bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic Analysis for Iron-Uptake System of Campylobacter spp. in humans and chickens
Authors: Kiourkou Mariklairi , Ketley Julian , Barratt Natalie 
Published: May 2022

Asymptomatic Campylobacter jejuni colonisation is highly prevalent in chickens, however, it’s a major cause of bacterial foodborne disease in humans. Iron is an essential co-factor in many physiological processes and Campylobacter strains employ several non-redundant iron acquisition systems for survival and colonization. The outer membrane receptors CfrA and CfrB are involved in iron acquisition fromcatecholamine siderophores and are required for colonisation of the chicken GI tract. In contrast, ChuAB are part of an uptake system, enabling the utilization of iron in haem and is not required for colonisation. This study aims to compare differences in the iron-uptake systems present in Campylobacter strains isolated from chickens or humans.
Analysis of Campylobacter jejuni/coli genome sequences in PubMLST (https://pubmlst.org/organisms/campylobacter-jejunicoli [https://pubmlst.org/organisms/campylobacter-jejunicoli]) added from the UK in 2018 reveals differences in sequence type (ST) and chuA, chuB, cfrA and cfrB between isolates from chicken (CI) or human (HI) sources. ST828 was the most common ST for the C. coliCI (45%) and ST827 (32%) for the HI. C. jejuniST5136 was the most common of the HI (10%) and CI (13%), ST50 (8%) for the HI and ST21 (7%) for the CI. >95% of isolates contained chuAand chuB, we also found the Chu system to be highly conserved. For cfrA81% of HI and 74% of CI contained the gene, and 92% of HI and 96% of CI harboured cfrB.<3% of all isolates had neither cfrAor cfrB, cfrBmore associated with CI than HI. This data analysis reveals potential gene targets towards vaccine development against Campylobacter strains.
Controlling the lytic switch; can m6A-modified RNA be used as an Anti-Viral Target?
Authors: Barker Amy , Fullenkamp Chris , Roder Konstanin , Pasquali Samuela , Schneekloth Jay , Whitehouse Adrian 
Published: May 2022

KSHV has a biphasic life cycle encompassing a latent state and lytic replication. The KSHV replication and transcription activator viral protein, encoded from open reading frame 50 (ORF50), is the key viral protein which drives the switch between the latent and lytic phases (Guito and Lukac, 2012). We have recently demonstrated that KSHV manipulates the host cell N6-methyl adenosine (m6A) RNA modification pathway to enhance viral gene expression. Specifically, we have shown that the KSHV ORF50 transcript is m6A methylated, allowing the recruitment of the m6A reader protein, Staphylococcal nuclease domain-containing protein 1 (SND1), resulting in the stabilisation of the ORF50 transcript and efficient KSHV lytic replication (Baquero-Perez et al. 2019).
Further analysis of the m6A modified site with the ORF50 transcript has identified an RNA stem-loop, termed ORF50-1, which is a m6A-modified 43-mer, essential for SND-1 binding, thought to occur in a secondary structure/ sequence-dependent manner.
Generating in silico 3D structures of the ORF50-1 RNA in its native ‘N’ and m6A-modified ‘M’ form confirms that the presence of the m6A-modification has repercussions in the lower part of the stem-loop and predicts a different secondary structure(collab. Pasquale and Roeder).
Due to the obvious structural differences anticipated, RNA-binding ligands have been identified using Small Molecule Microarrays (SMMS) (collab. Fullenkamp and Schneekloth). By investigating these ligands in biophysicalexperiments, we have verified RNA-binding and optimised cell-based assays to assess anti-viral properties. It is hoped these experiments will highlight the importance of A versus m6A within the lytic phase of KSHV’s lifecycle.
Failing to control Maedi-Visna
Authors: Jones Scott , Lovatt Fiona , Davies Peers , Dunham Stephen , Tarlinton Rachael 
Published: May 2022

Maedi-Visna is a lentivirus of sheep that causes lung disease and chronic wasting. It has been designated an “Iceberg disease” by the UK sheep industry levy board with a very large burden of subclinical disease that is often not apparent until losses in an individual flock become catastrophic. Disease prevalence in the UK is thought to have doubled in the last 10 years, however farmer and veterinary awareness of the disease is poor. There is no vaccine and treatment is not cost effective, meaning that the only realistic control option is culling of affected animals.
Current testing protocols use MV gag protein ELISAs. A long lag time between infection and antibody production means that many animals are missed on flock screening and repeated rounds of testing over a period of years are necessary to remove all infected animals. Preliminary testing of flocks that have attempted eradication indicates that those that do not keep testing until all animals are negative fail to eliminate the disease and that prevalence rates can even increase substantially in these flocks. The viruses extreme variability confounded attempts to develop a qPCR capable of detecting all variants, indeed deep sequencing was required to establish which strains of virus are currently present in UK sheep as there has been substantial genetic drift since the last sequencing studies (performed more than 20 years ago). More promisingly virus was detectable in nasal swabs of experimental animals at least offering sampling methods that can be done by farmers themselves.
Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant
Authors: He Xiaoling , Lu Huibin , Hu Wenzhe , Deng Tongchu , Gong Xiaofan , Yang Xunan , Song Da , He Mei , Xu Meiying 
Published: May 2022

Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus

Novosphingobium

. The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of

Novosphingobium

species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1
ω7c, C18 : 0, C16 : 1
ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of

Novosphingobium

, for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.
Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER Programs
Authors: Reese Justin T. , Blau Hannah , Bergquist Timothy , Loomba Johanna J. , Callahan Tiffany , Laraway Bryan , Antonescu Corneliu , Casiraghi Elena , Coleman Ben , Gargano Michael , Wilkins Kenneth J. , Cappelletti Luca , Fontana Tommaso , Ammar Nariman , Antony Blessy , Murali T. M. , Karlebach Guy , McMurry Julie A , Williams Andrew , Moffitt Richard , Banerjee Jineta , Solomonides Anthony E. , Davis Hannah , Kostka Kristin , Valentini Giorgio , Sahner David , Chute Christopher G. , Madlock-Brown Charisse , Haendel Melissa A , Robinson Peter N. ,   the RECOVER Consortium
Published: May 2022

AbstractAccurate stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, the natural history of long COVID is incompletely understood and characterized by an extremely wide range of manifestations that are difficult to analyze computationally. In addition, the generalizability of machine learning classification of COVID-19 clinical outcomes has rarely been tested. We present a method for computationally modeling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning procedures. Using k-means clustering of this similarity matrix, we found six distinct clusters of PASC patients, each with distinct profiles of phenotypic abnormalities. There was a significant association of cluster membership with a range of pre-existing conditions and with measures of severity during acute COVID-19. Two of the clusters were associated with severe manifestations and displayed increased mortality. We assigned new patients from other healthcare centers to one of the six clusters on the basis of maximum semantic similarity to the original patients. We show that the identified clusters were generalizable across different hospital systems and that the increased mortality rate was consistently observed in two of the clusters. Semantic phenotypic clustering can provide a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.
Exploring county-level spatio-temporal patterns in opioid overdose related emergency department visits
Authors: Acharya Angeela , Izquierdo Alyssa M , Gonçalves Stefanie F , Bates Rebecca A , Taxman Faye S , Slawski Martin P , Rangwala Huzefa S , Sikdar Siddhartha 
Published: May 2022

AbstractOpioid overdoses within the United States continue to rise and have been negatively impacting the social and economic status of the country. In order to effectively allocate resources and identify policy solutions to reduce the number of overdoses, it is important to understand the geographical differences in opioid overdose rates and their causes. In this study, we utilized data on emergency department opioid overdose (EDOOD) visits to explore the county-level spatio-temporal distribution of opioid overdose rates within the state of Virginia and their association with aggregate socio-ecological factors. The analyses were performed using a combination of techniques including Moran’s I and multilevel modeling. Using data from 2016-2021, we found that Virginia counties had notable differences in their EDOOD visit rates with significant neighborhood-level associations: many counties in the southwestern region were consistently identified as the hotspots (areas with a higher concentration of EDOOD visits) whereas many counties in the northern region were consistently identified as the coldspots (areas with a lower concentration of EDOOD visits). In most Virginia counties, EDOOD visit rates declined from 2017 to 2018. In more recent years (since 2019), the visit rates showed an increasing trend. The multilevel modeling revealed that the change in clinical care factors (i.e., access to care and quality of care) and socio-economic factors (i.e., levels of education, employment, income, family and social support, and community safety) were significantly associated with the change in the EDOOD visit rates. The findings from this study have the potential to assist policymakers in proper resource planning thereby improving health outcomes.
Dementia and Alzheimer’s disease in former contact sports participants: population-based cohort study, systematic review, and meta-analysis
Authors: Batty G. David , Frank Philipp , Kujala Urho M. , Sarna Seppo J. , Valencia-Hernández Carlos A. , Kaprio Jaakko 
Published: May 2022

SummaryImportanceThere is uncertainty regarding the long-term risk of dementia in individuals with a history of participation in sports characterised by repetitive head impact, and whether the occurrence of this disease differs between former amateur and professional athletes.ObjectiveTo quantify the dementia risk in former athletes with a background in contact sports using new cohort study data incorporated into a meta-analysis.Data sources and study selectionThe cohort study comprised 2005 male retired athletes who had competed internationally for Finland (1920-1965) and a general population comparison group (N=1386). For the systematic review, we searched PubMed and Embase from their inception to August 23 2022, including cohort studies published in English that reported standard estimates of association and variance.Data extraction and synthesisStudies were screened and results extracted independently by two authors. Study-specific estimates were aggregated using random-effect meta-analysis. An adapted Cochrane Risk of Bias Tool was used to assess study quality.Main outcomes and measuresThe primary outcomes were dementia and Alzheimer’s disease.ResultsThe systematic review identified 827 potentially eligible published articles, of which 7 met the inclusion criteria. Incorporating the new results from the Finnish cohort study with those from the systematic review revealed that former boxers had higher rates of dementia (2 studies: summary risk ratio 3.14 [95% CI 1.72, 5.74], I2=34%) and Alzheimer’s disease (2 studies: 3.07 [1.01, 9.38], I2=55%), as did retired soccer players (3 studies of dementia: 2.78 [1.69, 4.59], I2=86%; 2 studies of Alzheimer’s disease: 3.22 [1.34, 7.75], I2=81%). While the pooled estimate for dementia in retired American football players was less convincing (4 studies: 1.63 [0.76, 3.49], I2=75%), disease occurrence in onetime professionals was markedly higher (2.96 [1.66, 5.30]) than amateurs in whom there was no association (0.90 [0.52, 1.56]). There was also a risk differential for retired professional (3.61 [2.92, 4.45]) and amateur (1.60 [1.11, 2.30]) soccer players.Conclusion and relevanceBased on studies exclusively comprising men, former participants in contact sports subsequently experienced poorer brain health, and there was a suggestion that retired professionals had the greatest risk.Key pointsQuestionDo former participants in contact sports have a greater risk of dementia than the general population?FindingsCompared with general population controls, retired male participants from the contact sports of boxing, soccer, and American football appeared to have an elevated risk of dementia at follow-up. For soccer and American football, the risk in former professionals was higher than erstwhile amateurs.MeaningRetired male contact sports participants seem to subsequently experience poorer brain health.
In the Midst of a Pandemic, Introverts May Have a Mortality Advantage
Authors: Glei Dana A. , Weinstein Maxine 
Published: May 2022

ABSTRACTExtroverts may enjoy lower mortality than introverts under normal circumstances, but the relationship may be different during an airborne pandemic when social contact can be deadly. We used data for midlife Americans surveyed in 1995-96 with mortality follow-up through December 31, 2020 to investigate whether the association between extroversion and mortality changed during the COVID-19 pandemic. We hypothesized that excess mortality during the pandemic will be greater for extroverts than for introverts. Results were based on a Cox model estimating age-specific mortality controlling for sex, race/ethnicity, the period trend in mortality, and an additional indicator for the pandemic period (Mar-Dec 2020). We interacted extroversion with the pandemic indicator to test whether the relationship differed between prepandemic and pandemic periods. Prior to the pandemic, extroversion was associated with somewhat lower mortality (HR=0.93 per SD, 95% CI 0.88-0.97), but the relationship reversed during the pandemic: extroverted individuals appeared to suffer higher mortality than their introverted counterparts, although the effect was not significant (HR=1.20 per SD, 95% CI 0.93-1.54).Extroversion was associated with greater pandemic-related excess mortality (HR=1.20/0.93=1.29 per SD, 95% CI 1.00-1.67). Compared with someone who scored at the mean level of extroversion, mortality rates prior to the pandemic were 10% lower for a person who was very extroverted (i.e., top 12% of the sample at Wave 1), while they were 12% higher for someone who was very introverted (i.e., 11th percentile). In contrast, mortality rates during the pandemic appeared to be higher for very extroverted individuals (HR=1.15, 95% CI 0.77-1.71) and lower for those who were very introverted (HR=0.70, 95% CI 0.43-1.14) although the difference was not significant because of limited statistical power. In sum, the slight mortality advantage enjoyed by extroverts prior to the pandemic disappeared during the first 10 months of the COVID-19 pandemic. It remains to be seen whether that pattern continued into 2021-22. We suspect that the mortality benefit of introversion during the pandemic is largely a result of reduced exposure to the risk of infection, but it may also derive in part from the ability of introverts to adapt more easily to reduced social interaction without engaging in self-destructive behavior (e.g., drug and alcohol abuse). Introverts have been training for a pandemic their whole lives.
Pattern, preferences, barriers, and correlates of self-reported physical activity in adults with borderline personality disorder: An online survey in western countries
Authors: St-Amour Samuel , Cailhol Lionel , Lapointe Josyanne , Ducasse Déborah , Landry Gabrielle , Bernard Paquito 
Published: May 2022

AbstractBorderline personality disorder (BPD) is characterized by an instability of self-image, interpersonal relationships, and emotions and is highly comorbid with other disorders. Physical activity has shown great results in treating these disorders. Physical activity intervention should be built considering the preferences and barriers of the targeted individuals. However, to this day no study analyzed the preferences and barriers to physical activity in individuals with BPD, which is the goal of this study. We used an online survey to question 192 adults with a self-reported diagnosis of BPD from Canada, France, the United States, England, Switzerland, and New Zealand. Participants complete 607 minutes of physical activity weekly on average. They prefer walking (66.7%), biking (33.3%), aquatic activities (29.0%), and running (24.2%). Their main barriers to physical activity are having a friend over, having other engagements, and recovering from an injury. They also prefer doing individual supervised physical activity outside and in a long session of moderate intensity. Finally, a majority of participants are interested in receiving physical activity advice, but most did not. The professionals from whom they would prefer to receive advice are trainers, psychiatrists, physical therapists, and psychologists. These results are important to better tailor future physical activity interventions for adults with BPD.
The effects of reduced nicotine content cigarettes in smokers with mood or anxiety disorders: a double-blind randomized trial
Authors: Foulds Jonathan , Veldheer Susan , Pachas Gladys , Hrabovsky Shari , Hameed Ahmad , Allen Sophia I , Cather Corinne , Azzouz Nour , Yingst Jessica , Hammett Erin , Modesto Jennifer , Krebs Nicolle M , Lester Courtney , Trushin Neil , Reinhart Lisa , Wasserman Emily , Zhu Junjia , Liao Jason , Muscat Joshua E , Richie John P , Evins A Eden 
Published: May 2022

ABSTRACTBACKGROUNDThe U.S. Food and Drug Administration and the government of New Zealand have proposed a reduction of the nicotine content in cigarettes to very low levels. This study examined the likely effects of this regulation in smokers with affective disorders.METHODSIn a randomized controlled trial conducted at two sites (Penn State Hershey and Massachusetts General Hospital, Boston) 188 adult smokers with a current or lifetime anxiety or unipolar mood disorder, not planning to quit in the next 6 months, were randomly assigned to smoke either Usual Nicotine Content (UNC) (11.6 mg nicotine/cigarette) cigarettes, or Reduced Nicotine Content (RNC) cigarettes where the nicotine content per cigarette was progressively reduced to 0.2 mg in five steps over 18 weeks. Participants were then offered the choice to either receive assistance to quit smoking, receive free research cigarettes, or resume using their own cigarette brand during a 12-week follow-up period. Main outcomes were biomarkers of nicotine and toxicant exposure, smoking behavior and dependence and severity of psychiatric symptoms.RESULTSAfter switching to the lowest nicotine content cigarettes, compared to smokers in the UNC group, the RNC group had significantly lower plasma cotinine (metabolite of nicotine), urine NNAL (metabolite of NNK, a lung carcinogen), exhaled carbon-monoxide, cigarette consumption, and cigarette dependence. There were no significant effects on psychiatric symptoms. At the end of the 12-week treatment choice phase, those randomized to the RNC group were more likely to have quit smoking (18% RNC v 4% UNC, p=0.004).CONCLUSIONReducing nicotine content in cigarettes to very low levels reduces toxicant exposure and cigarette addiction and increases smoking cessation in smokers with mood and/or anxiety disorders, without worsening mental health.Trial registrationTRN: NCT01928758, registered August 21, 2013