bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the molecular inter-relationship of SRPK1 and SRSFs during Human Rhinovirus (HRV)-infection and their subsequent effects on viral replication
Authors: Rozario Christoforos , Graham Sheila , Stevenson Andrew , Maciewicz Rose 
Published: April 2019

Introduction
HRV infections cause asthma exacerbations, while HRV-induced wheezing in pre-school children is associated with asthma development in later life. Molecular mechanisms underlying this pathophysiology remain elusive, while HRV-C is increasingly associated with disease severity. Transcriptomic analysis of human respiratory (nasal) epithelia from an in vivo HRV-C infection model revealed changes in expression of cellular Serine/Arginine Protein Kinase 1 (SRPK1) and its substrates, the Serine/Arginine Splicing Factors (SRSFs) suggesting that HRV infection targets pre-mRNA splicing and/or its regulating factors.

Hypothesis
1) HRV splicing modulation results in host transcriptome changes, leading to impaired anti-viral responses and/or immunoregulation; 2) HRV-induced changes to SR proteins result in enhanced HRV-translation and replication.

Methods
HRV-A RNA was synthesised by in-vitro transcription from pRV16.11. HRV replication was measured by RT-qPCR and titration in HeLa cells. Protein expression was monitored by western blotting and confocal microscopy. SPRIN340 was used as a specific SRPK1 inhibitor. Alternatively, SRPK1 was depleted via siRNA interference.

Results
1) SRPK1, SRSF1-6 and SRSF9 are expressed in both A549 and HeLa cells; levels were greater in the latter. 2) SRPIN340 and siSRPK1 treatments decrease the levels of SRPK1 leading to decreased expression of SRSFs in HeLa and A549 cells. 3) HRV16 infection decreased SRPK1, SRSF1-6 and SRSF9 expression in HeLa and A549 cells.

Conclusion
Our initial data suggest that HRV-infection specifically alters molecules involved in pre-mRNA splicing, providing us with insights into the molecular mechanisms underlying the distinct pathology of HRV infection, as well as the aetiology of HRV-associated asthma.
The secretome profiling of a pediatric airway epithelium infected with human respiratory syncytial virus (hRSV) identified aberrant apical/basolateral trafficking and novel immune modulating (CXCL6, CXCL16, CSF3) and antiviral (CEACAM1) proteins
Authors: Touzelet Olivier , Broadbent Lindsay , Armstrong Stuart , Aljabr Waleed , Cloutman-Green Elaine , Power Ultan , Hiscox Julian 
Published: April 2019

Rationale
The respiratory epithelium comprises polarized cells at the interface between the environment and airway tissues. Polarized apical and basolateral protein secretions are a feature of airway epithelium homeostasis. Human respiratory syncytial virus (hRSV) is a major human pathogen that primarily targets the respiratory epithelium. However, the consequences of hRSV infection on epithelium secretome polarity and content remains poorly understood.

Objective
To investigate the impact of hRSV on the secretome of pediatric respiratory epithelium.

Methods
A proteomics approach was combined with an ex-vivo pediatric airway epithelial model (HAE) (n=3 donors) of hRSV infection to identify the apical and basolateral secretome of hRSV-infected cultures.

Measurements and main results
Following hRSV infection, many host proteins lost their apical- or basolateral-restricted secretion or displayed altered apical/basolateral abundance ratios. Fifty three proteins were specifically associated with RSV infection, including modulators of neutrophil and lymphocyte activation (CXCL6, CSF3, SECTM1 or CXCL16), and antiviral proteins (BST2 or CEACAM1) that were never previously associated with hRSV. Importantly, CXCL6, CXCL16, CSF3 was also detected in nasopharyngeal aspirates (NPA) from hRSV-infected infants but not non-infected controls. Furthermore, the antiviral activity of CEACAM1 against RSV was confirmed in vitro using BEAS-2B cells.

Conclusions
hRSV infection disrupted the polarity of the pediatric respiratory epithelial secretome. It also specifically induced immune modulating (CXCL6, CXCL16, CSF3) and an antiviral protein (CEACAM1) that are new to hRSV infection or disease. This study, therefore, provides novel insights into RSV pathogenesis and endogenous antiviral responses in pediatric airway epithelium.
Protein families are the punchline of the pangenomes
Authors: Crossman Lisa 
Published: April 2019

Short-read draft whole genome assemblies can contain many contigs and be impacted on by repeat regions, such as those caused by mobile element activity or inherently repetitive gene structure. Annotating such assemblies for gene content and functional activity can be challenging. This can be especially true if the predicted genes are fragmented across contigs, very large, repetitive or of unusual nucleotide content. Very high and low %GC genomes also come with additional issues. The Pfam domain database 1 is a widely-used large collection of protein families, each represented by multiple sequence alignments and Hidden Markov Models (HMMs). Rather than studying the predicted whole gene content of draft genomes, or presence/absence of specific genes in pan-core genome analyses, we examined predicted protein content by Pfam domain complement. Here we present Punchline, a workflow written in Python 3, to study the genetic content of pangenome assemblies including draft assemblies by looking at the complement of short protein domains. The domains can be used in statistical comparisons of Bacterial groups of interest as provided to the workflow of Punchline. In addition, we show the application of Punchline to specific genomic data.
1. The Pfam protein families database in 2019: S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn Nucleic Acids Research (2019) doi: 10.1093/nar/gky995
Lyme disease in Northern Ireland – a look back on serological testing
Authors: McCorry Louise , McCaughey Conall 
Published: April 2019

Background
Lyme disease is an illness caused by the spirochete Borrrelia burgdoferi. NICE guidance suggests an approach to diagnosis resting on clinical presentation, presence in an epidemiologically plausible area, and positive serology. It is however, well documented that serological diagnostics in European Lyme disease is problematic. There is a movement for Lyme advocacy, a voice that emphasises the poor diagnostics in this infection. With the spotlight on Lyme disease, we are increasingly seeing patients presenting in Northern Ireland across a broad range of specialities. Currently there is minimal data looking at the local epidemiology of Lyme disease. We present previously unpublished data looking at the demographics of those testing positive for Borrelia burgdoferi antibodies.

Methods
We collected data from all patients tested for Lyme disease in Northern Ireland from 2013–2018. We excluded negative results. A randomised selection of 300 cases were chosen. We recorded patient age, gender, origins of testing, home postcode, tick bite history, relevant travel history, duration of symptoms, timings of testing, antibody results including confirmatory testing and treatment.

Results
Of the 300 selected patients 241 (80 %) were IgM positive and 83 (30 %) IgG positive using DiaSorin, Liason CLIA. The average age of presentation was 39 years old. There was a predominance of females tested (62%). 32 % of tests originated in primary care. Of the IgM positives only 41 (17 %) were confirmed by C6 peptide or lineblot in the reference laboratory (RIPL, Porton Down). The results highlight the likely low seroprevalence of Lyme disease in Northern Ireland.
Oxford Nanopore sequencing elucidates a novel stx2f carrying prophage in a Shiga toxin producing Escherichia coli(STEC) O63:H6 associated with a case of haemolytic uremic syndrome (HUS)
Authors: Greig David , Dallman Timothy , Jenkins Claire 
Published: April 2019

Aim
The aim of this study was to use Oxford Nanopore sequencing to characterise a Shiga-toxin producing Escherichia coli(STEC) O63:H6 responsible for a recent case of haemolytic uremic syndrome (HUS).

Methods
STEC isolate 377323 and a comparator stxnegative E. coli isolate of the same lineage and serotype (382634) were sequenced on an Oxford Nanopore minION R9.4 flow cell and an Illumina HiSeq 2500. Nanopore FAST5 data were basecalled and demultiplexed by Albacore. Assemblies were generated using Unicycler and polished using Nanopolish, Pilon and Racon before screening for prophages using PHASTER.

Results
The Shiga toxin subtype was confirmed to be stx2f, which is rarely associated with the onset of HUS in STEC. Comparing the two genomes, the stxnegative isolate harboured five prophages compared to eleven prophages in the STEC isolate, with only one in common. Both samples contained an intact locus of enterocyte effacement pathogenicity island. The Shiga toxin encoding prophage was 42.5 kb in size and predicted to contain 71 coding sequences. 377323 also encoded an 85kbp IncFIB plasmid, not present in 382634. This plasmid encodes a traconjugation cassette and the virulence bfpcassette encoding for a type IV bundle forming pili.

Conclusion
Long read sequencing enabled the characterisation of a rare STEC and related E. coli IN relation to both prophage content and plasmid content and revealed significant differences in the pan-genome in addition to the acquisition of the novel Stx2f phage. This data contributes to the understanding of non-O157 STEC associated with HUS.
Investigating evolution of the paediatric cystic fibrosis lung microbiota using induced sputum sampling and culture-independent techniques
Authors: Weiser Rebecca , Oakley Juliette , Jones Cerith , Mahenthiralingam Eshwar , Forton Julian 
Published: April 2019

Background
Children with cystic fibrosis are frequently non-productive of sputum even during exacerbation. Current routine sampling methods are either invasive (Bronchoalveolar lavage; BAL) or insensitive (cough swab) which makes pathogen surveillance challenging. We investigated induced sputum (IS) as a promising complementary sampling technique, looking at both its comparison to BAL and the evolution of the lung microbiota across children aged 0.5–18 years.

Methods
BAL and IS samples were collected as part of the CF-SpIT study (UKCRN14615; ISRCTNR12473810). DNA was extracted from samples and Illumina NextSeq sequencing of the 16S rRNA gene V4 region was performed. Bioinformatics data processing was carried out using Mothur. Microsoft Excel and R statistical software were used for downstream analyses.

Results
Comparison of the microbiota of 30 BAL-IS matched patient samples indicated that at a presence/absence level, IS captured >80 % of the pathogens observed in BAL samples. These findings validated the expansion of the study to 136 un-matched IS sputum samples, and we found that as patient age increased, bacterial diversity decreased, and changes in the abundance of key genera occurred over time. Both Neisseria and Haemophilus decreased with age, whilst Pseudomonas and a sub-group of Prevotella increased.

Conclusions
Here we uniquely demonstrate using culture-independent techniques that IS captures the majority of the bacterial diversity observed in BAL samples. The age associated decline in lung microbiota diversity, previously documented using BAL samples, can also be captured using IS samples. This suggests that surveillance of microbiota evolution may be possible using this method.
Identification of novel factors associated with severe respiratory syncytial virus disease in infants
Authors: Parke Hong Guo , Groves Helen , Broadbent Lindsay , Touzelet Olivier , Douglas Isobel , Campos Guillermo Lopez , Canning Paul , Lyons Jeremy D. , Coyle Peter , Heaney Liam , Shields Michael D. , Power Ultan F. 
Published: April 2019

Background
Almost all infants are infected with RSV by 2 years. 1–3 % of RSV-infected infants are hospitalised with severe disease. Reasons for susceptibility to severe disease remain obscure. We aimed to identify factors that might explain such susceptibility.

Methods
We generated well-differentiated primary nasal epithelial cell (WD-PNEC) cultures from infants with histories of severe or mild RSV disease. Following infection with RSV BT2a (clinical isolate), virus growth kinetics, cytopathogenesis, chemokines, and IL-29/IFNλ1 responses and differential gene expression were determined. In an exciting development, 1 differentially expressed gene, ptn, encodes pleiotrophin (PTN), which interacts with nucleolin (NCL), an RSV entry co-factor. The PTN antiviral activity was determined in BEAS-2B cells and WD-PBECs (where B=bronchial).

Results
Viral growth kinetics, cell tropism, IP-10/CXCL10, TRAIL and RANTES/CCL5 responses did not differ significantly between cohorts. However, apical cell sloughing and IL-29/IFNλ1 were diminished in severe WD-PNECs following infection, while expression of isg15, ifi6, irf9, duox2 and tap1 was also reduced. Interestingly, diminished ptn expression was evident in severe WD-PNECs, irrespective of RSV infection. Furthermore, pre-treatment with PTN blocked RSV infection in BEAS-2B cells and WD-PBECs, while neutralisation of PTN with either antibodies or siRNAs resulted in increased RSV replication.

Conclusions
Diminished apical cell sloughing and expression/secretion of IL-29/IFNλ1 and specific interferon stimulated genes in WD-PNECs were associated with severe RSV. Importantly, PTN was identified as a novel endogenously expressed RSV antiviral protein in human airway epithelium. Lower expression of PTN in paediatric airway epithelium may explain, in part, increased susceptibility to severe disease.
First report of New Clonal groups ST706 and ST1088 from MDR Klebsiella pneumoniae Mexican strains
Authors: Córdova-Espinoza María Guadalupe , Hernández Arana Eder Daniel , Giono-Cerezo Silvia , Sierra Atanacio Erika Gabriela , Tapia Eduardo Carrillo , Carrillo Vázquez Laura Isabel , González-Vázquez Rosa 
Published: April 2019

AbstractMultidrug-resistant Klebsiella pneumoniae Mexican strains were characterized for the identification of endemic and pandemic clonal groups. The aims of this study were to know population structure and to identify endemic clonal groups inside K. pneumoniae Mexican strains isolated from clinical sources. We studied 93 isolated strains from three third level hospitals and one family clinic from Mexico City. Identification of the strains was done by conventional microbiological methods and an automated system (Vitek2®). The multidrug-resistant phenotype was confirmed following CLSI recommendations, and the strains were classified as MDR, XDR and PDR. Molecular characterization was done by Multilocus Sequence Typing scheme (rpoB, gapA, mdh, pgi, phoE, infB, y tonB). All strains were isolated from hospitalized patients, the most frequent sources were urine and blood cultures. Population structure of K. pneumoniae was clonal, 30 ST were identified, six of them are commonly found. The Clonal complex ST25, ST36, S5392, ST405 and ST551 were isolated from clinical sources, ST1088 was isolated from surfaces of hospital environment.
Enhancers facilitate the birth of de novo genes and their integration into regulatory networks
Authors: Majic Paco , Payne Joshua L. 
Published: April 2019

AbstractRegulatory networks control the spatiotemporal gene expression patterns that give rise to and define the individual cell types of multicellular organisms. In eumetazoa, distal regulatory elements called enhancers play a key role in determining the structure of such networks, particularly the wiring diagram of “who regulates whom.” Mutations that affect enhancer activity can therefore rewire regulatory networks, potentially causing changes in gene expression that are adaptive. Here, we use whole-tissue and single-cell transcriptomic and chromatin accessibility data from mouse to show that enhancers play an additional role in the evolution of regulatory networks: They facilitate network growth by creating transcriptionally active regions of open chromatin that are conducive to de novo gene evolution. Specifically, our comparative transcriptomic analysis with three other mammalian species shows that young, mouse-specific intergenic open reading frames are preferentially located near enhancers, whereas older open reading frames are not. Mouse-specific intergenic open reading frames that are proximal to enhancers are more highly and stably transcribed than those that are not proximal to enhancers or promoters, and they are transcribed in a limited diversity of cellular contexts. Furthermore, we report several instances of mouse-specific intergenic open reading frames that are proximal to promoters that show evidence of being repurposed enhancers. We also show that open reading frames gradually acquire specific interactions with enhancers over macro-evolutionary timescales, helping integrate new genes into existing regulatory networks. Taken together, our results highlight a dual role of enhancers in expanding and rewiring gene regulatory networks.
A comprehensive characterization of rhythmic spiking activity in the rat ventral striatum
Authors: van der Meer Matthijs A. A. , Gmaz Jimmie M. , Carmichael J. Eric 
Published: April 2019

AbstractThe ventral striatum (vStr) is anatomically interconnected with brain structures that exhibit prominent rhythmic activity, suggesting that oscillations in ventral striatal activity are potentially informative about systems-level interactions between these structures. However, rhythmic activity in ventral striatal neurons during behavior has only been characterized piecemeal, with individual studies focusing on a single cell type or frequency band. We performed a comprehensive analysis of (1) rhythmic activity in vStr neurons without reference to the local field potential, and (2) average as well as time-resolved spike-field relationships. Spike train rhythmicity tended to be limited to low frequencies such as delta and theta, whereas spike-field relationships were seen across a broad spectrum of frequencies, with about 90% of neurons showing spike-field locking to at least one rhythm. Using a novel time-resolved generalized linear model approach, we further show that the contribution of local field potential (LFP) phase to spike timing is dynamic over time, and enhanced by the inclusion of the LFP from the hippocampus – a new measure of inter-area coupling. These results provide a foundation for a more accurate interpretation of the ventral striatal LFP, suggest the possibility of an oscillatory taxonomy of ventral striatal neurons, and provide a starting point for understanding how rhythmic activity links cell-, circuit-, and systems-level phenomena in the ventral striatum.Significance StatementOscillations in neural activity are ubiquitous in the brain, readily accessible in the clinic and the lab, and shared by humans and animals to facilitate translational work. The ventral striatum (vStr) is a promising target structure for such a rhythmic activity perspective, not in the least because its local field potential (LFP) shows prominent task-related oscillations across a range of frequencies. However, recent work has shown that major components of the vStr LFP are in fact generated elsewhere in the brain, raising the question of how the LFP relates to local spiking activity. Unlike previous studies that focused on a specific cell type or frequency band of interest, we characterize rhythmic activity across a full range range of frequencies and cell types, and include novel analyses appropriate for a non-local LFP. Our results provide a foundation for more accurate interpretation of the vStr LFP and a starting point for an oscillatory taxonomy of vStr neurons.
SEC issues warning to analysts profiting from “short and distort” schemes, opens the door for civil claims
Authors: Weiner Perrie Michael , Totino Edward D. , Goodman Aaron 
Published: April 2019

Purpose
To analyze the evolution of market manipulation and fraud by short-sellers and online bloggers and mechanisms available for addressing and remediating the damage caused by such fraud, including recent activity by the US Securities and Exchange Commission (the “SEC” or “Commission”).

Design/methodology/approach
This article discusses the development of a modern market manipulation and fraud scheme – the “short and distort” – including a review of potential claims by the targeted companies and anticipated impediments to asserting such claims.It further examines the need for regulation and the possibility that the SEC has opened the door for civil claims for this type of fraud.

Findings
Companies wrongfully targeted by illegitimate short-sellers may pursue claims for securities violations, defamation, business interference, securities fraud and extortion, among other claims.However, each of these claims has had, and still has, both business and legal challenges, as the short-seller’s initial defense tends to be to attempt to prove the truth of their statements to the market or establish those statements as legitimate opinion.The SEC has made the pursuit easier but there is still a long way to go.

Originality/value
This article contains valuable information about recent SEC enforcement activity and practical guidance from experienced securities lawyers.
Exploring indigenous fermented foods of India for the presence of lactic acid bacteria
Authors: Lamba Joshita , Goomer Sangeeta , Nain Lata 
Published: April 2019

Purpose
The Indian diet is rich in all the essential nutrients required for the well-being of human life. Probiotics have always been part of our traditional diet but microbiota of traditional fermented foods has not been explored. This study aims to analyse various traditional Indian fermented products for their probiotic nature.

Design/methodology/approach
Fermented indigenous products such as kanji, vegetable pickles and curd were prepared under controlled conditions and stored at ambient temperatures for shelf life studies. During the shelf life study, pH, titratable acidity and Lactic acid bacteria (LAB) count were estimated.

Findings
LAB counts ranged between 106 and 108 cfu/g in all the products, reflective of the probiotic nature of the products. Growth was observed even at low pH of 2.77 in product such as lemon chilli and ginger pickle. The 16S RNA-based sequencing technique was used for the identification of probiotic organisms present in the product. Enterococcus lactis, enterococcus durans, bacillus subtilis and lactobacillus plantarum were detected in the products.

Practical implications
These observations emphasise the need to undertake in-depth analysis of the viability of LAB in these fermented Indian foods for improving their nutritional properties. A need exists to explore and popularise more indigenous fermented products as probiotics.

Originality/value
India has a very rich and diverse food culture which differs from one region to other. This is because of difference in climatic conditions which has led to variety of food products. There are many products prepared locally and are not studied scientifically. This study aimed to explore these products for the presence of LAB which could have a probiotic potential.