Mohammed , Trinidad Dennis , Smith Denelle , Browley Sharaka , Walker A Paige , Bullock Sandilyn , Eissenberg Thomas , Fagan Pebbles
Published: January 2021

Introduction

In 2018, the United States Food and Drug Administration (FDA) required that electronic cigarette (e-cigarette) manufacturers, packagers, importers, distributors, and retailers display an addictive or alternate warning statement on e-cigarette visual advertisements. Few studies have investigated the FDA-mandated and other warnings on social media. This study examined the prevalence and content of warning statements in e-cigarette-related YouTube videos.

Methods

In 2019, The Virginia Commonwealth University Center for the Study of Tobacco Products conducted bi-monthly (February-June) YouTube searches by relevance and view count to identify e-cigarette-related videos. Overall, 178 videos met the inclusion criteria. Staff coded each video for the presence of a visual/verbal warning statement, warning statement type (eg, FDA-mandated, addiction/tobacco, safety/toxic exposure, health effects), sponsorship, and tobacco product characteristics. A data extraction tool collected the video URL, title, upload date, and number of views, likes/dislikes, and comments.

Results

Only 5.1% of videos contained FDA-mandated and 21.9% contained non-mandated warnings. All videos with FDA-mandated and 46.2% of non-mandated warnings were represented visually. Only 13.1% of industry-sponsored videos uploaded after the mandate effective date had an FDA-mandated warning statement and videos with FDA-mandated and non-mandated (v. no) warnings had significantly fewer views, likes, dislikes, and comments. Among all non-mandated warnings, 31.3% featured an addiction/tobacco, 18.8% a safety/toxic exposure, and 37.5% a health effects warning.

Conclusions

The prevalence of FDA-mandated warning statements in e-cigarette related YouTube videos was low. FDA enforcement of the warning statement mandate on YouTube could increase the public’s understanding of the addictive nature of nicotine in e-cigarettes.

Implications

The FDA has the authority to regulate the advertisement and promotion of e-cigarettes on the Internet. These data can inform future FDA requirements related to the language content and visual representation of addiction/tobacco, safety/exposure, and health effects warning statements that appear in YouTube videos and other visual social media popular among young people. Such data would help consumers make informed decisions about purchasing e-cigarette products, using e-cigarettes, and avoiding unintentional harm related to e-cigarettes. In addition, these data may help social media platforms make decisions on whether they will prohibit advertisements that promote or facilitate the sale of tobacco products.
Health Claims, Marketing Appeals, and Warnings on Popular Brands of Waterpipe Tobacco Packaging Sold in the United States
Authors: Sutfin Erin L , Lazard Allison J , Soule Eric K , Kimes Caroline M , King Jessica , Jenson Desmond , Ross Jennifer Cornacchione
Published: January 2021

Introduction

Waterpipe tobacco (WT) smoking is associated with misperceptions of harm, especially among users. WT packaging contains imagery, flavor descriptors, and text claims that may contribute to misperceptions. The study goal was to characterize visual and text elements of WT packaging.

Aims and Methods

Using data from the U.S. Population Assessment on Tobacco and Health Study Wave 2 (October 2014–October 2015), we identified the 10 most popular WT brands. For each brand, we identified available flavors, including flavor collections with unique packaging elements. We randomly selected 10 flavors per brand for purchase (March–April 2018). We conducted descriptive content analysis to code all textual and visual design elements of each package.

Results

Over half (54%) of WT packages had modified risk tobacco product (MRTP) claims prohibited by federal law, including substance-free MRTP claims (43%) and the descriptor “natural” (11%). No MRTP reduced exposure or reduced risk claims were found. Over a quarter (26%) of packaging including one or more of terms that may imply reduced harm including “fresh,” “premium,” “quality,” and “pure.” All packages included a text-only warning, yet none appeared on the primary display panel. Almost all packaging (99%) included imagery, with 72% including flavor imagery. The majority of packages (72%) included a smoking cue. The most popular marketing appeals were “well-made” (57%), “enjoyable” (55%), and “patriotic” (47%).

Conclusions

Prohibited MRTP claims, other descriptors, and flavor imagery are common on WT packaging, despite federal law. Future research is needed to evaluate if this marketing contributes to misperceptions of reduced harm.

Implications

Tobacco packaging is used to convey health-related messages, both explicitly and implicitly; however, information about WT packaging is virtually nonexistent. We conducted a content analysis of WT packaging from the 10 most popular US brands. Over half (54%) of packages had prohibited MRTP claims and over a quarter (26%) included one or more descriptors that may be perceived as implying reduced harm. Use of imagery, including smoking cues, was common. The widespread use of prohibited MRTP claims, other descriptors, and imagery on WT packaging may contribute to misperceptions of reduced harm.
Successive variational approach with the tensor-optimized antisymmetrized molecular dynamics for the 5He nucleus
Authors: Myo Takayuki , Lyu Mengjiao , Toki Hiroshi , Horiuchi Hisashi
Published: January 2021

We study $^5$He variationally as the first $p$-shell nucleus in the tensor-optimized antisymmetrized molecular dynamics (TOAMD) using the bare nucleon–nucleon interaction without any renormalization. In TOAMD, the central and tensor correlation operators promote the AMD’s Gaussian wave function to a sophisticated many-body state including the short-range and tensor correlations with high-momentum nucleon pairs. We develop a successive approach by applying these operators successively with up to double correlation operators to get converging results. We obtain satisfactory results for $^5$He, not only for the ground state but also for the excited state, and discuss explicitly the correlated Hamiltonian components in each state. We also show the importance of the independent optimization of the correlation functions in the variation of the total energy beyond the condition assuming common correlation forms used in the Jastrow approach.
High-sensitivity cardiac troponin T and the risk of heart failure in postmenopausal women of the ARIC Study
Authors: Ebong Imo A. , Wilson Machelle D. , Bertoni Alain G. , Appiah Duke , Polonsky Tamar , Michos Erin D. , Ballantyne Christie , Chang Patricia
Published: January 2021

Objective:

We investigated isolated and joint effects of early menopause (occurrence before 45 y of age) and high-sensitivity cardiac troponin T elevation (hs-cTnT ≥ 14 ng/L) on heart failure (HF) incidence in postmenopausal women.

Methods:

We included 2,276 postmenopausal women, aged 67-90 years, with hs-cTnT measurements and without prevalent HF from the Atherosclerosis Risk in Communities study Visit 5 (2011-2013). Women were categorized according to early menopause and hs-cTnT group. Cox proportional hazards models were used for analysis.

Results:

Over a median follow-up of 5.5 years, we observed 104 HF events. The incidence rates of HF were greater in women with hs-cTnT elevation when compared to those without hs-cTnT elevation. In unadjusted analysis, the hazard ratios for incident HF were threefold greater in women with hs-cTnT elevation, with or without early menopause, (3.03 [95% CI, 1.59-5.77]) and (3.29 [95% CI, 2.08-5.21]), respectively, but not significantly greater in women with early menopause without hs-cTnT elevation, when compared to women with neither early menopause nor hs-cTnT elevation at Visit 5. After adjusting for HF risk factors and NT-pro B-type natriuretic peptide, these associations were attenuated and became nonsignificant for women with hs-cTnT elevation, but became stronger and significant for women with early menopause without hs-cTnT elevation (2.39 [95% CI, 1.28-4.46]).

Conclusions:

Irrespective of early menopause status, hs-cTnT elevation is associated with greater HF incidence but this association is partially explained by HF risk factors. Even in the absence of hs-cTnT elevation, early menopause is significantly associated with HF incidence after accounting for HF risk factors.

Video Summary:
http://links.lww.com/MENO/A693.
Treatment with a dual amylin and calcitonin receptor agonist improves metabolic health in an old, obese, and ovariectomized rat model
Authors: Katri Anna , Reker Ditte , Karsdal Morten A. , Bay-Jensen Anne-Christine , Henriksen Kim
Published: January 2021

Objectives:

Menopause is often characterized by detrimental metabolic changes, such as obesity, insulin resistance, and impaired glucose tolerance, often requiring treatment. KeyBioscience Peptides (KBPs) are Dual Amylin and Calcitonin Receptor Agonists which have shown promising metabolic effects in rats. The objective of this study was to investigate the in vivo effect of KBP on the metabolic health in a model driven by unhealthy diet, age, and menopause.

Methods:

Female Sprague Dawley rats were fed a high-fat diet (HFD) for 3 months before the initiation of the study. At 6 months of age the rats were randomized into groups (n = 12) and subjected to ovariectomy surgery and treatment with KBP: (1) Lean-Sham, (2) HFD-Sham, (3) Lean-OVX, (4) HFD-OVX, (5) HFD-OVX-KBP (10 μg/kg/d), (6) HFD-OVX-KBP (20 μg/kg/d), (7) HFD-OVX-EE2 (30 μg/d 17a-ethynylestradiol). Body weight, food intake, oral glucose tolerance tests (OGTTs), subcutaneous fat, visceral fat, liver weight, and uterus weight were assessed during the 6-month study. Statistical analyses were conducted by one-way ANOVA with Tukey post-hoc test for multiple comparisons.

Results:

Combination of OVX and HFD led to significant induction of obesity (31% weight increase, P < 0.001) and insulin resistance (13% increase in tAUCglucose during OGTT P < 0.01) compared with the relevant control groups (P < 0.05), and this could be completely rescued by EE2 therapy confirming the model system (P < 0.05).

Treatment of OVX-HFD rats with KBP for 26 weeks led to a significant reduction in body weight (13%, P < 0.001) in the high dose and 9% (P < 0.01) in the low dose, with corresponding improvements in fat depot sizes, all compared with HFD-OVX controls. As expected, food intake was suppressed, albeit mainly in the first 2 weeks of treatment, resulting in a reduction of overall caloric intake by 6.5% (P < 0.01) and 12.5% (P < 0.001) in the low and high doses respectively. Furthermore, treatment with KBP reduced the weight of visceral and subcutaneous fat tissues. Finally, KBP treatment significantly improved glucose tolerance, assessed using OGTTs at weeks 8, 16, and 24.

Conclusions:

The data presented here clearly indicate a positive and sustained effect of KBP treatment on body weight loss, fat depot size, and improved glucose tolerance, illustrating the potential of KBPs as treatments for metabolic complications of overweight and menopause.
Cosmetic Endocrinology
Authors: Gay Steven
Published: January 2021

Cosmetic endocrinology treats endocrine pathophysiologies to improve cosmetically bothersome physical exam findings for the patient. Here we review the general cosmetic changes in PCOS with an emphasis on targeted cosmetic medical therapies.
Sex- and Gender-Dependent Differences in Clinical and Preclinical Sepsis
Authors: Zhang Meng Qi , Macala Kimberly F. , Fox-Robichaud Alison , Mendelson Asher A. , Lalu Manoj M.
Published: January 2021

In this mini-review we provide an overview of sex- and gender-dependent issues in both clinical and preclinical sepsis. The increasing recognition for the need to account for sex and gender in biomedical research brings a unique set of challenges and requires researchers to adopt best practices when conducting and communicating sex- and gender-based research. This may be of particular importance in sepsis, given the potential contribution of sex bias in the failures of translational sepsis research in adults and neonates. Clinical evidence of sex-dependent differences in sepsis is equivocal. Since clinical studies are limited to observational data and confounded by a multitude of factors, preclinical studies provide a unique opportunity to investigate sex differences in a controlled, experimental environment. Numerous preclinical studies have suggested that females may experience favorable outcomes in comparison with males. The underlying mechanistic evidence for sex-dependent differences in sepsis and other models of shock (e.g., trauma-hemorrhage) largely centers around the beneficial effects of estrogen. Other mechanisms such as the immunosuppressive role of testosterone and X-linked mosaicism are also thought to contribute to observed sex- and gender-dependent differences in sepsis. Significant knowledge gaps still exist in this field. Future investigations can address these gaps through careful consideration of sex and gender in clinical studies, and the use of clinically accurate preclinical models that reflect sex differences. A better understanding of sex-and gender-dependent differences may serve to increase translational research success.
A novel mechanism of regulation of the transcription factor GLI3 by toll-like receptor signaling
Authors: Matissek Stephan J. , Han Weiguo , Hage Adam , Karbalivand Mona , Rajsbaum Ricardo , Elsawa Sherine F.
Published: January 2021

The transcription factor GLI3 is a member of the GLI family and has been shown to be regulated by canonical hedgehog (HH) signaling through smoothened (SMO). Little is known about SMO-independent regulation of GLI3. Here, we identify TLR signaling as a novel pathway regulating GLI3 expression. We show that GLI3 expression is induced by LPS/TLR4 in human monocyte cell lines and peripheral blood CD14+cells. Further analysis identified TRIF, but not MyD88, signaling as the adapter used by TLR4 to regulate GLI3. Using pharmacological and genetic tools, we identified IRF3 as the transcription factor regulating GLI3 downstream of TRIF. Furthermore, using additional TLR ligands that signal exclusively through TRIF such as the TLR4 ligand, MPLA and the TLR3 ligand, Poly(I:C), we confirm the role of TRIF-IRF3 in the regulation of GLI3. We found that IRF3 directly binds to the GLI3 promoter region and this binding was increased upon stimulation of TRIF-IRF3 with Poly(I:C). Furthermore, using IRF3−/−MEFs, we found that Poly(I:C) stimulation no longer induced GLI3 expression. Finally, using macrophages from mice lacking Gli3 expression in myeloid cells (M-Gli3−/−), we found that in the absence of Gli3, LPS stimulated macrophages secrete less CCL2 and TNF-α compared with macrophages from wild-type (WT)mice. Taken together, these results identify a novel TLR-TRIF-IRF3 pathway that regulates the expression of GLI3 that regulates inflammatory cytokines and expands our understanding of the non-canonical signaling pathways involved in the regulation of GLI transcription factors.
Lysosomal retargeting of Myoferlin mitigates membrane stress to enable pancreatic cancer growth
Authors: Gupta Suprit , Yano Julian , Htwe Htet Htwe , Shin Hijai R. , Cakir Zeynep , Ituarte Thomas , Wen Kwun W. , Kim Grace E. , Zoncu Roberto , Dawson David W. , Perera Rushika M.
Published: January 2021

Lysosomes must maintain integrity of their limiting membrane to ensure efficient fusion with incoming organelles and degradation of substrates within their lumen. Pancreatic cancer cells upregulate lysosomal biogenesis to enhance nutrient recycling and stress resistance, but whether dedicated programs for maintaining lysosomal membrane integrity facilitate pancreatic cancer growth is unknown. Using proteomic-based organelle profiling, we identify the Ferlin family plasma membrane repair factor, Myoferlin, as selectively and highly enriched on the membrane of pancreatic cancer lysosomes. Mechanistically, lysosome localization of Myoferlin is necessary and sufficient for maintenance of lysosome health and provides an early-acting protective system against membrane damage that is independent from the endosomal sorting complex required for transport (ESCRT)-mediated repair network. Myoferlin is upregulated in human pancreatic cancer, predicts poor survival, and its ablation severely impairs lysosome function and tumour growthin vivo. Thus, retargeting of plasma membrane repair factors enhances pro-oncogenic activities of the lysosome.
OPA1 Deletion in Brown Adipose Tissue Improves Thermoregulation and Systemic Metabolism via FGF21
Authors: Pereira Renata O. , Marti Alex , Olvera Angela C. , Tadinada Satya M. , Bjorkman Sarah H. , Weatherford Eric T. , Westphal Michael , Patel Pooja H. , Kirby Ana K. , Hewezi Rana , Bùi Trần William , Garcia Pena Luis M , Souvenir Rhonda A. , Mittal Monika , Adams Christopher M. , Potthoff Matthew J. , Abel E. Dale
Published: January 2021

Adrenergic stimulation of brown adipocytes alters mitochondrial dynamics, including proteolytic processing of the mitochondrial fusion protein optic atrophy 1 (OPA1). However, direct mechanisms linking OPA1 to brown adipose tissue (BAT) physiology are incompletely understood. By deleting OPA1 selectively in BAT (OPA1 BAT KO), we demonstrate that OPA1 is required for cold-induced thermogenesis. Unexpectedly, OPA1 deficiency induced fibroblast growth factor 21 (FGF21) as a BATokine in an activating transcription factor 4 (ATF4)- dependent manner. BAT-derived FGF21 mediates an adaptive response in OPA1 BAT KO mice, by inducing browning of white adipose tissue (WAT), increasing resting metabolic rates, and improving thermoregulation. However, FGF21 does not mediate the resistance to diet-induced obesity observed in these animals. These findings reveal a requirement for OPA1 in BAT thermogenesis, and uncovers a homeostatic mechanism of BAT-mediated metabolic protection governed by an ATF4-FGF21 axis, that is activated independently of BAT thermogenic function.
The impact of COVID-19 vaccination campaigns accounting for antibody-dependent enhancement
Authors: Adil Nessma M. Y. , Obama H. Christian Tsoungui , Ngucho Jordan Y. , Kwamou S. Frank , Kayanula Loyce , Kamanga George , Ibrahim Toheeb B. , Iliya Patience Bwanu , Iyanda Sulyman , Alawam Looli , Helle Kristina B. , Teboh-Ewungkem Miranda I. , Schneider Kristan A.
Published: January 2021

Background

COVID-19 vaccines are approved, vaccination campaigns are launched, and worldwide return to normality seems within close reach. Nevertheless, concerns about the safety of COVID-19 vaccines arose, due to their fast emergency approval. In fact, the problem of antibody-dependent enhancement was raised in the context of COVID-19 vaccines.

Methods and findings

We introduce a complex extension of the model underlying the pandemic preparedness tool CovidSim 1.1 (http://covidsim.eu/) to optimize vaccination strategies with regard to the onset of campaigns, vaccination coverage, vaccination schedules, vaccination rates, and efficiency of vaccines. Vaccines are not assumed to immunize perfectly. Some individuals fail to immunize, some reach only partial immunity, and – importantly – some develop antibody-dependent enhancement, which increases the likelihood of developing symptomatic and severe episodes (associated with higher case fatality) upon infection. Only a fraction of the population will be vaccinated, reflecting vaccination hesitancy or contraindications. The model is intended to facilitate decision making by exploring ranges of parameters rather than to be fitted by empirical data.

We parameterized the model to reflect the situation in Germany and predict increasing incidence (and prevalence) in early 2021 followed by a decline by summer. Assuming contact reductions (curfews, social distancing, etc.) to be lifted in summer, disease incidence will peak again. Fast vaccine deployment contributes to reduce disease incidence in the first quarter of 2021, and delay the epidemic outbreak after the summer season. Higher vaccination coverage results in a delayed and reduced epidemic peak. A coverage of 75% - 80% is necessary to prevent an epidemic peak without further drastic contact reductions.

Conclusions

With the vaccine becoming available, compliance with contact reductions is likely to fade. To prevent further economic damage from COVID-19, high levels of immunization need to be reached before next year’s flu season, and vaccination strategies and disease management need to be flexibly adjusted. The predictive model can serve as a refined decision support tool for COVID-19 management.
A workflow for simultaneous detection of coding and non-coding transcripts by ribosomal RNA-depleted RNA-Seq
Authors: Potemkin Nikita , Cawood Sophie M.F. , Treece Jackson , Guévremont Diane , Rand Christy J. , McLean Catriona , Stanton Jo-Ann L. , Williams Joanna M.
Published: January 2021

RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was highly efficient, resulting in less than 1.5% rRNA content in the final library, significantly better than other reported rRNA removal techniques. We identified >30,000 unique transcripts from all samples, including protein-coding genes and many unique species of non-coding RNA, in biologically-relevant proportions. Furthermore, normalized sequencing read count for select genes significantly negatively correlated with Ct values from RT-qPCR analysis from the same samples. These results indicate that this protocol accurately and consistently identifies and quantifies a wide variety of transcripts simultaneously. The highly efficient rRNA depletion, coupled with minimized sample handling and without complicated and high-loss size selection protocols, makes this protocol useful to researchers wishing to investigate whole transcriptomes.
Metronomic therapy prevents emergence of drug resistance by maintaining the dynamic of intratumor heterogeneity
Authors: Bondarenko Maryna , Grand Marion Le , Shaked Yuval , Raviv Ziv , Chapuisat Guillemette , Carrère Cécile , Montero Marie-Pierre , Rossi Mailys , Pasquier Eddy , Carré Manon , André Nicolas
Published: January 2021

Despite recent advances in deciphering cancer drug resistance mechanisms, relapse is a widely observed phenomenon in advanced cancers, mainly due to intratumor clonal heterogeneity. How tumor clones progress and impact each other remains elusive. By better understanding clone dynamics, we could reveal valuable biological insights and unveil vulnerabilities that could be therapeutically exploited. In this study, we developed 2D and 3D non-small cell lung cancer co-culture systems and defined a phenomenological mathematical model. Our results demonstrated a dominant role of the drug-sensitive clones over the drug-resistant ones under untreated conditions. Model predictions and their experimentalin vitroandin vivovalidations indicated that metronomic schedule leads to a better regulation of tumor cell heterogeneity over time than maximum-tolerated dose schedule, while achieving control of global tumor progression. We finally showed that drug-sensitive clones exert a suppressive effect on the proliferation of the drug-resistant ones through a paracrine mechanism way, which is linked to metabolic cell clone activity. Altogether, these computational and experimental approaches allow assessment of drug schedules controlling drug-sensitive and -resistant clone balance and highlight the potential of targeting cell metabolism to manage intratumor heterogeneity.

Significance

Combined computational and experimental models reveal how drug-sensitive tumor cells exert their dominance over drug-resistant cells and how it impacts optimal chemotherapy scheduling.
Genetic analysis of DinG-family helicase YoaA and its interaction with replication clamp-loader protein HolC inE. coli
Authors: Sutera Vincent A. , Sass Thalia H. , Leonard Scott E. , Wu Lingling , Glass David J. , Giordano Gabriela G. , Zur Yonatan , Lovett Susan T.
Published: January 2021

The XP-D/DinG family of DNA helicases contribute to genomic stability in all three domains of life. We investigate here the role of one of these proteins,YoaA, ofEscherichia coli. InE. coli,YoaA aids tolerance to the nucleoside azidothymidine (AZT), a DNA replication inhibitor and physically interacts with a subunit of the DNA polymerase III holoenzyme, HolC. We map the residues of YoaA required for HolC interaction to its C-terminus by yeast two-hybrid analysis. We propose that this interaction competes with HolC’s interaction with HolD and the rest of the replisome;YoaA indeed inhibits growth when overexpressed, dependent on this interaction region. By gene fusions we show YoaA is repressed by LexA and induced in response to DNA damage as part of the SOS response. Induction of YoaA by AZT is biphasic with an immediate response after treatment and a slower response that peaks in the late log phase of growth. This growth-phase dependent induction by AZT is not blocked bylexA3(Ind-), which normally negates its self-cleavage, implying another means to induce the DNA damage response that responds to the nutritional state of the cell. We propose that YoaA helicase activity increases access to the 3’ nascent strand during replication; consistent with this,YoaA appears to aid removal of potential A-to-T transversion mutations inndkmutants, which are prone to nucleotide misincorporation. YoaA and its paralog DinG also may initiate template-switching that leads to deletions between tandem repeats in DNA.

IMPORTANCE

Maintaining genomic stability is crucial for all living organisms. Replication of DNA frequently encounters barriers that must be removed to complete genome duplication. Balancing DNA synthesis with its repair is critical and not entirely understood at a mechanistic level.The YoaA protein, studied here, is required for certain types of DNA repair and interacts in an alternative manner with proteins that catalyze DNA replication. YoaA is part of the well-studied LexA-regulated response to DNA damage, the SOS response. We describe an unusual feature of its regulation that promotes induction after DNA damage as the culture begins to experience starvation. Replication fork repair integrates both DNA damage and nutritional signals. We also show that YoaA affects genomic stability.
Quantification of biologically and chemically bound phosphorus in activated sludge from full-scale plants with biological P-removal
Authors: Petriglieri Francesca , Petersen Jette F. , Peces Miriam , Nierychlo Marta , Hansen Kamilla , Baastrand Cecilie E. , Nielsen Ulla Gro , Reitzel Kasper , Nielsen Per Halkjær
Published: January 2021

Large amounts of phosphorus (P) are present in activated sludge from municipal wastewater treatment plants, where it exists in the form of metal salt precipitates or biologically bound into the biomass as nucleic acids, cell membrane components, and the extracellular polymeric substances or, in special polyphosphate-accumulating organisms (PAOs), as intracellular polyphosphate. Only recently, methods that reliably allow an absolute quantification of the different P-fractions, such as sequential extraction, Raman microspectroscopy, solid-state31P magic angle spinning (MAS) NMR, and solution state31P NMR have been developed. This study combines these techniques to obtain a comprehensive P mass-balance of activated sludge from four wastewater treatment plants with enhanced biological phosphate removal (EBPR). The total content of P and various cations was measured by chemical analysis (ICP-OES), and different P fractions were extracted for chemical characterization. Chemically bound P constituted 38-69% of total P, most likely in the form of Fe, Mg, or Al minerals, while organically bound P constituted 7-9%. By using Raman microspectroscopy and solution state31P NMR and31P MAS NMR spectroscopy before and after anaerobic P-release experiments, poly-P was quantified and constituted 22-54% of total P in the activated sludges and was found in approx. 25% of all bacterial cells. Moreover, Raman microspectroscopy in combination with fluorescencein situhybridization (FISH) was used to quantify the species-specific intracellular poly-P of known PAO genera (Tetrasphaera,Ca.Accumulibacter,Dechloromonas) and other microorganisms known to possess high level of poly-P, such as the filamentousCa.Microthrix. They were all abundant, as measured by quantitative-FISH and amplicon sequencing, and accumulated large amount of poly-P, depending on their cell-size, contributing substantially to the P-removal. Interestingly, in all four EBPR plants investigated, only 1-13% of total poly-P was stored by unidentified PAO, highlighting that most PAOs in the full-scale EBPR plants investigated are now known.

Highlights

Exhaustive P mass-balance of main organic and inorganic P-species in four EBPR plants

Quantification of poly-P of FISH-defined PAO and other species with high P content

Total P content was 36-50 mgP/gSS of which 31-62% was in biomass and as poly-P

A high fraction of all cells (25-30%) contained a high content of poly-P

Known PAOs contained almost all poly-P in the EBPR plants investigated
Functionality of the putative surface glycoproteins of the Wuhan spiny eel influenza virus
Authors: Arunkumar Guha Asthagiri , Strohmeier Shirin , Li Tiehai , Bhavsar Disha , Chromikova Veronika , Amanat Fatima , Bunyatov Mehman , Wilson Patrick C. , Ellebedy Ali H. , Boons Geert-Jan , Simon Viviana , de Vries Robert P. , Krammer Florian
Published: January 2021

A panel of novel influenza-like virus sequences were recently documented in jawless fish, ray-finned fish, and amphibians. Of these, the Wuhan spiny eel influenza virus (WSEIV) was found to phylogenetically cluster with influenza B viruses as a sister clade. Influenza B viruses have been historically documented to circulate only in humans, with certain virus isolates found in harbor seals. It is therefore interesting that a similar virus was potentially found in fish. Here we characterized the functionality and antigenicity of the putative hemagglutinin (HA) and neuraminidase (NA) surface glycoproteins of the WSEIV to better understand this virus and its pandemic potential. Upon functional characterization of NA, we identified that the WSEIV NA-like protein has sialidase activity comparable to B/Malaysia/2506/2004 influenza B virus NA, making it abona fideneuraminidase that could be inhibited by NA inhibitors. Testing of the functionality of HA was carried out including receptor specificity, stability, and preferential airway protease cleavage and showed very specific binding to monosialic ganglioside 2 (GM2). To probe the degree of conservation of target epitopes, binding of known broadly cross-reactive monoclonal antibodies targeting the influenza B HA and NA, respectively, were assessed through enzyme linked immunosorbent assays against recombinant WSEIV glycoproteins. Human serum samples of patients with antibodies to influenza B viruses were used to determine the cross-reactivity against these novel glycoproteins. Very few monoclonal antibodies – notably including pan NA antibody 1G01 - showed cross-reactivity and reactivity from human sera was basically absent. In summary, we have conducted a functional and antigenic characterization of the glycoproteins of the novel WSEIV to assess if it is indeed abona fideinfluenza virus potentially circulating in ray-finned fish.