bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Luminex-Based Multiplex Assay for Detection of Mutations Conferring Resistance to Echinocandins in Candida glabrata
Authors: Pham Cau D. , Bolden Carol B. , Kuykendall Randall J. , Lockhart Shawn R. 
Published: December 2013

ABSTRACT

Echinocandins are the recommended treatment for invasive candidiasis due to
Candida glabrata
. Resistance to echinocandins is known to be caused by nonsynonymous mutations in the hot spot-1 (HS1) regions of the
FKS1
and
FKS2
genes, which encode a subunit of the β-1,3-glucan synthase, the target of echinocandins. Here, we describe the development of a microsphere-based assay using Luminex MagPix technology to identify mutations in the
FKS1
HS1 and
FKS2
HS1 domains, which confer
in vitro
echinocandin resistance in
C. glabrata
isolates. The assay is rapid and can be performed with high throughput. The assay was validated using 102 isolates that had
FKS1
HS1 and
FKS2
HS1 domains previously characterized by DNA sequencing. The assay was 100% concordant with DNA sequencing results. The assay was then used for high-throughput screening of 1,032
C. glabrata
surveillance isolates. Sixteen new isolates with mutations, including a mutation that was new to our collection (del659F), were identified. This assay provides a rapid and cost-effective way to screen
C. glabrata
isolates for echinocandin resistance.
Effect of Microtubule Disruption on Neuronal Spread and Replication of Demyelinating and Nondemyelinating Strains of Mouse Hepatitis Virus
In Vitro
Authors: Biswas Kaushiki , Das Sarma Jayasri 
Published: December 2013

ABSTRACT
The isogenic host attachment spike protein recombinant demyelinating strain of mouse hepatitis virus (MHV) (RSA59) and the nondemyelinating strain (RSMHV2) differ in their abilities to infect distinct types of neural cells, spread from cell to cell, and induce subsequent demyelination and axonal loss. The differential demyelination properties of RSA59 and RSMHV2 may be a function of spike protein-mediated neuronal transport. Disruption of microtubules with colchicine and vinblastine significantly blocks neuronal transport and reduces the replication of RSA59, whereas RSMHV2 remains unaffected.
Human Enterovirus 71 Uncoating Captured at Atomic Resolution
Authors: Lyu Ke , Ding Jie , Han Jian-Feng , Zhang Yu , Wu Xiao-Yan , He Ya-Ling , Qin Cheng-Feng , Chen Rong 
Published: December 2013

ABSTRACT
Human enterovirus 71 (EV71) is the major causative agent of severe hand-foot-and-mouth diseases (HFMD) in young children, and structural characterization of EV71 during its life cycle can aid in the development of therapeutics against HFMD. Here, we present the atomic structures of the full virion and an uncoating intermediate of a clinical EV71 C4 strain to illustrate the structural changes in the full virion that lead to the formation of the uncoating intermediate prepared for RNA release. Although the VP1 N-terminal regions observed to penetrate through the junction channel at the quasi-3-fold axis in the uncoating intermediate of coxsackievirus A16 were not observed in the EV71 uncoating intermediate, drastic conformational changes occur in this region, as has been observed in all capsid proteins. Additionally, the RNA genome interacts with the N-terminal extensions of VP1 and residues 32 to 36 of VP3, both of which are situated at the bottom of the junction. These observations highlight the importance of the junction for genome release. Furthermore, EV71 uncoating is associated with apparent rearrangements and expansion around the 2- and 5-fold axes without obvious changes around the 3-fold axes. Therefore, these structures enabled the identification of hot spots for capsid rearrangements, which led to the hypothesis that the protomer interface near the junction and the 2-fold axis permits the opening of large channels for the exit of polypeptides and viral RNA, which is an uncoating mechanism that is likely conserved in enteroviruses.

IMPORTANCE
Human enterovirus 71 (EV71) is the major causative agent of severe hand-foot-and-mouth diseases (HFMD) in young children. EV71 contains an RNA genome protected by an icosahedral capsid shell. Uncoating is essential in EV71 life cycle, which is characterized by conformational changes in the capsid to facilitate RNA release into host cell. Here we present the atomic structures of the full virion and an uncoating intermediate of a clinical C4 strain of EV71. Structural analysis revealed drastic conformational changes associated with uncoating in all the capsid proteins near the junction at the quasi-3-fold axis and protein-RNA interactions at the bottom of the junction in the uncoating intermediate. Significant capsid rearrangements also occur at the icosahedral 2- and 5-fold axes but not at the 3-fold axis. Taking the results together, we hypothesize that the junction and nearby areas are hot spots for capsid breaches for the exit of polypeptides and viral RNA during uncoating.
Nucleic Acid Chaperone Activity Associated with the Arginine-Rich Domain of Human Hepatitis B Virus Core Protein
Authors: Chu Tien-Hua , Liou An-Ting , Su Pei-Yi , Wu Huey-Nan , Shih Chiaho 
Published: December 2013

ABSTRACT

Hepatitis B virus (HBV) DNA replication occurs within the HBV icosahedral core particles. HBV core protein (HBc) contains an arginine-rich domain (ARD) at its carboxyl terminus. This ARD domain of HBc 149-183 is known to be important for viral replication but not known to have a structure. Recently, nucleocapsid proteins of several viruses have been shown to contain nucleic acid chaperone activity, which can facilitate structural rearrangement of viral genome. Major features of nucleic acid chaperones include highly basic amino acid residues and flexible protein structure. To test the nucleic acid chaperone hypothesis for HBc ARD, we first used the disassembled full-length HBc from
Escherichia coli
to analyze the nucleic acid annealing and strand displacement activities. To exclude the potential contamination of chaperones from
E. coli
, we designed synthetic HBc ARD peptides with different lengths and serine phosphorylations. We demonstrated that HBc ARD peptide can behave like a bona fide nucleic acid chaperone and that the chaperone activity depends on basic residues of the ARD domain. The loss of chaperone activity by arginine-to-alanine substitutions in the ARD can be rescued by restoring basic residues in the ARD. Furthermore, the chaperone activity is subject to regulation by phosphorylation and dephosphorylation at the HBc ARD. Interestingly, the HBc ARD can enhance
in vitro
cleavage activity of RNA substrate by a hammerhead ribozyme. We discuss here the potential significance of the HBc ARD chaperone activity in the context of viral DNA replication, in particular, at the steps of primer translocations and circularization of linear replicative intermediates.

IMPORTANCE
Hepatitis B virus is a major human pathogen. At present, no effective treatment can completely eradicate the virus from patients with chronic hepatitis B. We report here a novel chaperone activity associated with the viral core protein. Our discovery could lead to a new drug design for more effective treatment against hepatitis B virus in the future.
Dispersed and Conserved Hydrophobic Residues of HIV-1 Vif Are Essential for CBFβ Recruitment and A3G Suppression
Authors: Zhou Xiaohong , Han Xue , Zhao Ke , Du Juan , Evans Sean L. , Wang Hong , Li Peng , Zheng Wenwen , Rui Yajuan , Kang Jian , Yu Xiao-Fang 
Published: December 2013

ABSTRACT

CBFβ was recently found to be a key regulator of the ability of human immunodeficiency virus type 1 (HIV-1) Vif to overcome host antiviral APOBEC3 proteins. However, the detailed molecular requirements for the Vif-CBFβ interaction are still not clear. Here, we mapped the minimum Vif domain required for CBFβ binding. In terms of CBFβ binding, the Vif N terminus was very sensitive to deletions. We determined that the Vif fragment from residues 5 to 126 was sufficient to form a stable complex with CBFβ
in vitro
. We also observed that ionic interactions were not the main contributor to the interaction between Vif and CBFβ. Instead, hydrophobic interactions were important for maintaining the Vif-CBFβ complex, since it could be disrupted by nonionic detergent. Site-directed mutagenesis of conserved hydrophobic amino acids revealed novel residues in Vif that were important for CBFβ binding and APOBEC3 inactivation. At least part of the well-characterized HCCH domain (residues 108 to 139) was required to form a stable Vif-CBFβ complex. Thus, the HCCH motif may have a dual role in binding both Cul5 and CBFβ. Considering the importance of Vif in HIV-1 infection, this unique Vif-CBFβ interaction represents an attractive pharmacological intervention target against HIV-1.

IMPORTANCE
Vif-induced APOBEC3 protein degradation was the first host antiviral mechanism against HIV-1/simian immunodeficiency virus to be revealed, yet details regarding which proteins are degraded are not fully demonstrated. Recently, host cellular factor CBFβ was found to be essential for Vif to function and promote viral infectivity. In this study, we present more critical information on the Vif-CBFβ interaction by revealing that hydrophobicity contributes the most to the Vif-CBFβ interaction and locating several novel hydrophobic sites (tryptophans and phenylalanines) that are conserved among Vif proteins from different lentiviruses and essential for Vif binding to CBFβ. Mutations on these sites result in a reduced/abolished Vif-CBFβ interaction, leading to the attenuated potency of Vif on both inducing the degradation of antiviral factors like APOBEC3G and promoting HIV-1 infectivity. Therefore, information from this study will help people to further understand how Vif acts against host antiviral mechanism, which is important for novel anti-HIV-1 drug development.
Incidental findings of elevated random plasma glucose in the ED as a prompt for outpatient diabetes screening: a retrospective study
Authors: Friedman Steven Marc , Vallipuram Janaki , Baswick Brenda 
Published: December 2013

ObjectiveTo determine whether random plasma glucose (RPG) collected from patients without known impaired glucose metabolism (IGM) in the emergency department (ED) is a useful screen for diabetes or prediabetes.DesignRetrospective cohort study.SettingED of a Canadian teaching hospital over 1 month.ParticipantsAdult patients in ED with RPG over 7 mmol/L were recruited for participation. Exclusion criteria included known diabetes, hospital admission and inability to consent. Participants were contacted by mail, encouraged to follow-up with their family physician (FP) for further testing and subsequently interviewed.Outcome measuresThe primary outcome measure was the proportion of patients in the ED with RPG over 7 mmol/L and no previous diagnosis of IGM who were diagnosed with diabetes or prediabetes after secondary testing by FP with oral glucose tolerance test or fasting plasma glucose (FPG). Secondary outcomes included patient characteristics (age, gender, body mass index and language) and (2) compliance with advice to seek an appropriate follow-up care.ResultsRPG was drawn on approximately one-third (33%, n=1149) of the 3470 patients in the ED in March 2010. RPG over 7 mmol/L was detected in 24% (n=278) of patients, and after first telephone follow-up, 32% (n=88/278) met the inclusion criteria and were advised to seek confirmatory testing. 41% (n=114/278) of patients were excluded for known diabetes. 73% of patients contacted (n=64/88) followed up with their FP. 12.5% (n=11/88) of patients had abnormal FPG, and of these 11% (n=10/88) were encouraged to initiate lifestyle modifications and 1% (n=1/88) was started on an oral hypoglycaemic agent. For 7% (n=6/88) of patients, FP's declined to do follow-up fasting blood work.ConclusionsElevated RPG in the ED is useful for identification of patients at risk for IGM and in need of further diabetic screening. Emergency physicians should advise patients with elevated RPG to consider screening for diabetes. For ED screening to be successful, patient education and collaboration with FPs are essential.
Patient safety culture in China: a case study in an outpatient setting in Beijing
Authors: Liu Chaojie , Liu Weiwei , Wang Yuanyuan , Zhang Zhihong , Wang Peng 
Published: December 2013

ObjectivesTo investigate the patient safety culture in an outpatient setting in Beijing and explore the meaning and implications of the safety culture from the perspective of health workers and patients.MethodsA mixed methods approach involving a questionnaire survey and in-depth interviews was adopted. Among the 410 invited staff members, 318 completed the Hospital Survey of Patient Safety Culture (HSOPC). Patient safety culture was described using 12 subscale scores. Inter-subscale correlation analysis, ANOVA and stepwise multivariate regression analyses were performed to identify the determinants of the patient safety culture scores. Interviewees included 22 patients selected through opportunity sampling and 27 staff members selected through purposive sampling. The interview data were analysed thematically.ResultsThe survey respondents perceived high levels of unsafe care but had personally reported few events. Lack of ‘communication openness’ was identified as a major safety culture problem, and a perception of ‘penalty’ was the greatest barrier to the encouragement of error reporting. Cohesive ‘teamwork within units’, while found to be an area of strength, conversely served as a protective and defensive mechanism for medical practice. Low levels of trust between providers and consumers and lack of management support constituted an obstacle to building a positive patient safety culture.ConclusionsThis study in China demonstrates that a punitive approach to error is still widespread despite increasing awareness of unsafe care, and managers have been slow in acknowledging the importance of building a positive patient safety culture. Strong ‘teamwork within units’, a common area of strength, could fuel the concealment of errors.
Characterising emergency department high-frequency users in a rural hospital
Authors: Hardie Thomas L , Polek Carolee , Wheeler Erlinda , McCamant Karen , Dixson Melinda , Gailey Robert , Lafrak Karen 
Published: December 2013

ObjectivePatients who are frequent users (≥4 visits/year) comprise ∼10% of patients, but account for ∼34% of total yearly emergency department (ED) visits. Non-emergent care provided to frequent ED users affects operating costs and usage. The majority of reports characterising frequent ED use are from urban teaching centres. This study describes frequent users of ED services in a rural community setting and the association between counts of patient's visits and discrete diagnoses.DesignRetrospective study of 1652 frequent ED adult patients from a rural US hospital over a one-year period. Descriptive statistics and Poisson regression were used to explore the characteristics of frequent users and their patterns of diagnoses.ResultsFrequent user visits ranged from 4 to 66 per patient. Frequent users were 9.41% of patient volume accounting for 33.94% of the total visits and were younger compared with patients with <4 visits. Approximately 36% of frequent user visits were generated by 20 diagnoses when the diagnoses were concatenated into domains which covered ∼76% of the visits. There was a high correlation between the number of visits and discrete diagnoses in frequent users.ConclusionsThese findings suggest a more complex picture of rural ED services and their relationship with primary care and dental services, which needs to be defined before policy development to reduce ED use.
Non-resuscitative first-aid training for children and laypeople: a systematic review
Authors: He Zhimin , Wynn Persephone , Kendrick Denise 
Published: December 2013

BackgroundRelatively little is currently known about the effectiveness of first-aid training for children and laypeople. We have undertaken a systematic review to synthesise the evidence and inform policy and practice in this area.MethodsA range of bibliographic databases were searched. Studies were eligible if they used experimental designs, provided first-aid training to laypeople or children and reported first-aid knowledge, skills behaviours or confidence. Studies were selected for inclusion, data extracted and risk of bias assessed by two independent reviewers. Findings were synthesised narratively.Results23 studies (14 randomised controlled trials and 9 non-randomised studies) were included, 12 of which recruited children or young people (≤19 years old). Most studies reported significant effects favouring the intervention group; 11 out of 16 studies reported significant increases in first-aid knowledge; 11 out of 13 studies reported significant increases in first-aid skills; 2 out of 5 studies reported significant improvements in helping behaviour; and 2 out of 3 studies reported significant increases in confidence in undertaking first aid. Only one study undertook an economic evaluation; finding an intensive instructor-led course was more effective, but had significantly higher costs than either a less-intensive instructor-led course or a video-delivered course. Most studies were at risk of bias, particularly selection, performance or detection bias.ConclusionsThere is some evidence to support provision of first-aid training, particularly for children or young people, but many studies were judged to be at risk of bias. Conclusions cannot be drawn about which first-aid training courses or programmes are most effective or the age at which training can be most effectively provided. Few studies evaluated training in adult laypeople. High-quality studies are required assessing effectiveness and cost-effectiveness of standardised first-aid training to inform policy development and provision of first-aid training.
Case suitability for definitive through knee amputation following lower extremity blast trauma: analysis of 146 combat casualties, 2008–2010
Authors: Singleton James A G , Walker N M , Gibb I E , Bull A M J , Clasper J C 
Published: December 2013

IntroductionAnalysis of recent UK Armed Forces combat casualty data has highlighted a significant number of through joint traumatic amputations (TAs), most commonly through knee (through knee amputations (TKAs)). Previously, a consensus statement on lower limb amputation from the UK Defence Medical Services reported better outcomes in some patients with TKAs when compared with those with above knee amputations. This study sought to define the proportion of recent combat casualties sustaining severe lower extremity trauma with acute osseous and soft tissue injury anatomy amenable to definitive TKA.MethodsThe UK Joint Theatre Trauma Registry and post mortem CT (PM-CT) databases were used to identify all UK Armed Forces personnel (survivors and fatalities) sustaining a major extremity TA (through/proximal to wrist or ankle joint) between August 2008 and August 2010. Through knee and all below knee TAs were grouped as ‘potential TKAs’ (pTKAs), that is, possible candidates for definitive TKA.Results146 Cases (75 survivors and 71 fatalities) sustaining 271 TAs (130 in survivors, 141 in fatalities) were identified. The through-joint TA rate was 47/271 (17.3%); 34/47 through-joint injuries (72.3%) were TKAs. Overall, 63/130 TAs in survivors and 66/140 TAs in fatalities merited analysis as the pTKA group. Detailed anatomical data on pre-debridement osseous and soft tissue injury levels were only consistently available for fatalities through PM-CT findings. Further analysis of the soft tissue injury profile revealed that a definitive TKA in the pTKA group (all BKAs as well as TKAs) would have been proximal to the zone of injury (ZOI) in only 3/66 cases.ConclusionsTraumatic TKAs following explosive blast are more common than previously reported. The majority of lower limb TAs are skeletally amenable to a definitive TKA. Maximising residual stump length carries the risks of definitive level amputation within the original ZOI but this study demonstrates that the proximal extent of the soft tissue injury may frequently make this unavoidable. Further work is required to determine the relative merits of definitive below, through and above knee amputations in the short, medium and long term to ensure survivors are subject to minimal complications while maintaining capacity to achieve optimal functional outcomes.
Cysteine Catabolism: A Novel Metabolic Pathway Contributing to Glioblastoma Growth
Authors: Prabhu Antony , Sarcar Bhaswati , Kahali Soumen , Yuan Zhigang , Johnson Joseph J. , Adam Klaus-Peter , Kensicki Elizabeth , Chinnaiyan Prakash 
Published: December 2013

Abstract
The relevance of cysteine metabolism in cancer has gained considerable interest in recent years, largely focusing on its role in generating the antioxidant glutathione. Through metabolomic profiling using a combination of high-throughput liquid and gas chromatography–based mass spectrometry on a total of 69 patient-derived glioma specimens, this report documents the discovery of a parallel pathway involving cysteine catabolism that results in the accumulation of cysteine sulfinic acid (CSA) in glioblastoma. These studies identified CSA to rank as one of the top metabolites differentiating glioblastoma from low-grade glioma. There was strong intratumoral concordance of CSA levels with expression of its biosynthetic enzyme cysteine dioxygenase 1 (CDO1). Studies designed to determine the biologic consequence of this metabolic pathway identified its capacity to inhibit oxidative phosphorylation in glioblastoma cells, which was determined by decreased cellular respiration, decreased ATP production, and increased mitochondrial membrane potential following pathway activation. CSA-induced attenuation of oxidative phosphorylation was attributed to inhibition of the regulatory enzyme pyruvate dehydrogenase. Studies performed in vivo abrogating the CDO1/CSA axis using a lentiviral-mediated short hairpin RNA approach resulted in significant tumor growth inhibition in a glioblastoma mouse model, supporting the potential for this metabolic pathway to serve as a therapeutic target. Collectively, we identified a novel, targetable metabolic pathway involving cysteine catabolism contributing to the growth of aggressive high-grade gliomas. These findings serve as a framework for future investigations designed to more comprehensively determine the clinical application of this metabolic pathway and its contributory role in tumorigenesis. Cancer Res; 74(3); 787–96. ©2013 AACR.