bluuebunny/crossref_metadata_2025 huggingface dataset:
Re-use of trial data in the first 10 years of the data-sharing policy of the Annals of Internal Medicine: a survey of published studies
Authors: Pellen Claude , Caquelin Laura , Bail Alexia Jouvance-Le , Gaba Jeanne , Vérin Mathilde , Moher David , Ioannidis John P. A. , Naudet Florian
Published: June 2020

Background

The Annals of Internal Medicine (AIM) has adopted a policy encouraging data-sharing since 2007.

Objective

To explore the impact of the AIM data-sharing policy for randomized controlled trials (RCTs) in terms of output from data-sharing (i.e. publications re-using the data).

Design

Retrospective study.

Setting

AIM.

Participants

RCTs published in the AIM between 2007 and 2017 were retrieved on PubMed. Publications where the data had been re-used were identified on Web of Science. Searches were performed by two independent reviewers.

Interventions

Intention to share data (or not) expressed in a data-sharing statement.

Measurements

The primary outcome was any published re-use of the data (i.e. re-analysis, secondary analysis, or meta-analysis of individual participant data [MIPD]), where the first, last and corresponding authors were not among the authors of the RCT. Components of the primary outcome and analyses without any author restriction were secondary outcomes. Analyses used Cox (primary analysis) models adjusting for RCT characteristics.

Results

185 RCTs were identified. 106 (57%) mentioned willingness to share data and 79 (43%) did not. 208 secondary analyses, 67 MIPD and no re-analyses were identified. No significant association was found between intent to share and re-use where the first, last and corresponding authors were not among the authors of the primary RCT (adjusted hazard ratio = 1.04 [0.47-2.30]). Secondary outcomes also showed no association between intent to share and re-use.

Limitations

Possibility of residual confounding and limited power.

Conclusion

Over ten years, RCTs published in AIM expressing an intention to share data were not associated with more extensive re-use of the data.

Registration

https://osf.io/8pj5e/

Funding Source

Grants from the Fondation pour la Recherche Médicale, Région Bretagne, and French National Research Agency.
Potent Neutralizing Antibodies Directed to Multiple Epitopes on SARS-CoV-2 Spike
Authors: Liu Lihong , Wang Pengfei , Nair Manoj S. , Yu Jian , Rapp Micah , Wang Qian , Luo Yang , Chan Jasper F-W. , Sahi Vincent , Figueroa Amir , Guo Xinzheng V. , Cerutti Gabriele , Bimela Jude , Gorman Jason , Zhou Tongqing , Chen Zhiwei , Yuen Kwok-Yung , Kwong Peter D. , Sodroski Joseph G. , Yin Michael T. , Sheng Zizhang , Huang Yaoxing , Shapiro Lawrence , Ho David D.
Published: June 2020

The SARS-CoV-2 pandemic rages on with devasting consequences on human lives and the global economy1,2. The discovery and development of virus-neutralizing monoclonal antibodies could be one approach to treat or prevent infection by this novel coronavirus. Here we report the isolation of 61 SARS-CoV-2-neutralizing monoclonal antibodies from 5 infected patients hospitalized with severe disease. Among these are 19 antibodies that potently neutralized the authentic SARS-CoV-2in vitro, 9 of which exhibited exquisite potency, with 50% virus-inhibitory concentrations of 0.7 to 9 ng/mL. Epitope mapping showed this collection of 19 antibodies to be about equally divided between those directed to the receptor-binding domain (RBD) and those to the N-terminal domain (NTD), indicating that both of these regions at the top of the viral spike are immunogenic. In addition, two other powerful neutralizing antibodies recognized quaternary epitopes that are overlapping with the domains at the top of the spike. Cryo-electron microscopy reconstructions of one antibody targeting RBD, a second targeting NTD, and a third bridging two separate RBDs revealed recognition of the closed, “all RBD-down” conformation of the spike. Several of these monoclonal antibodies are promising candidates for clinical development as potential therapeutic and/or prophylactic agents against SARS-CoV-2.
The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins
Authors: Conceicao Carina , Thakur Nazia , Human Stacey , Kelly James T. , Logan Leanne , Bialy Dagmara , Bhat Sushant , Stevenson-Leggett Phoebe , Zagrajek Adrian K. , Hollinghurst Philippa , Varga Michal , Tsirigoti Christina , Hammond John A. , Maier Helena J. , Bickerton Erica , Shelton Holly , Dietrich Isabelle , Graham Stephen C. , Bailey Dalan
Published: June 2020

SARS-CoV-2 emerged in late 2019, leading to the COVID-19 pandemic that continues to cause significant global mortality in human populations. Given its sequence similarity to SARS-CoV, as well as related coronaviruses circulating in bats, SARS-CoV-2 is thought to have originated in Chiroptera species in China. However, whether the virus spread directly to humans or through an intermediate host is currently unclear, as is the potential for this virus to infect companion animals, livestock and wildlife that could act as viral reservoirs. Using a combination of surrogate entry assays and live virus we demonstrate that, in addition to human ACE2, the Spike glycoprotein of SARS-CoV-2 has a broad host tropism for mammalian ACE2 receptors, despite divergence in the amino acids at the Spike receptor binding site on these proteins. Of the twenty-two different hosts we investigated, ACE2 proteins from dog, cat and rabbit were the most permissive to SARS-CoV-2, while bat and bird ACE2 proteins were the least efficiently used receptors. The absence of a significant tropism for any of the three genetically distinct bat ACE2 proteins we examined indicates that SARS-CoV-2 receptor usage likely shifted during zoonotic transmission from bats into people, possibly in an intermediate reservoir. Interestingly, while SARS-CoV-2 pseudoparticle entry was inefficient in cells bearing the ACE2 receptor from bats or birds the live virus was still able to enter these cells, albeit with markedly lower efficiency. The apparently broad tropism of SARS-CoV-2 at the point of viral entry confirms the potential risk of infection to a wide range of companion animals, livestock and wildlife.
Small Non-coding RNAome of ageing chondrocytes
Authors: Balaskas Panagiotis , Green Jonathan A. , Haqqi Tariq M. , Dyer Philip , Kharaz Yalda A. , Fang Yongxiang , Liu Xuan , Welting Tim J.M. , Peffers Mandy J.
Published: June 2020

Background

Ageing is one of the leading risk factors predisposing cartilage to musculoskeletal diseases, including osteoarthritis. Cumulative evidence suggests that small non-coding RNAs play a role in cartilage-related pathological changes. However, little research has been conducted on the effect of ageing on the expression of small non-coding RNAs in cartilage. By using small RNA sequencing, we investigated changes in the expression of small non-coding RNAs between young and old equine chondrocytes.

Methods

Chondrocytes were extracted from five young (4±1 years) and five old (17.4±1.9 years) macroscopically normal equine metacarpophalangeal joints. Following RNA extraction cDNA libraries were prepared and subjected to small RNA sequencing using the Illumina MiSeq platform. Differential expression analysis was performed in R using package DESeq2. For tRNA fragment analysis, tRNA reads were aligned to horse tRNA sequences using Bowtie2 version 2.2.5. Selected microRNA and small nucleolar RNA findings were validated using qRT-PCR in an extended cohort of equine chondrocytes. tRNA fragments were further investigated in low and high grade OA human cartilage tissue.

Results

In total, 83 sncRNAs were differentially expressed between young and old equine chondrocytes, including microRNAs, snoRNAs, snRNAs and tRNAs. Of these, 34 were expressed higher and 49 were expressed lower in old chondrocytes compared to young. qRT-PCR analysis confirmed findings in an extended cohort of equine chondrocytes. Ingenuity Pathway Analysis of differentially expressed microRNAs and their predicted target genes linked them to cartilage and OA-related pathways and diseases. tRNA fragment analysis revealed that tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1 were reduced in both high grade OA human cartilage and old equine chondrocytes.

Conclusion

For the first time, we have measured the effect of ageing on the expression of small non-coding RNAs in equine chondrocytes. Changes were detected in a number of different sncRNA species, including microRNAs, small nucleolar RNAs and tRNA fragments. This study supports a role for small non-coding RNAs in ageing cartilage and their potential involvement in age-related cartilage diseases.
Ozone-induced changes in murine lung extracellular vesicle number and small RNA content
Authors: Smith Gregory J. , Tovar Adelaide , Kanke Matt , Sethupathy Praveen , Kelada Samir N. P.
Published: June 2020

Inhalation exposure to ozone (O3) causes adverse respiratory health effects that result from airway inflammation, a complex response mediated by changes to airway cellular transcriptional programs. These programs may be regulated in part by a subset of microRNAs transferred between cells (e.g. epithelial cells and macrophages) via extracellular vesicles (EV miRNA). To explore this, we exposed female C57BL/6J mice to filtered air (FA), 1, or 2 ppm O3by inhalation and collected bronchoalveolar lavage fluid (BALF) 21 hours later for markers of airway inflammation, EVs, and EV miRNA. Both concentrations of O3significantly increased markers of inflammation (neutrophils and total protein) and the number of EVs in the BALF. Using high-throughput small RNA sequencing, we identified several differentially expressed (DE) BALF EV miRNAs after 1 ppm (16 DE miRNAs) and 2 ppm (99 DE miRNAs) O3versus FA exposure. O3concentration response patterns in EV miRNA expression were apparent, particularly for the two most highly expressed (miR-2137 and miR-126-3p) and lowly expressed (miR-378-3p and miR-351-5p) miRNAs. Integrative analysis of EV miRNA expression and airway cellular mRNA expression identified EV miR-22-3p as a candidate regulator of transcriptomic responses to O3in airway macrophages. In contrast, we did not identify candidate miRNA regulators of mRNA expression data from conducting airways (predominantly composed of epithelial cells). In summary, our data show that O3exposure alters EV release and EV miRNA expression, suggesting that further investigation of EVs may provide insight into their effects on airway macrophage function and other mechanisms of O3-induced respiratory inflammation.
Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization
Authors: Sharanowski Barbara J. , Ridenbaugh Ryan D. , Piekarski Patrick K. , Broad Gavin R. , Burke Gaelen R. , Deans Andrew R. , Lemmon Alan R. , Lemmon Emily C. Moriarty , Diehl Gloria J. , Whitfield James B. , Hines Heather M.
Published: June 2020

Ichneumonoidea is one of the most diverse lineages of animals on the planet with more than 48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp’s genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.
Comparative phylogeography reveals how a barrier filters and structures taxa in North American warm deserts
Authors: Provost Kaiya L. , Myers Edward A. , Smith Brian Tilston
Published: June 2020

The study of biogeographic barriers have been instrumental in understanding the evolution and distribution of taxa. Now with the increased availability of empirical datasets, it is possible to infer emergent patterns from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data for a barrier and perform spatially-explicit simulations to quantify temporal and spatial patterns of divergence, the influence of species traits on these patterns, and understand the statistical power of differentiating alternative diversification modes. We incorporate published datasets to examine taxa around the Cochise Filter Barrier, separating the Sonoran and Chihuahuan deserts of North America, to synthesize phylogeographic structuring across the community with respect to organismal functional traits. We then use a simulation and machine learning pipeline to assess the power of phylogeographic model selection. Taxa distributed across the Cochise Filter Barrier show heterogeneous responses to the barrier in levels of gene flow, phylogeographic structure, divergence timing, barrier width, and divergence mechanism. These responses vary concordantly with locomotor and thermoregulatory traits. Many taxa show a Pleistocene population genetic break, often with introgression after divergence. Allopatric isolation and isolation-by-environment are the primary mechanisms purported to structure taxa. Simulations reveal that in spatially-explicit isolation-with-migration models across the barrier, age of divergence, presence of gene flow, and presence of isolation-by-distance can confound the interpretation of evolutionary history and model selection by producing easily-confusable results. By synthesizing phylogeographic data for the Cochise Filter Barrier we show a pattern where barriers interact with species traits to differentiate taxa in communities over millions of years. Identifying the modes of differentiation across the barriers for these taxa remains challenging because commonly invoked demographic models may not be identifiable across a range of likely parameter space.
A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine
Authors: Cranford Matthew T. , Kaszubowski Joseph D. , Trakselis Michael A.
Published: June 2020

During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves ‘on-the-fly’ translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol for bypass of the lesion. The length of TLS must be long enough for effective bypass, but it must also be regulated to minimize replication errors by the TLS Pol. The exact position where the TLS Pol ends and the HiFi Pol resumes (i.e. the length of the TLS patch) has not been described. We use steady-state and pre-steady-state kinetic assays to characterize lesion bypass intermediates formed by different archaeal polymerase holoenzyme complexes that include PCNA123 and RFC. After bypass of 8-oxoG by TLS PolY, products accumulate at the template position three base pairs beyond the lesion. PolY is catalytically poor for subsequent extension from this +3 position beyond 8-oxoG, but this inefficiency is overcome by rapid extension of HiFi PolB1. The reciprocation of Pol activities at this intermediate indicates a defined position where TLS Pol extension is limited and where the DNA substrate is handed back to the HiFi Pol after bypass of 8-oxoG.
The mechanisms behind perivascular fluid flow
Authors: Daversin-Catty Cécile , Vinje Vegard , Mardal Kent-André , Rognes Marie E.
Published: June 2020

Flow of cerebrospinal fluid (CSF) in perivascular spaces (PVS) is one of the key concepts involved in theories concerning clearance from the brain. Experimental studies have demonstrated both net and oscillatory movement of microspheres in PVS (Mestre et al. (2018), Bedussi et al. (2018)). The oscillatory particle movement has a clear cardiac component, while the mechanisms involved in net movement remain disputed. Using computational fluid dynamics, we computed the CSF velocity and pressure in a PVS surrounding a cerebral artery subject to different forces, representing arterial wall expansion, systemic CSF pressure changes and rigid motions of the artery. The arterial wall expansion generated velocity amplitudes of 60–260µm/s, which is in the upper range of previously observed values. In the absence of a static pressure gradient, predicted net flow velocities were small (<0.5µm/s), though reaching up to 7µm/s for non-physiological PVS lengths. In realistic geometries, a static systemic pressure increase of physiologically plausible magnitude was sufficient to induce net flow velocities of 20–30µm/s. Moreover, rigid motions of the artery added to the complexity of flow patterns in the PVS. Our study demonstrates that the combination of arterial wall expansion, rigid motions and a static CSF pressure gradient generates net and oscillatory PVS flow, quantitatively comparable with experimental findings. The static CSF pressure gradient required for net flow is small, suggesting that its origin is yet to be determined.

Significance Statement

Cerebrospinal fluid flow along perivascular spaces is hypothesized to be instrumental for clearance of metabolic waste from the brain, such as e.g. clearance of amyloid-beta, a protein known to accumulate as plaque within the brain in Alzheimer’s patients. Arterial pulsations have been proposed as the main driving mechanism for perivascular fluid flow, but it is unclear whether this mechanism alone is sufficient. Our results show that arterial pulsations drive oscillatory movement in perivascular spaces, but also indicate that a pressure gradient is required for net flow. However, the required pressure gradient is relatively small, thus suggesting that its origins can be associated with physiological processes within the brain and/or experimental procedures.
Local and global analysis of macromolecular Atomic Displacement Parameters
Authors: Masmaliyeva Rafiqa C , Babai Kaveh H , Murshudov Garib N
Published: June 2020

This paper describes the global and local analyses of Atomic Displacement Parameters (ADP) of macromolecules solved and refined using X-ray crystallography method. It is shown that the distribution of ADPs follows the (mixture of) Shifted Inverse Gamma distribution(s). The parameters of the mixture of SIGDs are estimated using Expectation/Maximisation methods. In addition, a method for resolution and individual ADP dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of the mismodelled atoms and indicates potential identity of heavy metal atoms. It also helps in detecting of disordered and/or wrongly modelled ligands. Both global and local analyses can be used to detect errors in atomic structures thus helping in (re)building, refinement and validation of macromolecular structures. It can also serve as an additional validation tool during data deposition to the PDB.

Synopsis

Macromolecular atomic B value distributions have been modelled using a mixture of Shifted Inverse Gamma Distribution. Also, B value and resolution dependent local ADP differences have been applied for validation of heavy atoms and ligands.
Y disruption, autosomal hypomethylation and poor male lung cancer survival
Authors: Willis-Owen Saffron A.G. , Sabugo Clara Domingo , Starren Elizabeth , Liang Liming , Freidin Maxim B. , Arseneault Madeleine , Zhang Youming , Lu Shir Kiong , Popat Sanjay , Lim Eric , Nicholson Andrew G. , Riazalhosseini Yasser , Lathrop Mark , Cookson William O.C. , Moffatt Miriam F.
Published: June 2020

Lung cancer is the most frequent cause of cancer death worldwide1. It is male predominant and for reasons that are unknown also associated with significantly worse outcomes in men2. Here we compared gene co-expression networks in affected and unaffected pulmonary tissue derived from 126 patients with Stage IA–IV lung cancer. We observed marked degradation of a sex-associated gene co-expression network in tumour tissue. The disturbance was linked to fractional loss of the Y chromosome and was detected in 28% of male tumours in the discovery dataset and 27% of male tumours in a 123 sample replication dataset. Depression of Y chromosome expression was accompanied by extensive autosomal DNA hypomethylation. The male specific H3K4 demethylase, KDM5D, was identified as an apex hub within this co-expression network. Male patients exhibiting relative tumour KDM5D deficiency had an increased risk of death in the discovery dataset (Hazard Ratio [HR] 3.80, 95% CI 1.40 – 10.3, P=0.009) and in an independent sample of 1,100 male lung tumours (HR 1.67, 95% CI 1.4-2.0, P=1.2⨯10−10). Our findings identify tumour-specific weakening of male-specific expression, in particular deficiency of KDM5D, as a common replicable prognostic marker and credible mechanism underlying sex disparity in cancer.
The Endothelial Dysfunction and Pyroptosis Might Drive the SARS-CoV-2 Lung Injury to the Systemic Immunothrombosis
Authors: Nagashima Seigo , Mendes Monalisa C. , Martins Ana Paula C. , Borges Nicolas H. , Godoy Thiago M. , dos Santos Miggiolaro Anna Flavia Ribeiro , Dezidério Felipe S. , de Noronha Lucia , Machado-Souza Cleber
Published: June 2020

Objective

Endothelial cells that are close to the alveolar-capillary exchange membranes can be activated by SARS-CoV-2 infection leading to cytokine release and macrophage activation syndrome. This could trigger endothelial dysfunction, pyroptosis, and immunothrombosis, which are the vascular changes commonly referred to as COVID-19 endotheliopathy. Thus, this study aimed to identify tissue biomarkers associated with endothelial activation/dysfunction and the pyroptosis pathway in the lung and myocardial samples of COVID-19 patients and to compare them to pandemic Influenza A virus H1N1 subtype – 2009 and Control cases.

Approach and Results

Post-mortem lung (COVID-19 group=6 cases; H1N1 group=10 cases, and Control group=11 cases) and myocardial samples (COVID-19=2 cases and control=1 case) were analyzed using immunohistochemistry and the following monoclonal primary antibodies: anti-CD163, anti-interleukin-6 (IL-6), anti-tumor necrosis factor-alpha (TNF-alpha), anti-intercellular adhesion molecule-1 (ICAM-1), and anti-caspase-1. From the result, IL-6, TNF-alpha, ICAM-1, and caspase-1 showed higher tissue expression in the COVID-19 group than in the H1N1 and control groups.

Conclusion

Our results demonstrated the presence of endotheliopathy and suggest the participation of the pyroptosis pathway in both the pulmonary and myocardial samples. These conditions might lead to systemic immunothrombotic events that could impair the efforts of clinical staff to avoid fatal outcomes. One of the goals of health professionals should be to identify the high-risk of immunothrombosis patients early to block endotheliopathy and its consequences.
FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy
Authors: Fiore Josè Ramòn , Centra Michele , De Carlo Armando , Granato Tommaso , Rosa Annamaria , Sarno Michelina , De Feo Lucia , Di Stefano Mariantonietta , D’Errico Maria L. , Caputo Sergio Lo , De Nittis Rosella , Arena Fabio , Corso Gaetano , Margaglione Maurizio , Santantonio Teresa Antonia
Published: June 2020

Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors from a low incidence COVID-19 area (Apulia region, South Eastern Italy).

Among 904 subjects tested, only in 9 cases (0.99%) antibodies against SARS-CoV-2 were demonstrated. All the 9 seropositive patients were negative for the research of viral RNA by RT-PCR in nasopharyngeal swab.

These data, along with those recently reported from other countries, clearly show that we are very far from herd immunity and that the containment measures are at the moment the only realistic instrument we have to slow the spread of the pandemic.
UV-C Tower for point-of-care decontamination of filtering facepiece respirators
Authors: Kayani Badar J. , Weaver Davis T. , Gopalakrishnan Vishvaan , King Eshan S. , Dolson Emily , Krishnan Nikhil , Pelesko Julia , Scott Michael J. , Hitomi Masahiro , Cadnum Jennifer L. , Li Daniel F. , Donskey Curtis J. , Scott Jacob G. , Charnas Ian
Published: June 2020

Filtering facepiece respirators (FFR) are critical for protecting essential personnel and limiting the spread of disease. Due to the current COVID-19 pandemic, FFR supplies are dwindling in many health systems, necessitating re-use of potentially contaminated FFR. Multiple decontamination solutions have been developed to meet this pressing need, including systems designed for bulk decontamination of FFR using vaprous hydrogen peroxide or UV-C radiation. However, the large scale on which these devices operate may not be logistically practical for small or rural health care settings or for ad hoc use at points-of-care. Here, we present the Synchronous UV Decontamination System (SUDS), a novel device for rapidly deployable, point-of-care decontamination using UV-C germicidal irradiation. We designed a compact, easy-to-use device capable of delivering over 2 J· cm−2 of UV-C radiation in one minute. We experimentally tested SUDS’ microbicidal capacity and found that it eliminates near all virus from the surface of tested FFRs, with less efficacy against pathogens embedded in the inner layers of the masks. This short decontamination time should enable care-providers to incorporate decontamination of FFR into a normal donning and doffing routine following patient encounters.
Toward patient-centered tuberculosis preventive treatment: preferences for regimens and formulations in Lima, Peru
Authors: Yuen Courtney M. , Millones Ana K. , Galea Jerome T. , Puma Daniela , Jimenez Judith , Lecca Leonid , Becerra Mercedes C. , Keshavjee Salmaan
Published: June 2020

Background

To ensure patient-centered TB preventive treatment, it is important to consider factors that make it easier for patients to complete treatment. However, there is little published literature about patient preferences for different preventive treatment regimen options, particularly from countries with high tuberculosis burdens.

Methods

We conducted a qualitative research study using a framework analysis approach to understand preventive treatment preferences among household contacts. We conducted three focus group discussions with 16 members of families affected by TB in Lima, Peru. Participants were asked to vote for preferred preventive treatment regimens and discuss the reasons behind their choices. Coding followed a deductive approach based on prior research, with data-driven codes added.

Results

In total, 7 (44%) participants voted for 3 months isoniazid and rifapentine, 4 (25%) chose 3 months isoniazid and rifampicin, 3 (19%) chose 4 months rifampicin, and 2 (13%) chose 6 months isoniazid. Preferences for shorter regimens over 6 months of isoniazid were driven by concerns over “getting tired” or “getting bored” of taking medications, the difficulty of remembering to take medications, side effects, and interference with daily life. For some, weekly dosing was perceived as being easier to remember and less disruptive, leading to a preference for 3 months isoniazid and rifapentine, which is dosed weekly. However, among caregivers, having a child-friendly formulation was more important than regimen duration. Caregivers reported difficulty in administering pills to children, and preferred treatments available as syrup or dispersible formulations.

Conclusions

There is demand for shorter regimens and child-friendly formulations for preventive treatment in a high-burden setting. Individual preferences differ, suggesting that patient-centered care would best be supported by having multiple shorter regimens available.
Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variablehsdSspecificity genes that randomly switch methyltransferase specificity by recombination
Authors: Atack John M. , Guo Chengying , Litfin Thomas , Yang Long , Blackall Patrick J. , Zhou Yaoqi , Jennings Michael P.
Published: June 2020

N6-adenine DNA methyltransferases associated with some Type I and Type III restriction-modification (R-M) systems are able to randomly switch expression by variation in the length of locus-encoded simple sequence repeats (SSRs). SSR tract-length variation causes ON/OFF switching of methyltransferase expression, resulting in genome-wide methylation differences, and global changes in gene expression. These epigenetic regulatory systems are called phasevarions, phase-variable regulons, and are widespread in bacteria. A distinct switching system has also been described in Type I R-M systems, based on recombination-driven changes inhsdSgenes, which dictate the DNA target site. In order to determine the prevalence of recombination-driven phasevarions, we generated a program called RecombinationRepeatSearch to interrogate REBASE and identify the presence and number of inverted repeats ofhsdSdownstream of Type I R-M loci. We report that 5.9% of Type I R-M systems have duplicated variablehsdSgenes containing inverted repeats capable of phase-variation. We report the presence of these systems in the major pathogensEnterococcus faecalisandListeria monocytogenes, which will have important implications for pathogenesis and vaccine development. These data suggest that in addition to SSR-driven phasevarions, many bacteria have independently evolved phase-variable Type I R-M systems via recombination between multiple, variablehsdSgenes.

Importance

Many bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems called phasevarions (phase-variable regulons) control the expression of multiple genes by global methylation changes. In every previously characterised phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with methyltransferase switching. A systematic study to determine the extent of phasevarions controlled by invertible Type I R-M systems has never before been performed. Understanding how bacteria regulate genes is key to the study of physiology, virulence, and vaccine development; therefore it is critical to identify and characterize phase-variable methyltransferases controlling phasevarions.
The Distribution of Enset Pests and Pathogens and a Genomic Survey of Enset Xanthomonas Wilt
Authors: Yemataw Zerihun , Borrell James S. , Biswas Manosh Kumar , White Oliver , Mengesha Wendawek , Muzemil Sadik , Darbar Jaypal N. , Ondo Ian , Harrison Pat J.S. Heslop , Blomme Guy , Wilkin Paul
Published: June 2020

Mapping the distribution of crop pests and pathogens is essential to safeguard food security and sustainable livelihoods. However, these data are unavailable for many neglected and underutilised crops, particularly in developing countries. In Ethiopia, the world’s largest historic recipient of food aid, the indigenous banana relative enset (Ensete ventricosum) is threatened by multiple pests and pathogens whilst providing the staple starch source for 20 million people. Foremost among these isXanthomonasWilt of enset (EXW), caused byXanthomonas vasicolapv.musacearum(Xvm), a globally important disease of bananas (Musasp.) that likely originated in enset. Here we collate 1069 farm surveys to map the distribution and relative prevalence of enset pests and pathogens across the entire enset growing region. We find that EXW is the most frequently encountered pathogen, and that farmers consistently ranked EXW as the most significant constraint on enset agriculture. Our surveys also showed that corm rot, and the pests root mealybug, mole rat and porcupine are all virtually ubiquitous. Finally, we apply genotyping-by-sequencing to the detection ofXvmand demonstrate that it is present even in asymptomatic domesticated and wild enset samples, suggesting that management of plants displaying symptoms alone may not be sufficient to reduce disease transmission. Holistic understanding of pests and pathogen distributions in enset may have significant benefits for both food security in Ethiopia, and preventing proliferation in related crops such as banana across central and east Africa.
Smooth muscle-specific MMP17 (MT4-MMP) defines the intestinal ECM niche
Authors: Martín-Alonso Mara , Lindholm Håvard T. , Iqbal Sharif , Vornewald Pia , Hoel Sigrid , Damen Mirjam J. , Altelaar A.F.Maarten , Katajisto Pekka , Arroyo Alicia G. , Oudhoff Menno J.
Published: June 2020

Smooth muscle is an essential component of the intestine, both to maintain its structure and produce peristaltic and segmentation movements. However, very little is known about other putative roles that smooth muscle may have. Here, we show that smooth muscle is the dominant supplier of BMP antagonists, which are niche factors that are essential for intestinal stem cell maintenance. Furthermore, muscle-derived factors can render epithelium reparative and fetal-like, which includes heightened YAP activity. Mechanistically, we find that the matrix metalloproteinase MMP17, which is exclusively expressed by smooth muscle, is required for intestinal epithelial repair after inflammation- or irradiation-induced injury. Furthermore, we provide evidence that MMP17 affects intestinal epithelial reprogramming indirectly by cleaving the matricellular protein PERIOSTIN, which itself is able to activate YAP. Together, we identify an important signaling axis that firmly establishes a role for smooth muscle as a modulator of intestinal epithelial regeneration and the intestinal stem cell niche.
The failure of B cells to induce non-canonicalMYD88splice variants correlates with lymphomagenesis via sustained NF-κB signaling
Authors: Gloria Yamel Cardona , Bernhart Stephan H. , Fillinger Sven , Wolz Olaf-Oliver , Dickhöfer Sabine , Admard Jakob , Ossowski Stephan , Nahnsen Sven , Siebert Reiner , Weber Alexander N.R.
Published: June 2020

Gain-of-function mutations of the TLR adaptor and oncoprotein MyD88 drive B cell lymphomagenesis via sustained NF-κB activation. In myeloid cells, sustained TLR activation and NF-κB activation lead to the induction of inhibitoryMYD88splice variants that restrain prolonged NF-κB activation. We therefore sought to investigate whether such a negative feedback loop exists in B cells. AnalyzingMYD88splice variants in normal B cells and different primary B cell malignancies, we observed thatMYD88splice variants in transformed B cells are dominated by the canonical, strongly NF-κB-activating isoform ofMYD88and contain at least three novel, so far uncharacterized signaling-competent splice isoforms. TLR stimulation in B cells unexpectedly reinforces splicing of NF-κB-promoting, canonical isoforms rather than the ‘MyD88s’, a negative regulatory isoform that is typically induced by TLRs in myeloid cells. This suggests that an essential negative feedback loop restricting TLR signaling in myeloid cells at the level of alternative splicing, is missing in B cells, rendering B cells vulnerable to sustained NF-κB activation and eventual lymphomagenesis. Our results uncoverMYD88alternative splicing as an unappreciated promoter of B cell lymphomagenesis and provide a rationale why oncogenicMYD88mutations are exclusively found in B cells.
Enterococcal PrgA extends far outside the cell and provides surface exclusion to protect against unwanted conjugation
Authors: Schmitt Andreas , Hirt Helmut , Järvå Michael A. , Sun Wei-Sheng , Beek Josy ter , Dunny Gary M. , Berntsson Ronnie P-A
Published: June 2020

Horizontal gene transfer between Gram-positive bacteria leads to a rapid spread of virulence factors and antibiotic resistance. This transfer is often facilitated via Type 4 Secretion Systems (T4SS), which frequently are encoded on conjugative plasmids. However, donor cells that already contain a particular conjugative plasmid resist acquisition of a 2ndcopy of said plasmid. They utilize different mechanisms, including surface exclusion for this purpose.Enterococcus faecalisPrgA, encoded by the conjugative plasmid pCF10, is a surface protein that has been implicated to play a role in both virulence and surface exclusion, but the mechanism by which this is achieved has not been fully explained. Here, we report the structure of full-length PrgA, which shows that PrgA protrudes far out from the cell wall (approximately 40 nm), where it presents a protease domain.In vivoexperiments show that PrgA provides a physical barrier to cellular adhesion, thereby reducing cellular aggregation. This function of PrgA contributes to surface exclusion, reducing the uptake of its cognate plasmid by approximately one order of magnitude. Using variants of PrgA with mutations in the catalytic site we show that the surface exclusion effect is dependent on the activity of the protease domain of PrgA.In silicoanalysis suggest that PrgA can interact with another enterococcal adhesin, PrgB, and that these two proteins have co-evolved. PrgB is a strong virulence factor, and PrgA is involved in post-translational processing of PrgB. Finally, competition mating experiments show that PrgA provides a significant fitness advantage to plasmid-carrying cells.
Anomalous incisor morphology indicates tissue-specific roles forTfap2aandTfap2bin tooth development
Authors: Woodruff Emily D. , Gutierrez Galaxy C. , Van Otterloo Eric , Williams Trevor , Cohn Martin J.
Published: June 2020

Mice possess two types of teeth that differ in their cusp patterns; incisors have one cusp and molars have multiple cusps. The patterning of these two types of teeth relies on fine-tuning of the reciprocal molecular signaling between dental epithelial and mesenchymal tissues during embryonic development. Here we show that the incisors are populated only at early time points by the neural crest, whereas the molars continue to receive contributions at later stages, revealing a temporal difference that could alter epithelial-mesenchymal signaling dynamics between these two types of teeth. The AP-2 transcription factors, particularlyTfap2aandTfap2b, are essential components of such epithelial-mesenchymal signaling interactions that coordinate craniofacial development in mice and other mammals, but little is known about their roles in the regulation of tooth development and shape. We demonstrate that incisors and molars differ in their temporal and spatial expression ofTfap2aandTfap2b; in particular, at the bud stage,Tfap2ais expressed in both the epithelium and mesenchyme of the incisors and molars but expression ofTfap2bis restricted to the mesenchyme of the molars. Tissue-specific deletions show that loss of the epithelial domain ofTfap2aandTfap2baffects the number and spatial arrangement of the incisors, notably resulting in duplicated lower incisors. In contrast, deletion of these two genes in the mesenchymal domain has little effect on tooth development. Collectively these results implicate epithelial expression ofTfap2aandTfap2bin dorsal-ventral patterning of the incisors and suggest that these genes contribute to morphological differences between anterior (incisor) and posterior (molar) teeth within the mammalian dentition.

Highlights

Late-migrating cranial neural crest cells contribute extensively to the developing molar tooth germs but minimally to the incisors.

During tooth development, transcription factorsTfap2aandTfap2bare expressed in spatially and temporally dynamic patterns and differ between incisor and molar tooth germs.

Epithelial expression ofTfap2aandTfap2bis necessary for incisor development, but mesenchymal expression of these genes is not required.
3D-printed drug testing platform based on a 3D model of aged human skeletal muscle
Authors: Mestre Rafael , García Nerea , Patiño Tania , Guix Maria , Fuentes Judith , Valerio-Santiago Mauricio , Almiñana Núria , Sánchez Samuel
Published: June 2020

Three-dimensional engineering of skeletal muscle is becoming increasingly relevant for tissue engineering, disease modeling and bio-hybrid robotics, where flexible, versatile and multidisciplinary approaches for the evaluation of tissue differentiation, functionality and force measurement are required. This works presents a 3D-printed platform of bioengineered human skeletal muscle which can efficiently model the three-dimensional structure of native tissue, while providing information about force generation and contraction profiles. Proper differentiation and maturation of myocytes is demonstrated by the expression of key myo-proteins using immunocytochemistry and analyzed by confocal microscopy, and the functionality assessedviaelectrical stimulation and analysis of contraction kinetics. To validate the flexibility of this platform for complex tissue modelling, the bioengineered muscle is treated with tumor necrosis factor α to mimic the conditions of aging, which is supported by morphological and functional changes. Moreover, as a proof of concept, the effects of Argireline®Amplified peptide, a cosmetic ingredient that causes muscle relaxation, are evaluated in both healthy and aged tissue models. Therefore, the results demonstrate that this 3D-bioengineered human muscle platform could be used to assess morphological and functional changes in the aging process of muscular tissue with potential applications in biomedicine, cosmetics and bio-hybrid robotics.
Nonlinear ridge regression improves cell-type-specific differential expression analysis
Authors: Takeuchi Fumihiko , Kato Norihiro
Published: June 2020

Background

Epigenome-wide association studies (EWAS) and differential gene expression analyses are generally performed on tissue samples, which consist of multiple cell types. Cell-type-specific effects of a trait, such as disease, on the omics expression are of interest but difficult or costly to measure experimentally. By measuring omics data for the bulk tissue, cell type composition of a sample can be inferred statistically. Subsequently, cell-type-specific effects are estimated by linear regression that includes terms representing the interaction between the cell type proportions and the trait. This approach involves two issues, scaling and multicollinearity.

Results

First, although cell composition is analyzed in linear scale, differential methylation/expression is analyzed suitably in the logit/log scale. To simultaneously analyze two scales, we applied nonlinear regression. Second, we show that the interaction terms are highly collinear, which is obstructive to ordinary regression. To cope with the multicollinearity, we applied ridge regularization. In simulated data, nonlinear ridge regression attained well-balanced sensitivity, specificity and precision. Marginal model attained the lowest precision and highest sensitivity and was the only algorithm to detect weak signal in real data.

Conclusion

Nonlinear ridge regression performed cell-type-specific association test on bulk omics data with well-balanced performance. The omicwas package for R implements nonlinear ridge regression for cell-type-specific EWAS, differential gene expression and QTL analyses. The software is freely available fromhttps://github.com/fumi-github/omicwas
Quantifying risk factors associated with light-induced potato tuber greening in retail stores
Authors: Tanios Sabine , Eyles Alieta , Corkrey Ross , Tegg Robert S. , Thangavel Tamilarasan , Wilson Calum R.
Published: June 2020

Light conditions in retail stores may contribute to potato greening. In this study, we aimed to develop a potato tuber greening risk rating model for retail stores based on light quality and intensity parameters. This was achieved by firstly exposing three potato varieties (Nicola, Maranca and Kennebec) to seven specific light wavelengths (370, 420, 450, 530, 630, 660 and 735 nm) to determine the tuber greening propensity. Detailed light quality and intensity measurements from 25 retail stores were then combined with the greening propensity data to develop a tuber greening risk rating model. Our study showed that maximum greening occurred under blue light (450 nm), while 53%, 65% and 75% less occurred under green (530 nm), red (660 nm) and orange (630 nm) light, respectively. Greening risk, which varied between stores, was found to be related to light intensity level, and partially explained potato stock loss in stores. Our results from this study suggested that other in-store management practices, including lighting duration, average potato turnover, and light protection during non-retail periods, likely influence tuber greening risk.
Evaluation validation of a qPCR curve analysis method and conventional approaches
Authors: Zhang Yashu , Li Hongping , Shang Shucheng , Meng Shuoyu , Lin Ting , Zhang Yanhui
Published: June 2020

Real-time quantitative polymerase chain reaction (qPCR) is a sensitive and reliable method for mRNA quantification and rapid analysis of gene expression from a large number of starting templates. It is based on the statistical significance of the beginning of exponential phase in real-time PCR kinetics, reflecting quantitative cycle of the initial target quantity and the efficiency of the PCR reaction (the fold increase of product per cycle). We used the large clinical biomaker dataset and 94-replicates-4-dilutions set which was published previously as research tools, then proposed a new qPCR curve analysis method——CqMAN, to determine the position of quantitative cycle as well as the efficiency of the PCR reaction and applied in the calculations. To verify algorithm performance, 20 genes from biomarker and partial data with concentration gradients from 94-replicates-4-dilutions set of MYCN gene were used to compare various publicly available curve analysis methods with our method and established a suitable evaluation index system. The results show that CqMAN method is comparable to other methods and can be a feasible method which applied to our self-developed qPCR data processing and analysis software, providing a simple tool for qPCR analysis.