bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copy Number Heterogeneity of JC Virus Standards
Authors: Greninger Alexander L. , Bateman Allen C. , Atienza Ederlyn E. , Wendt Sharon , Makhsous Negar , Jerome Keith R. , Cook Linda 
Published: January 2017

ABSTRACT
Quantitative PCR is a diagnostic mainstay of clinical virology, and accurate quantitation of viral load among labs requires the use of international standards. However, the use of multiple passages of viral isolates to obtain sufficient material for international standards may result in genomic changes that complicate their use as quantitative standards. We performed next-generation sequencing to obtain single-nucleotide resolution and relative copy number of JC virus (JCV) clinical standards. Strikingly, the WHO international standard and the Exact v1/v2 prototype standards for JCV showed 8-fold and 4-fold variation in genomic coverage between different loci in the viral genome, respectively, due to large deletions in the large T antigen region. Intriguingly, several of the JCV standards sequenced in this study with large T antigen deletions were cultured in cell lines immortalized using simian virus 40 (SV40) T antigen, suggesting the possibility of transcomplementation in cell culture. Using a cutoff 5% allele fraction for junctional reads, 7 different rearrangements were present in the JC virus sequences present in the WHO standard across multiple library preparations and sequencing runs. Neither the copy number differences nor the rearrangements were observed in a clinical sample with a high copy number of JCV or a plasmid control. These results were also confirmed by the quantitative real-time PCR (qPCR), droplet digital PCR (ddPCR), and Sanger sequencing of multiple rearrangements. In summary, targeting different regions of the same international standard can result in up to an 8-fold difference in quantitation. We recommend the use of next-generation sequencing to validate standards in clinical virology.
Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain
Authors: Naito Tadasuke , Mori Kotaro , Ushirogawa Hiroshi , Takizawa Naoki , Nobusawa Eri , Odagiri Takato , Tashiro Masato , Ohniwa Ryosuke L. , Nagata Kyosuke , Saito Mineki 
Published: January 2017

ABSTRACT
Vaccination is considered the most effective preventive means for influenza control. The development of a master virus with high growth and genetic stability, which may be used for the preparation of vaccine viruses by gene reassortment, is crucial for the enhancement of vaccine performance and efficiency of production. Here, we describe the generation of a high-fidelity and high-growth influenza vaccine master virus strain with a single V43I amino acid change in the PB1 polymerase of the high-growth A/Puerto Rico/8/1934 (PR8) master virus. The PB1-V43I mutation was introduced to increase replication fidelity in order to design an H1N1 vaccine strain with a low error rate. The PR8-PB1-V43I virus exhibited good replication compared with that of the parent PR8 virus. In order to compare the efficiency of egg adaptation and the occurrence of gene mutations leading to antigenic alterations, we constructed 6:2 genetic reassortant viruses between the A(H1N1)pdm09 and the PR8-PB1-V43I viruses; hemagglutinin (HA) and neuraminidase (NA) were from the A(H1N1)pdm09 virus, and the other genes were from the PR8 virus. Mutations responsible for egg adaptation mutations occurred in the HA of the PB1-V43I reassortant virus during serial egg passages; however, in contrast, antigenic mutations were introduced into the HA gene of the 6:2 reassortant virus possessing the wild-type PB1. This study shows that the mutant PR8 virus possessing the PB1 polymerase with the V43I substitution may be utilized as a master virus for the generation of high-growth vaccine viruses with high polymerase fidelity, low error rates of gene replication, and reduced antigenic diversity during virus propagation in eggs for vaccine production.

IMPORTANCE
Vaccination represents the most effective prophylactic option against influenza. The threat of emergence of influenza pandemics necessitates the ability to generate vaccine viruses rapidly. However, as the influenza virus exhibits a high mutation rate, vaccines must be updated to ensure a good match of the HA and NA antigens between the vaccine and the circulating strain. Here, we generated a genetically stable master virus of the A/Puerto Rico/8/1934 (H1N1) backbone encoding an engineered high-fidelity viral polymerase. Importantly, following the application of the high-fidelity PR8 backbone, no mutation resulting in antigenic change was introduced into the HA gene during propagation of the A(H1N1)pdm09 candidate vaccine virus. The low error rate of the present vaccine virus should decrease the risk of generating mutant viruses with increased virulence. Therefore, our findings are expected to be useful for the development of prepandemic vaccines and live attenuated vaccines with higher safety than that of the present candidate vaccines.
Matrix Metalloproteinase Activity in Infections by an Encephalitic Virus, Mouse Adenovirus Type 1
Authors: Ashley Shanna L. , Pretto Carla D. , Stier Matthew T. , Kadiyala Padma , Castro-Jorge Luiza , Hsu Tien-Huei , Doherty Robert , Carnahan Kelly E. , Castro Maria G. , Lowenstein Pedro R. , Spindler Katherine R. 
Published: January 2017

ABSTRACT

Mouse adenovirus type 1 (MAV-1) infection causes encephalitis in susceptible strains of mice and alters the permeability of infected brains to small molecules, which indicates disruption of the blood-brain barrier (BBB). Under pathological conditions, matrix metalloproteinases (MMPs) can disrupt the BBB through their proteolytic activity on basement membrane and tight junction proteins. We examined whether MAV-1 infection alters MMP activity
in vivo
and
in vitro
. Infected MAV-1-susceptible SJL mice had higher MMP2 and MMP9 activity in brains, measured by gelatin zymography, than mock-infected mice. Infected MAV-1-resistant BALB/c mice had MMP activity levels equivalent to those in mock infection. Primary SJL mouse brain endothelial cells (a target of MAV-1
in vivo
) infected
ex vivo
with MAV-1 had no difference in activities of secreted MMP2 and MMP9 from mock cells. We show for the first time that astrocytes and microglia are also infected
in vivo
by MAV-1. Infected mixed primary cultures of astrocytes and microglia had higher levels of MMP2 and MMP9 activity than mock-infected cells. These results indicate that increased MMP activity in the brains of MAV-1-infected susceptible mice may be due to MMP activity produced by endothelial cells, astrocytes, and microglia, which in turn may contribute to BBB disruption and encephalitis in susceptible mice.

IMPORTANCE
RNA and DNA viruses can cause encephalitis; in some cases, this is accompanied by MMP-mediated disruption of the BBB. Activated MMPs degrade extracellular matrix and cleave tight-junction proteins and cytokines, modulating their functions. MAV-1 infection of susceptible mice is a tractable small-animal model for encephalitis, and the virus causes disruption of the BBB. We showed that MAV-1 infection increases enzymatic activity of two key MMPs known to be secreted and activated in neuroinflammation, MMP2 and MMP9, in brains of susceptible mice. MAV-1 infects endothelial cells, astrocytes, and microglia, cell types in the neurovascular unit that can secrete MMPs.
Ex vivo
MAV-1 infection of these cell types caused higher MMP activity than mock infection, suggesting that they may contribute to the higher MMP activity seen
in vivo
. To our knowledge, this provides the first evidence of an encephalitic DNA virus in its natural host causing increased MMP activity in brains.
A Point Mutation in the N-Terminal Amphipathic Helix α
0
in NS3 Promotes Hepatitis C Virus Assembly by Altering Core Localization to the Endoplasmic Reticulum and Facilitating Virus Budding
Authors: Yan Yu , He Ying , Boson Bertrand , Wang Xuesong , Cosset François-Loïc , Zhong Jin 
Published: January 2017

ABSTRACT

The assembly of hepatitis C virus (HCV), a complicated process in which many viral and cellular factors are involved, has not been thoroughly deciphered. NS3 is a multifunctional protein that contains an N-terminal amphipathic α helix (designated helix α
0
), which is crucial for the membrane association and stability of NS3 protein, followed by a serine protease domain and a C-terminal helicase/NTPase domain. NS3 participates in HCV assembly likely through its C-terminal helicase domain, in which all reported adaptive mutations enhancing virion assembly reside. In this study, we determined that the N-terminal helix α
0
of NS3 may contribute to HCV assembly. We identified a single mutation from methionine to threonine at amino acid position 21 (M21T) in helix α
0
, which significantly promoted viral production while having no apparent effect on the membrane association and protease activity of NS3. Subsequent analyses demonstrated that the M21T mutation did not affect HCV genome replication but rather promoted virion assembly. Further study revealed a shift in the subcellular localization of core protein from lipid droplets (LD) to the endoplasmic reticulum (ER). Finally, we showed that the M21T mutation increased the colocalization of core proteins and viral envelope proteins, leading to a more efficient envelopment of viral nucleocapsids. Collectively, the results of our study revealed a new function of NS3 helix α
0
and aid understanding of the role of NS3 in HCV virion morphogenesis.

IMPORTANCE
HCV NS3 protein possesses the protease activity in its N-terminal domain and the helicase activity in its C-terminal domain. The role of NS3 in virus assembly has been mainly attributed to its helicase domain, because all adaptive mutations enhancing progeny virus production are found to be within this domain. Our study identified, for the first time to our knowledge, an adaptive mutation within the N-terminal helix α
0
domain of NS3 that significantly enhanced virus assembly while having no effect on viral genome replication. The mechanistic studies suggested that this mutation promoted the relocation of core proteins from LD to the ER, leading to a more efficient envelopment of viral nucleocapsids. Our results revealed a possible new function of helix α
0
in the HCV life cycle and provided new clues to understanding the molecular mechanisms for the action of NS3 in HCV assembly.
Headache outcomes in children undergoing foramen magnum decompression for Chiari I malformation
Authors: Raza-Knight Saba , Mankad Kshitij , Prabhakar Prab , Thompson Dominic 
Published: January 2017

ObjectiveA common symptom of Chiari I malformation (CIM) is headache, which is diagnosed using non-validated criteria from the International Headache Society (IHS). CIM-associated headaches should resolve following neurosurgical treatment of the malformation by foramen magnum decompression (FMD). We aimed to validate the IHS criteria and determine (1) the efficacy of FMD in treating headache and (2) whether duraplasty confers an advantage over simple bony decompression in the treatment of this symptom.MethodsA retrospective review of CIM cases treated with FMD at Great Ormond Street Hospital from 1989 to 2014 was carried out. Clinical headache characteristics were compared against IHS criteria and correlated with outcome following FMD.ResultsHeadache was a presenting symptom in 57/102 (55.9%) of patients. Of these, 42/57 (73.7%) could be classified as Chiari I-type headache. Following FMD, 42/57 (73.7%) of all presenting headaches showed a sustained improvement (>3 months) compared with 32/39 (82.1%) of Chiari I-type headaches. Duraplasty led to a sustained improvement in headache in 32/38 (84.2%) cases compared with 9/16 (56.3%) cases treated with bone-only decompression.ConclusionsOur data suggest that 80% of headaches classified as Chiari I-type will show a sustained improvement following FMD, and, as such, the IHS criteria are clinically useful in evaluating symptoms attributable to CIM. For all headaches associated with CIM, duraplasty may confer a benefit in terms of long-term improvement, compared with bone-only decompression.
‘There were more wires than him’: the potential for wireless patient monitoring in neonatal intensive care
Authors: Bonner Oliver , Beardsall Kathryn , Crilly Nathan , Lasenby Joan 
Published: January 2017

BackgroundThe neonatal intensive care unit (NICU) can be one of the most stressful hospital environments. Alongside providing intensive clinical care, it is important that parents have the opportunity for regular physical contact with their babies because the neonatal period is critical for parent–child bonding. At present, monitoring technology in the NICU requires multiple wired sensors to track each baby's vital signs. This study describes the experiences that parents and nurses have with the current monitoring methods, and reports on their responses to the concept of a wireless monitoring system.MethodsSemistructured interviews were conducted with six parents, each of whom had babies on the unit, and seven nurses who cared for those babies. The interviews initially focused on the participants’ experiences of the current wired system and then on their responses to the concept of a wireless system. The transcripts were analysed using a general inductive approach to identify relevant themes.ResultsParticipants reported on physical and psychological barriers to parental care, the ways in which the current system obstructed the efficient delivery of clinical care and the perceived benefits and risks of a wireless system. The parents and nurses identified that the wires impeded baby–parent bonding; physically and psychologically. While a wireless system was viewed as potentially enabling greater interaction, staff and parents highlighted potential concerns, including the size, weight and battery life of any new device.ConclusionsThe many wires required to safely monitor babies within the NICU creates a negative environment for parents at a critical developmental period, in terms of physical and psychological interactions. Nurses also experience challenges with the existing system, which could negatively impact the clinical care delivery. Developing a wireless system could overcome these barriers, but there remain challenges in designing a device suitable for this unique environment.
Health hackathons: theatre or substance? A survey assessment of outcomes from healthcare-focused hackathons in three countries
Authors: Olson Kristian R , Walsh Madeline , Garg Priya , Steel Alexis , Mehta Sahil , Data Santorino , Petersen Rebecca , Guarino Anthony J , Bailey Elizabeth , Bangsberg David R 
Published: January 2017

BackgroundHealthcare-focused hackathons are 48-hour platforms intended to accelerate novel medical technology. However, debate exists about how much they contribute to medical technology innovation. The Consortium for Affordable Medical Technologies (CAMTech) has developed a three-pronged model to maximise their effectiveness. To gauge the success of this model, we examined follow-up outcomes.MethodsOutcomes of 12 hackathons from 2012 to 2015 in India, Uganda and the USA were measured using emailed surveys. To minimise response bias, non-responding teams were coded as having made no progress.Results331 individuals provided information on 196 of 356 projects (55.1% response rate), with no difference in responses from teams participating in different countries (Cramer's V=0.09, p=0.17). 30.3% of projects had made progress after a mean of 12.2 months. 88 (24.7%) teams had initiated pilot testing, with 42 (11.8%) piloting with care providers and 24 (6.7%) with patients. Overall, 97 teams (8.1 per hackathon) drafted business plans, 22 (1.8 per hackathon) had filed patents on their innovations and 15 (1.3 per hackathon) had formed new companies. Teams raised US$64.08 million in funding (average US$5.34 million per hackathon; median award size of $1800). In addition, 108 teams (30.3%) reported at least one member working on additional technologies with people they met at a hackathon. Individual confidence to address medical technology challenges was significantly increased after attending (t(1282)=192.77, p 0.001).ConclusionCAMTech healthcare hackathons lead to consistent output with respect to medical technology innovation, including clinical trials, business plan development, securing investment capital/funding and new company formation.
Acupuncture and PC6 stimulation for the prevention of postoperative nausea and vomiting in patients undergoing elective laparoscopic resection of colorectal cancer: a study protocol for a three-arm randomised pilot trial
Authors: Kim Kun Hyung , Kim Dae Hun , Bae Ji Min , Son Gyung Mo , Kim Kyung Hee , Hong Seung Pyo , Yang Gi Young , Kim Hee Young 
Published: January 2017

IntroductionThis study aims to assess the feasibility of acupuncture and a Pericardium 6 (PC6) wristband as an add-on intervention of antiemetic medication for the prevention of postoperative nausea and vomiting (PONV) in patients undergoing elective laparoscopic colorectal cancer resection.Methods and analysisA total of 60 participants who are scheduled to undergo elective laparoscopic resection of colorectal cancer will be recruited. An enhanced recovery after surgery protocol using standardised antiemetic medication will be provided for all participants. Participants will be equally randomised into acupuncture plus PC6 wristband (Acupuncture), PC6 wristband alone (Wristband), or no acupuncture or wristband (Control) groups using computer-generated random numbers concealed in opaque, sealed, sequentially numbered envelopes. For the acupuncture combined with PC6 wristband group, the embedded auricular acupuncture technique for preoperative anxiolysis and up to three sessions of acupuncture treatments with manual and electrical stimulation within 48 hours after surgery will be provided by qualified Korean medicine doctors. The PC6 wristband will be applied in the Acupuncture and Wristband groups, beginning 1 hour before surgery and lasting 48 hours postoperatively. The primary outcome will be the number of participants who experience moderate or severe nausea, defined as nausea at least 4 out of 10 on a severity numeric rating scale or vomiting at 24 hours after surgery. Secondary outcomes, including symptom severity, participant global assessments and satisfaction, quality of life, physiological recovery, use of medication and length of hospital stay, will be assessed. Adverse events and postoperative complications will be measured for 1 month after surgery.Ethics and disseminationAll participants will provide written informed consent. The study has been approved by the institutional review board (IRB). This pilot trial will inform a full-scale randomised trial of acupuncture combined with PC6 stimulation for the prevention of PONV in patients undergoing elective laparoscopic colorectal cancer surgery.Trial registration numberNCT02509143.
Microscale distribution and dynamic surface tension of pulmonary surfactant normalize the recruitment of asymmetric bifurcating airways
Authors: Yamaguchi Eiichiro , Nolan Liam P. , Gaver Donald P. 
Published: January 2017

We investigate the influence of bifurcation geometry, asymmetry of daughter airways, surfactant distribution, and physicochemical properties on the uniformity of airway recruitment of asymmetric bifurcating airways. To do so, we developed microfluidic idealized in vitro models of bifurcating airways, through which we can independently evaluate the impact of carina location and daughter airway width and length. We explore the uniformity of recruitment and its relationship to the dynamic surface tension of the lining fluid and relate this behavior to the hydraulic (PHyd) and capillary (PCap) pressure drops. These studies demonstrate the extraordinary importance of PCap in stabilizing reopening, even in highly asymmetric systems. The dynamic surface tension of pulmonary surfactant is integral to this stability because it modulates PCap in a velocity-dependent manner. Furthermore, the surfactant distribution at the propagating interface can have a very large influence on recruitment stability by focusing surfactant preferentially to specific daughter airways. This implies that modification of the surfactant distribution through novel modes of ventilation could be useful in inducing uniformly recruited lungs, aiding in gas exchange, and reducing ventilator-induced lung injury. NEW & NOTEWORTHY The dynamic surface tension of pulmonary surfactant is integral to the uniformity of asymmetric bifurcation airway recruitments because it modulates capillary pressure drop in a velocity-dependent manner. Also, the surfactant distribution at the propagating interface can have a very large influence on recruitment stability by focusing surfactant preferentially to specific daughter airways. This implies that modification of the surfactant distribution through novel modes of ventilation could be useful in inducing uniformly recruited lungs, reducing ventilator-induced lung injury.
O ensino de literatura: perspectivas comparatistas e a formação de professores à luz da Lei 11.645/08
Authors: Sarteschi Rosangela 
Published: January 2017

O presente texto tem por objetivo fazer uma breve reflexão conceitual e teórica sobre a formação dos futuros professores do componente curricular “Língua Portuguesa” da rede pública e privada da educação básica no âmbito da área dos Estudos Comparados de Literaturas de Língua Portuguesa, do Departamento de Letras Clássicas e Vernáculas da Faculdade de Filosofia, Letras e Ciências Humanas da USP.
El Apellido Judío como Marcador de Identidad
Authors: Dzienciarsky Damian 
Published: January 2017

O nome, além de ser uma designação ou denominação oral que se dá a uma pessoa, é uma ferramenta identificatória. A utilização do nome garante, de certa forma, a preservação da identidade. Os sobrenomes não são apenas palavras, eles escondem, também, diversos significados.A Bíblia, o Talmud e os demais textos judaicos, foram fontes de nomes e sobrenomes. Entretanto, concretamente, somente nos séculos X e XI os sobrenomes, por diferentes motivos, começaram a propagar-se dentro do povo judeu.Este trabalho analisa o sobrenome seguindo os passos da história. A fundamentação metodológica deste artigo está baseada em uma análise histórica diacrônica da adoção de sobrenomes pela população europeia em geral e judaica em particular.É estudada a situação dos sobrenomes e sua consolidação na Idade Média, tratando a situação dos judeus sefardis e asquenazis separadamente. É investigado o sobrenome na época do Iluminismo destacando a origem do nome “Polônia” e a identidade judaica.Esta pesquisa tem por objetivo refletir sobre os processos que desencadearam e geraram os diferentes sobrenomes judaicos através dos tempos, marcando e definindo a identidade judaica.
Uma Bibliografia do Violão Brasileiro (1916-1990)
Authors: Castagna Paulo , Schwarz Werner 
Published: January 2017

Este artigo é a primeira tentativa de reunir as publicações feitas entre 1916 e 1990, sobre a música "erudita" e "popular" para violão e instrumentos similares (viola, cavaquinho, guitarra, etc.), violonistas, professores e construtores brasileiros, sem as quais seria impossível iniciar estudos de maiores proporções sobre o assunto. 1916 é, ao mesmo tempo, a data dos textos mais antigos que encontramos e o ano em que o violão começa a ser aceito, no país, como instrumento solista e de concerto. As 490 referências bibliográficas que apresentamos foram colecionadas durante 5 anos e encontradas em bibliografias e/ou nos acervos pesquisados.