bluuebunny/crossref_metadata_2025_split huggingface dataset:
High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea
Authors: Cortey Martí , Díaz Ivan , Vidal Anna , Martín-Valls Gerard , Franzo Giovanni , Gómez de Nova Pedro José , Darwich Laila , Puente Héctor , Carvajal Ana , Martín Marga , Mateu Enric 
Published: December 2019

Abstract
Background
Diarrhoea is a major cause of death in neonate pigs and most of the viruses that cause it are RNA viruses. Next Generation Sequencing (NGS) deeply characterize the genetic diversity among rapidly mutating virus populations at the interspecific as well as the intraspecific level. The diversity of RNA viruses present in faeces of neonatal piglets suffering from diarrhoea in 47 farms, plus 4 samples from non-diarrhoeic piglets has been evaluated by NGS. Samples were selected among the cases submitted to the Veterinary Diagnostic Laboratories of Infectious Diseases of the Universitat Autònoma de Barcelona (Barcelona, Spain) and Universidad de León (León, Spain).

Results
The analyses identified the presence of 12 virus species corresponding to 8 genera of RNA viruses. Most samples were co-infected by several viruses. Kobuvirus and Rotavirus were more commonly reported, with Sapovirus, Astrovirus 3, 4 and 5, Enterovirus G, Porcine epidemic diarrhoea virus, Pasivirus and Posavirus being less frequently detected. Most sequences showed a low identity with the sequences deposited in GenBank, allowing us to propose several new VP4 and VP7 genotypes for Rotavirus B and Rotavirus C.

Conclusions
Among the cases analysed, Rotaviruses were the main aetiological agents of diarrhoea in neonate pigs. Besides, in a small number of cases Kobuvirus and Sapovirus may also have an aetiological role. Even most animals were co-infected in early life, the association with enteric disease among the other examined viruses was unclear. The NGS method applied successfully characterized the RNA virome present in faeces and detected a high level of unreported intraspecific diversity.
A female patient with retinoblastoma and severe intellectual disability carrying an X;13 balanced translocation without rearrangement in the RB1 gene: a case report
Authors: Tsutsumi Makiko , Hattori Hiroyoshi , Akita Nobuhiro , Maeda Naoko , Kubota Toshinobu , Horibe Keizo , Fujita Naoko , Kawai Miki , Shinkai Yasuko , Kato Maki , Kato Takema , Kawamura Rie , Suzuki Fumihiko , Kurahashi Hiroki 
Published: December 2019

AbstractBackgroundFemale carriers of a balanced X; autosome translocation generally undergo selective inactivation of the normal X chromosome. This is because inactivation of critical genes within the autosomal region of the derivative translocation chromosome would compromise cellular function. We here report a female patient with bilateral retinoblastoma and a severe intellectual disability who carries a reciprocal X-autosomal translocation.Case presentationCytogenetic and molecular analyses, a HUMARA (Human androgen receptor) assay, and methylation specific PCR (MSP) and bisulfite sequencing were performed using peripheral blood samples from the patient. The patient’s karyotype was 46,X,t(X;13)(q28;q14.1) by G-banding analysis. Further cytogenetic analysis located the entireRB1gene and its regulatory region on der(X) with no translocation disruption. The X-inactivation pattern in the peripheral blood was highly skewed but not completely selected. MSP and deep sequencing of bisulfite-treated DNA revealed that an extensive 13q region, including theRB1promoter, was unusually methylated in a subset of cells.ConclusionsThe der(X) region harboring theRB1gene was inactivated in a subset of somatic cells, including the retinal cells, in the patient subject which acted as the first hit in the development of her retinoblastoma. In addition, the patient’s intellectual disability may be attributable to the inactivation of the der(X), leading to a 13q deletion syndrome-like phenotype, or to an active X-linked gene on der (13) leading to Xq28 functional disomy.
Smoking heroin with cannabis versus injecting heroin: unexpected impact on treatment outcomes
Authors: Morgan Nirvana , Daniels William , Subramaney Ugasvaree 
Published: December 2019

Abstract
Background
In several countries, especially in Africa, the dominant method of heroin intake is smoking a joint of cannabis laced with heroin. There is no data exploring the impact of smoking heroin with cannabis on treatment outcomes.

Aim
To compare treatment outcomes between people who inject heroin and people who smoke heroin with cannabis.

Methodology
Three hundred heroin users were assessed on admission to inpatient rehabilitation and after treatment. We compared drug use, psychopathology, criminality, social functioning and general health between heroin injectors and heroin-cannabis smokers at treatment entry, and at 3 and 9 months after rehabilitation.

Results
The sample comprised 211 (70.3%) heroin-cannabis smokers and 89 (29.7%) heroin injectors. Eighty-four percent were followed up at 3 months and 75% at 9 months. At 9 months, heroin-cannabis smokers had a higher proportion of those who relapsed to heroin use compared with intravenous (IV) users (p = 0.036). The median number of heroin use episodes per day was lower for IV users than heroin-cannabis smokers at both follow-up points (p = 0.013 and 0.0019). A higher proportion of IV users was HIV positive (p = 0.002). There were no significant differences in psychopathology, general health, criminality and social functioning between IV users and heroin-cannabis smokers at all three time points.

Conclusions
Heroin users who do not inject drugs but use other routes of administration may have increased risk for relapse to heroin use after inpatient rehabilitation and should therefore have equal access to harm reduction treatment services. Advocating a transition from injecting to smoking heroin in an African context may pose unique challenges.
Family composition and age at menarche: Findings from the international Health Behaviour in School-aged Children study
Authors: Steppan Martin , Whitehead Ross , McEachran Juliet , Currie Candace 
Published: December 2019

AbstractBackgroundEarly menarche has been associated with father absence, stepfather presence and adverse health consequences in later life. This article assesses the association of different family compositions with the age at menarche. Pathways are explored which may explain any association between family characteristics and pubertal timing.MethodsCross-sectional, international data on the age at menarche, family structure and covariates (age, psychosomatic complaints, media consumption, physical activity) were collected from the 2009–2010 Health Behaviour in School-aged Children (HBSC) survey. The sample focuses on 15-year old girls comprising 36,175 individuals across 40 countries in Europe and North America (N = 21,075 for age at menarche). The study examined the association of different family characteristics with age at menarche. Regression and path analyses were applied incorporating multilevel techniques to adjust for the nested nature of data within countries.ResultsLiving with mother (Cohen’s d = .12), father (d = .08), brothers (d = .04) and sisters (d = .06) are independently associated with later age at menarche. Living in a foster home (d = −.16), with ‘someone else’ (d = −.11), stepmother (d = −.10) or stepfather (d = −.06) was associated with earlier menarche. Path models show that up to 89% of these effects can be explained through lifestyle and psychological variables.ConclusionsEarlier menarche is reported amongst those with living conditions other than a family consisting of two biological parents. This can partly be explained by girls’ higher Body Mass Index in these families which is a biological determinant of early menarche. Lower physical activity and elevated psychosomatic complaints were also more often found in girls in these family environments.
The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon
Authors: Cheng Jinghua , Tao Jie , Li Benqiang , Shi Ying , Liu Huili 
Published: December 2019

Abstract
Background
Nonstructural protein 1 (NS1) is a virulence factor encoded by influenza A virus (IAV) that is expressed in the nucleus and cytoplasm of host cells during the earliest stages of infection. NS1 is a multifunctional protein that plays an important role in virus replication, virulence and inhibition of the host antiviral immune response. However, to date, the phosphorylation sites of NS1 have not been identified, and the relationship between phosphorylation and protein function has not been thoroughly elucidated.

Method
In this study, potential phosphorylation sites in the swine influenza virus (SIV) NS1 protein were bioinformatically predicted and determined by Phos-tag SDS-PAGE analysis. To study the role of NS1 phosphorylation sites, we rescued NS1 mutants (Y73F and S83A) of A/swine/Shanghai/3/2014(H1N1) strain and compared their replication ability, cytokine production as well as the intracellular localization in cultured cells. Additionally, we used small interfering RNA (siRNA) assay to explore whether changes in the type I IFN response with dephosphorylation at positions 73 and 83 were mediated by the RIG-I pathway.

Results
We checked 18 predicted sites in 30 SIV NS1 genes to exclude strain-specific sites, covering H1N1, H1N2 and H3N2 subtypes and identified two phosphorylation sites Y73 and S83 in the H1N1 SIV protein by Phos-tag SDS-PAGE analysis. We found that dephosphorylation at positions 73 and 83 of the NS1 protein attenuated virus replication and reduced the ability of NS1 to antagonize IFN-β expression but had no effect on nuclear localization. Knockdown of RIG-I dramatically impaired the induction of IFN-β and ISG56 in NS1 Y73F or S83A mutant-infected cells, indicating that RIG-I plays a role in the IFN-β response upon rSIV NS1 Y73F and rSIV NS1 S83A infection.

Conclusion
We first identified two functional phosphorylation sites in the H1N1 SIV protein: Y73 and S83. We found that dephosphorylation at positions 73 and 83 of the NS1 protein affected the antiviral state in the host cells, partly through the RIG-I pathway.
PCR-based reverse genetics strategy for bluetongue virus recovery
Authors: Xu Qingyuan , Ge Jinying , Li Maolin , Sun Encheng , Zhou Yawei , Guo Yunze , Wu Donglai , Bu Zhigao 
Published: December 2019

Abstract
Background
Bluetongue virus (BTV), an emerging insect vector mediated pathogen affecting both wild ruminants and livestock, has a genome consisting of 10 linear double-stranded RNA genome segments. BTV has a severe economic impact on agriculture in many parts of the world. Current reverse genetics (RG) strategy to rescue BTV mainly rely on in vitro synthesis of RNA transcripts from cloned complimentary DNA (cDNA) corresponding to viral genome segments with the aid of helper plasmids. RNA synthesis is a laborious job which is further complicated with a need for expensive reagents and a meticulous operational procedure. Additionally, the target genes must be cloned into a specific vector to prepare templates for RNA transcription.

Result
In this study, we have developed a PCR based BTV RG system with easy two-step transfection. Viable viruses were recovered following a first transfection with the seven helper plasmids and a second transfection with the 10 PCR products on the BSR cells. Further, recovered viruses were characterized with indirect immunofluorescence assays (IFA) and gene sequencing. And the proliferation properties of these viruses were also compared with wild type BTV. Interestingly, we have identified that viruses containing the segment 2 of the genome from reassortant BTV, grew slightly slower than the others.

Conclusion
In this study, a convenient PCR based RG platform for BTV is established, and this strategy could be an effective alternative to the original available BTV rescue methods. Furthermore, this RG strategy is likely applicable for other Orbiviruses.
Non-invasive diagnosis of viability in seeds and lichens by infrared thermography under controlled environmental conditions
Authors: Fernández-Marín Beatriz , Buchner Othmar , Kastberger Gerald , Piombino Federica , García-Plazaola José Ignacio , Kranner Ilse 
Published: December 2019

Abstract
Background
Non-invasive procedures for the diagnosis of viability of plant or fungal tissues would be valuable for scientific, industrial and biomonitoring purposes. Previous studies showed that infrared thermography (IRT) enables non-invasive assessment of the viability of individual "orthodox" (i.e. desiccation tolerant) seeds upon water uptake. However, this method was not tested for rehydrating tissues of other desiccation tolerant life forms. Furthermore, evaporative cooling could obscure the effects of metabolic processes that contribute to heating and cooling, but its effects on the shape of the "thermal fingerprints" have not been explored. Here, we further adapted this method using a purpose-built chamber to control relative humidity (RH) and gaseous atmosphere. This enabled us to test (i) the influence of relative humidity on the thermal fingerprints during the imbibition of Pisum sativum (Garden pea) seeds, (ii) whether thermal fingerprints can be correlated with viability in lichens, and (iii) to assess the potential influence of aerobic metabolism on thermal fingerprints by controlling the oxygen concentration in the gaseous atmosphere around the samples. Finally, we developed a method to artificially "age" lichens and validated the IRT-based method to assess lichen viability in three lichen species.

Results
Using either 30% or 100% RH during imbibition of pea seeds, we showed that "live" and "dead" seeds produced clearly discernible "thermal fingerprints", which significantly differed by > |0.15| °C in defined time windows, and that RH affected the shape of these thermal fingerprints. We demonstrated that IRT can also be used to assess the viability of the lichens Lobaria pulmonaria, Pseudevernia furfuracea and Peltigera leucophlebia. No clear relationship between aerobic metabolism and the shape of thermal fingerprints was found.

Conclusions
Infrared thermography appears to be a promising method for the diagnosis of viability of desiccation-tolerant tissues at early stages of water uptake. For seeds, it is possible to diagnose viability within the first hours of rehydration, after which time they can still be re-dried and stored until further use. We envisage our work as a baseline study for the use of IR imaging techniques to investigate physiological heterogeneity of desiccation tolerant life forms such as lichens, which can be used for biomonitoring, and for sorting live and dead seeds, which is potentially useful for the seed trade.
The last 10 years: any changes in perceptions of the seriousness of alcohol, cannabis, and substance use in Canada?
Authors: Cunningham John A. , Koski-Jännes Anja 
Published: December 2019

AbstractBackgroundOver the last decade, there have been a number of changes in the Canadian landscape - the deconstruction of alcohol policy in some provinces, the legalization of cannabis, increased availability of gambling options, and the increase in opioid use and its associated problems. Have there been concomitant changes in societal images of addictions?MethodsA general population survey on societal images of addictions was conducted in multiple countries in 2008 - Finland, Sweden, Canada (Canadian sample size:N = 864; 40% response rate), and part of Russia (St Petersburg). We repeated the same survey in 2018 in Canada (N = 813; response rate = 23%). The survey assessed perceptions of the seriousness of different issues to society - including items about alcohol, tobacco, marijuana, gambling, misuse of medical drugs, and drugs like amphetamine, cocaine, or heroin - among other items (e.g., pollution, violent crime, prostitution).ResultsThere were increases in perceptions of the seriousness of misuse of medical drugs (p = .001), of illicit drugs (p = .005), ratings of the seriousness of cannabis use (p = .02), and a decrease in ratings of gambling as a social problem (p = .04). Ratings of the seriousness of alcohol and tobacco as social problems did not display significant changes over time (p > .05).ConclusionsThere has been some variation in societal perceptions of the seriousness of different addictions. Increases in perceptions of the seriousness of misusing medical drugs and the use of illicit drugs may reflect increases in societal concerns about opioid use and its associated problems. Despite substantial changes in alcohol control policies, the legalization of cannabis, and the increased availability of options for gambling, there appears to be very little associated change in societal perceptions regarding these addictive behaviours.
Does increased implementation support improve community clinics’ guideline-concordant care? Results of a mixed methods, pragmatic comparative effectiveness trial
Authors: Gold Rachel , Bunce Arwen , Cowburn Stuart , Davis James V. , Nelson Joan C. , Nelson Christine A. , Hicks Elisabeth , Cohen Deborah J. , Horberg Michael A. , Melgar Gerardo , Dearing James W. , Seabrook Janet , Mossman Ned , Bulkley Joanna 
Published: December 2019

Abstract
Background
Disseminating care guidelines into clinical practice remains challenging, partly due to inadequate evidence on how best to help clinics incorporate new guidelines into routine care. This is particularly true in safety net community health centers (CHCs).

Methods
This pragmatic comparative effectiveness trial used a parallel mixed methods design. Twenty-nine CHC clinics were randomized to receive increasingly intensive implementation support (implementation toolkit (arm 1); toolkit + in-person training + training webinars (arm 2); toolkit + training + webinars + offered practice facilitation (arm 3)) targeting uptake of electronic health record (EHR) tools focused on guideline-concordant cardioprotective prescribing for patients with diabetes. Outcomes were compared across study arms, to test whether increased support yielded additive improvements, and with 137 non-study CHCs that share the same EHR as the study clinics. Quantitative data from the CHCs’ EHR were used to compare the magnitude of change in guideline-concordant ACE/ARB and statin prescribing, using adjusted Poisson regressions. Qualitative data collected using diverse methods (e.g., interviews, observations) identified factors influencing the quantitative outcomes.

Results
Outcomes at CHCs receiving higher-intensity support did not improve in an additive pattern. ACE/ARB prescribing did not improve in any CHC group. Statin prescribing improved overall and was significantly greater only in the arm 1 and arm 2 CHCs compared with the non-study CHCs. Factors influencing the finding of no additive impact included: aspects of the EHR tools that reduced their utility, barriers to providing the intended implementation support, and study design elements, e.g., inability to adapt the provided support. Factors influencing overall improvements in statin outcomes likely included a secular trend in awareness of statin prescribing guidelines, selection bias where motivated clinics volunteered for the study, and study participation focusing clinic staff on the targeted outcomes.

Conclusions

Efforts to implement care guidelines should: ensure adaptability when providing implementation support and conduct formative evaluations to determine the optimal form of such support for a given clinic; consider how study data collection influences adoption; and consider barriers to clinics’ ability to use/accept implementation support as planned. More research is needed on supporting change implementation in under-resourced settings like CHCs.

Trial registration
ClinicalTrials.gov, NCT02325531. Registered 15 December 2014.
Epidemiology and prognosis of anti-infective therapy in the ICU setting during acute pancreatitis: a cohort study
Authors: Montravers Philippe , Kantor Elie , Constantin Jean-Michel , Lefrant Jean-Yves , Lescot Thomas , Nesseler Nicolas , Paugam Catherine , Jabaudon Matthieu , Dupont Hervé 
Published: December 2019

Abstract
Background
Recent international guidelines for acute pancreatitis (AP) recommend limiting anti-infective therapy (AIT) to cases of suspected necrotizing AP or nosocomial extrapancreatic infection. Limited data are available concerning empirical and documented AIT prescribing practices in patients admitted to the intensive care unit (ICU) for the management of AP.

Methods
Using a multicentre, retrospective (2009–2014), observational database of ICU patients admitted for AP, our primary objective was to assess the incidence of AIT prescribing practices during the first 30 days following admission. Secondary objectives were to assess the independent impact of centre characteristics on the incidence of AIT and to identify factors associated with crude hospital mortality in a logistic regression model.

Results
In this cohort of 860 patients, 359 (42%) received AIT on admission. Before day 30, 340/359 (95%) AIT patients and 226/501 (45%) AIT-free patients on admission received additional AIT, mainly for intra-abdominal and lung infections. A large heterogeneity was observed between centres in terms of the incidence of infections, therapeutic management including AIT and prognosis. Administration of AIT on admission or until day 30 was not associated with an increased mortality rate. Patients receiving AIT on admission had increased rates of complications (septic shock, intra-abdominal and pulmonary infections), therapeutic (surgical, percutaneous, endoscopic) interventions and increased length of ICU stay compared to AIT-free patients. Patients receiving delayed AIT after admission and until day 30 had increased rates of complications (respiratory distress syndrome, intra-abdominal and pulmonary infections), therapeutic interventions and increased length of ICU stay compared to those receiving AIT on admission. Risk factors for hospital mortality assessed on admission were age (adjusted odds ratio [95% confidence interval] 1.03 [1.02–1.05]; p < 0.0001), Balthazar score E (2.26 [1.43–3.56]; p < 0.0001), oliguria/anuria (2.18 [1.82–4.33]; p < 0.0001), vasoactive support (2.83 [1.73–4.62]; p < 0.0001) and mechanical ventilation (1.90 [1.15–3.14]; p = 0.011), but not AIT (0.63 [0.40–1.01]; p = 0.057).

Conclusions
High proportions of ICU patients admitted for AP receive AIT, both on admission and during their ICU stay. A large heterogeneity was observed between centres in terms of incidence of infections, AIT prescribing practices, therapeutic management and outcome. AIT reflects the initial severity and complications of AP, but is not a risk factor for death.