bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-Genome Sequence of Human Rhinovirus C47, Isolated from an Adult Respiratory Illness Outbreak in Butte County, California, 2017
Authors: Pan Chao-Yang , Padilla Tasha , Yagi Shigeo , Lewis Linda S. , Ng Terry Fei Fan , Marine Rachel L. , Nix William Allan , Wadford Debra A. 
Published: January 2018

ABSTRACT
Here, we report the full coding sequence of rhinovirus C47 (RV-C47), obtained from a patient respiratory sample collected during an acute respiratory illness investigation in Butte County, California, in January 2017. This is the first whole-genome sequence of RV-C47 to be reported.
Cross-sectional epidemiology of hearing loss in Australian children aged 11–12 years old and 25-year secular trends
Authors: Wang Jing , le Clercq Carlijn M P , Sung Valerie , Carew Peter , Liu Richard S , Mensah Fiona K , Burt Rachel A , Gold Lisa , Wake Melissa 
Published: January 2018

ObjectiveIn a national study of Australian children aged 11–12 years old, we examined the (1) prevalence and characteristics of hearing loss, (2) its demographic risk factors and (3) evidence for secular increases since 1990.MethodsThis is a cross-sectional CheckPoint wave within the Longitudinal Study of Australian Children. 1485 children (49.8% retention; 49.7% boys) underwent air-conduction audiometry. Aim 1: hearing loss (≥16 decibels hearing level (dB HL)) was defined in four ways to enable prior/future comparisons: high Fletcher Index (mean of 1, 2 and 4 kHz; primary outcome relevant to speech perception), four-frequency (1, 2, 4 and 8 kHz), lower frequency (1 and 2 kHz) and higher frequency (4 and 8 kHz); aim 2: logistic regression of hearing loss by age, gender and disadvantage index; and aim 3: P for trend examining CheckPoint and reported prevalence in studies arranged by date since 1990.ResultsFor high Fletcher Index, the prevalence of bilateral and unilateral hearing loss ≥16 dB HL was 9.3% and 13.3%, respectively. Slight losses (16–25 dB HL) were more prevalent than mild or greater (≥26 dB HL) losses (bilateral 8.5% vs 0.8%; unilateral 12.5% vs 0.9%), and lower frequency more prevalent than higher frequency losses (bilateral 11.0% vs 6.9%; unilateral 15.4% vs 11.5%). Demographic characteristics did not convincingly predict hearing loss. Prevalence of bilateral/unilateral lower and higher frequency losses ≥16 dB HL has risen since 1990 (all P for trend <0.001).Conclusions and relevanceChildhood hearing loss is prevalent and has risen since 1990. Future research should investigate the causes, course and impact of these changes.
Understanding the informational needs of patients with IPF and their caregivers: ‘You get diagnosed, and you ask this question right away, what does this mean?’
Authors: Ramadurai Deepa , Corder Stephanie , Churney Tara , Graney Bridget , Harshman Andrea , Meadows Sarah , Swigris Jeffrey J 
Published: January 2018

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive, incurable lung disease whose intrusive symptoms rob patients of their quality of life. Patients with IPF rely on their caregivers for support and assistance in amounts that vary according to patients’ individual circumstances and disease severity. Knowledgeable and well-informed patients and caregivers are best suited to deal with life-altering conditions like IPF.MethodsWe conducted two hour-long focus groups with 13 patients with IPF and 4 caregivers of patients with IPF to better understand their informational needs and in what format such information should be delivered.ResultsPatients discussed the challenges IPF creates in their daily lives. They wanted information on how to live well despite having IPF, practical information on how they could remain active and travel and how they could preserve their quality of life despite living with a life-threatening disease like IPF. Caregivers wanted information on the general aspects of IPF, because it would help them understand what patients were going through. They also wanted specific information on how to give care to a patient with IPF, even when physical care may not be needed (as in earlier phases of the disease). Patients and caregivers both needed efficient information delivery from trustworthy sources, including the healthcare team involved in their care. They considered both spoken and written information valuable, and ease of access was critical.ConclusionThis study provides valuable insight regarding the informational needs of IPF patients and their caregivers. It is hoped that identifying or creating sources of this information, and insuring that patients and caregivers have access to it, will improve well-being for patients with IPF and their caregivers.
Practical guide for the comparison of two next-generation sequencing systems for solid tumour analysis in a universal healthcare system
Authors: Maxwell Perry , Hynes Seán O , Fuchs Marc , Craig Stephanie , McGready Claire , McLean Fiona , McQuaid Stephen , James Jacqueline , Salto-Tellez Manuel 
Published: January 2018

AimsAlthough there have been excellent reports in the literature of validating next-generation sequencing, comparisons between two systems are not often published due to cost and time. We set out to establish that targetable mutations could be reliably detected with different gene panels and different chemistries using a common bioinformatics pipeline for meaningful comparisons to be made.MethodsAfter running selected formalin-fixed, paraffin-embedded samples through QPCR, Sanger sequencing and the 50 gene hotspot v2 panel from Life Technologies to determine standard-of-care variants, we compared the Oncomine panel from Life Technologies performed on a Personal Genome Machine (PGM) and the eight-gene actionable panel from Qiagen performed on a MiSeq platform. We used a common bioinformatics program following the creation of respective VCF files.ResultsBoth panels were accurate to above 90%, the actionable panel workflow was easier to perform but the lowest effective starting DNA load was obtained on the Oncomine workflow at 4 ng. Such minimal DNA can help with samples where there is limited material such as those for lung cancer molecular studies. We also discuss gene panel content and propose that increasing the gene profile of a panel will not benefit clinical laboratories where standard-of-care testing is all that is required.ConclusionsOnce recognised, it may be cost-effective for such laboratories to begin validation with an appropriate bioinformatics pipeline for targeted multigene hotspot molecular testing.
Duchenne muscular dystrophy: genome editing gives new hope for treatment
Authors: Crispi Vassili , Matsakas Antonios 
Published: January 2018

AbstractDuchenne muscular dystrophy (DMD) is a progressive wasting disease of skeletal and cardiac muscles, representing one of the most common recessive fatal inherited genetic diseases with 1:3500–1:5000 in yearly incidence. It is caused by mutations in the DMD gene that encodes the membrane-associated dystrophin protein. Over the years, many have been the approaches to management of DMD, but despite all efforts, no effective treatment has yet been discovered. Hope for the development of potential therapeutics has followed the recent advances in genome editing and gene therapy. This review gives an overview to DMD and summarises current lines of evidence with regard to treatment and disease management alongside the appropriate considerations.
Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations
Authors: Mayhew David , Devos Nathalie , Lambert Christophe , Brown James R , Clarke Stuart C , Kim Viktoriya L , Magid-Slav Michal , Miller Bruce E , Ostridge Kristoffer K , Patel Ruchi , Sathe Ganesh , Simola Daniel F , Staples Karl J , Sung Ruby , Tal-Singer Ruth , Tuck Andrew C , Van Horn Stephanie , Weynants Vincent , Williams Nicholas P , Devaster Jeanne-Marie , Wilkinson Tom M A 
Published: January 2018

BackgroundAlterations in the composition of the lung microbiome associated with adverse clinical outcomes, known as dysbiosis, have been implicated with disease severity and exacerbations in COPD.ObjectiveTo characterise longitudinal changes in the lung microbiome in the AERIS study (Acute Exacerbation and Respiratory InfectionS in COPD) and their relationship with associated COPD outcomes.MethodsWe surveyed 584 sputum samples from 101 patients with COPD to analyse the lung microbiome at both stable and exacerbation time points over 1 year using high-throughput sequencing of the 16S ribosomal RNA gene. We incorporated additional lung microbiology, blood markers and in-depth clinical assessments to classify COPD phenotypes.ResultsThe stability of the lung microbiome over time was more likely to be decreased in exacerbations and within individuals with higher exacerbation frequencies. Analysis of exacerbation phenotypes using a Markov chain model revealed that bacterial and eosinophilic exacerbations were more likely to be repeated in subsequent exacerbations within a subject, whereas viral exacerbations were not more likely to be repeated. We also confirmed the association of bacterial genera, including Haemophilus and Moraxella, with disease severity, exacerbation events and bronchiectasis.ConclusionsSubtypes of COPD have distinct bacterial compositions and stabilities over time. Some exacerbation subtypes have non-random probabilities of repeating those subtypes in the future. This study provides insights pertaining to the identification of bacterial targets in the lung and biomarkers to classify COPD subtypes and to determine appropriate treatments for the patient.Trial registration numberResults, NCT01360398.
Routine repeat head CT may not be necessary for patients with mild TBI
Authors: Rosen Claire B , Luy Diego D , Deane Molly R , Scalea Thomas M , Stein Deborah M 
Published: January 2018

BackgroundRoutine repeat cranial CT (RHCT) is standard of care for CT-verified traumatic brain injury (TBI). Despite mixed evidence, those with mild TBI are subject to radiation and expense from serial CT scans. Thus, we investigated the necessity and utility of RHCT for patients with mild TBI. We hypothesized that repeat head CT in these patients would not alter patient care or outcomes.MethodsWe retrospectively studied patients suffering from mild TBI (Glasgow Coma Scale (GCS) score 13–15) and treated at the R Adams Cowley Shock Trauma Center from November 2014 through January 2015. The primary outcome was the need for surgical intervention. Outcomes were compared using paired Student’s t-test, and stratified by injury on initial CT, GCS change, demographics, and presenting vital signs (mean ± SD).ResultsEighty-five patients met inclusion criteria with an average initial GCS score=14.6±0.57. Our center sees about 2800 patients with TBI per year, or about 230 per month. This includes patients with concussions. This sample represents about 30% of patients with TBI seen during the study period. Ten patients required operation (four based on initial CT and others for worsening GCS, headaches, large unresolving injury). There was progression of injury on repeat CT scan in only two patients that required operation, and this accompanied clinical deterioration. The mean brain Abbreviated Injury Scale (AIS) score was 4.8±0.3 for surgical patients on initial CT scan compared with 3.4±0.6 (P<0.001) for non-surgical patients. Initial CT subdural hematoma size was 1.1±0.6 cm for surgical patients compared with 0.49±0.3 cm (P=0.05) for non-surgical patients. There was no significant difference between intervention groups in terms of other intracranial injuries, demographics, vital signs, or change in GCS. Overall, 75 patients that did not require surgical intervention received RHCT. At $340 per CT, $51 000 was spent on unnecessary imaging ($367 000/year, extrapolated).DiscussionIn an environment of increased scrutiny on healthcare expenditures, it is necessary to question dogma and eliminate unnecessary cost. Our data questions the use of routine repeat head CT scans in every patient with anatomic TBI and suggests that clinically stable patients with small injury can simply be followed clinically.Level of evidenceLevel III.
Complexity analysis on public transport networks of 97 large- and medium-sized cities in China
Authors: Tian Zhanwei , Zhang Zhuo , Wang Hongfei , Ma Li 
Published: January 2018

The traffic situation in Chinese urban areas is continuing to deteriorate. To make a better planning and designing of the public transport system, it is necessary to make profound research on the structure of urban public transport networks (PTNs). We investigate 97 large- and medium-sized cities’ PTNs in China, construct three types of network models — bus stop network, bus transit network and bus line network, then analyze the structural characteristics of them. It is revealed that bus stop network is small-world and scale-free, bus transit network and bus line network are both small-world. Betweenness centrality of each city’s PTN shows similar distribution pattern, although these networks’ size is various. When classifying cities according to the characteristics of PTNs or economic development level, the results are similar. It means that the development of cities’ economy and transport network has a strong correlation, PTN expands in a certain model with the development of economy.
Rapid Screening and Preparative Isolation of Antioxidants fromAlpinia officinarumHance Using HSCCC Coupled with DPPH-HPLC Assay and Evaluation of Their Antioxidant Activities
Authors: Fang Lei , Zhang Hua , Zhou Jie , Geng Yanling , Wang Xiao 
Published: January 2018

An efficient method using high-speed counter-current chromatography (HSCCC) coupled with DPPH-HPLC assay has been developed for rapid screening and preparative isolation of antioxidants from ethyl acetate fraction ofAlpinia officinarumHance. Target-guided by DPPH-HPLC assay, two antioxidants, galangin and kaempferide, were targeted and further separated with purities of 99.3% and 98.5% by HSCCC using petroleum ether–ethyl acetate–methanol–water (0.8 : 1 : 1 : 0.8,v/v) as the solvent system. The antioxidant activities of galangin and kaempferide were further evaluated by measuring their inhibiting effects on superoxide anion radical, hydroxyl radical, and hydrogen peroxide in different luminol chemiluminescence (CL) systems. As a result, galangin and kaempferide both showed potent antioxidant activities. Results of the present study indicated that the combinative method by offline coupling DPPH-HPLC and HSCCC could be widely applied for rapid screening and isolation of antioxidants from complex TCM extract.
CD301b/MGL2
+
Mononuclear Phagocytes Orchestrate Autoimmune Cardiac Valve Inflammation and Fibrosis
Authors: Meier Lee A. , Auger Jennifer L. , Engelson Brianna J. , Cowan Hannah M. , Breed Elise R. , Gonzalez-Torres Mayra I. , Boyer Joshua D. , Verma Mayank , Marath Aubyn , Binstadt Bryce A. 
Published: January 2018

Background:
Valvular heart disease is common and affects the mitral valve (MV) most frequently. Despite the prevalence of MV disease (MVD), the cellular and molecular pathways that initiate and perpetuate it are not well understood.

Methods:

K/B.g7 T-cell receptor transgenic mice spontaneously develop systemic autoantibody-associated autoimmunity, leading to fully penetrant fibroinflammatory MVD and arthritis. We used multiparameter flow cytometry, intracellular cytokine staining, and immunofluorescent staining to characterize the cells in inflamed K/B.g7 MVs. We used genetic approaches to study the contribution of mononuclear phagocytes (MNPs) to MVD in this model. Specifically, we generated K/B.g7 mice in which either CX3CR1 or CD301b/macrophage galactose
N
-acetylgalactosamine–specific lectin 2 (MGL2)–expressing MNPs were ablated. Using K/B.g7 mice expressing
Cx3Cr1
-Cre, we conditionally deleted critical inflammatory molecules from MNPs, including the Fc-receptor signal-transducing tyrosine kinase Syk and the cell adhesion molecule very late antigen–4. We performed complementary studies using monoclonal antibodies to block key inflammatory molecules. We generated bone marrow chimeric mice to define the origin of the inflammatory cells present in the MV and to determine which valve cells respond to the proinflammatory cytokine tumor necrosis factor (TNF). Finally, we examined specimens from patients with rheumatic heart disease to correlate our findings to human pathology.

Results:

MNPs comprised the vast majority of MV-infiltrating cells; these MNPs expressed CX3CR1 and CD301b/MGL2. Analogous cells were present in human rheumatic heart disease valves. K/B.g7 mice lacking CX3CR1 or in which CD301b/MGL2-expressing MNPs were ablated were protected from MVD. The valve-infiltrating CD301b/MGL2
+
MNPs expressed tissue-reparative molecules including arginase-1 and resistin-like molecule α. These MNPs also expressed the proinflammatory cytokines TNF and interleukin-6, and antibody blockade of these cytokines prevented MVD. Deleting Syk from CX3CR1-expressing MNPs reduced their TNF and interleukin-6 production and also prevented MVD. TNF acted through TNF receptor–1 expressed on valve-resident cells to increase the expression of vascular cell adhesion molecule–1. Conditionally deleting the vascular cell adhesion molecule-1 ligand very late antigen–4 from CX3CR1-expressing MNPs prevented MVD.

Conclusions:

CD301b/MGL2
+
MNPs are key drivers of autoimmune MVD in K/B.g7 mice and are also present in human rheumatic heart disease. We define key inflammatory molecules that drive MVD in this model, including Syk, TNF, interleukin-6, very late antigen–4, and vascular cell adhesion molecule–1.
Transport by Lagrangian Vortices in the Eastern Pacific
Authors: Abernathey Ryan , Haller George 
Published: January 2018

AbstractRotationally coherent Lagrangian vortices (RCLVs) are identified from satellite-derived surface geostrophic velocities in the eastern Pacific (180°–130°W) using the objective (frame invariant) finite-time Lagrangian coherent structure detection method of Haller et al. based on the Lagrangian-averaged vorticity deviation. RCLVs are identified for 30-, 90-, and 270-day intervals over the entire satellite dataset, beginning in 1993. In contrast to structures identified using Eulerian eddy-tracking methods, the RCLVs maintain material coherence over the specified time intervals, making them suitable for material transport estimates. Statistics of RCLVs are compared to statistics of eddies identified from sea surface height (SSH) by Chelton et al. RCLVs and SSH eddies are found to propagate westward at similar speeds at each latitude, consistent with the Rossby wave dispersion relation. However, RCLVs are uniformly smaller and shorter-lived than SSH eddies. A coherent eddy diffusivity is derived to quantify the contribution of RCLVs to meridional transport; it is found that RCLVs contribute less than 1% to net meridional dispersion and diffusion in this sector, implying that eddy transport of tracers is mostly due to incoherent motions, such as swirling and filamentation outside of the eddy cores, rather than coherent meridional translation of eddies themselves. These findings call into question prior estimates of coherent eddy transport based on Eulerian eddy identification methods.
Complications of surgery for infectious lung cavities
Authors: Cortés-Julián Gildardo , Valencia Luis C. , Ríos-Pascual Silviano , de la Rosa-Abarroa Marco A , Guzmán-de Alba Enrique 
Published: January 2018

Background Infectious lung cavities are a common entity for the respiratory physician. Sometimes these lesions require surgical treatment, but surgery is challenging, and complications are common. Methods Patients with infectious lung cavities amenable to surgical treatment were included in a case-control study. The control group included patients with no complications. The cases group comprised patients with any of the following complications up to 90 days after surgery: death, persistence of hemoptysis, empyema, operative blood loss > 500 mL, vascular lesion requiring repair, massive transfusion (>5 units of packed red blood cells per 48 h) or reoperation for bleeding, postoperative mechanical ventilation, intensive care unit stay > 48 h, prolonged air leak, and persistent atelectasis. The potential risk factors for complications analyzed were demographic data, exposure to contaminants, comorbidities, preoperative embolization, surgical indication, spirometry results, and sputum test positive for Mycobacterium tuberculosis. Results Forty-five patients were included in the study and divided into 24 cases and 21 controls. We found a significant difference in the time to removal of chest tubes in favor of the noncomplicated cases (6.45 vs. 4.05 days, p = 0.030), and persistent active infection at the time of surgery tended to be a risk factor for complications (odds ratio = 6.6, 95% confidence interval: 0.7–60, p = 0.061). Conclusion The presence of persistent active infection at the time of surgery could be a risk factor for complications in resection surgery for infectious lung cavities.
Distal Clavicular Osteochondral Autograft Augmentation for Glenoid Bone Loss: A Comparison of Radius of Restoration Versus Latarjet Graft
Authors: Kwapisz Adam , Fitzpatrick Kelly , Cook Jay B. , Athwal George S. , Tokish John M. 
Published: January 2018

Background: Bone loss in shoulder instability is a well-recognized cause of failure after stabilization surgery. Many approaches have been described to address glenoid bone loss, including coracoid transfer. This transfer can be technically difficult and has been associated with high complication rates. An ideal alternative to coracoid transfer would be an autologous source of fresh osteochondral graft with enough surface area to replace significant glenoid bone loss. The distal clavicle potentially provides such a graft source that is readily available and low-cost. Purpose: To evaluate distal clavicular autograft reconstruction for instability-related glenoid bone loss, specifically comparing the width of the clavicular autograft with the width of an ipsilateral coracoid graft as prepared for a Latarjet procedure. Further, we sought to compare the articular cartilage thickness of the distal clavicle graft with that of the native glenoid. Study Design: Controlled laboratory study. Methods: Twenty-seven fresh-frozen cadaver specimens were dissected, and an open distal clavicle excision was performed. The coracoid process in each specimen was prepared as has been described for a classic Latarjet coracoid transfer. In each specimen, the distal clavicle graft was compared with the coracoid graft for size and potential of glenoid articular radius of restoration. The distal clavicle graft was also compared with the native glenoid for cartilage thickness. Results: In all specimens, the distal clavicle grafts provided a greater radius of glenoid restoration than the coracoid grafts ( P < .0001). On average, the clavicular graft was able to reconstruct 44% of the glenoid diameter, compared with 33% for the coracoid graft ( P < .0001). The articular cartilage of the glenoid was significantly thicker (1.4 mm thicker, P < .0001) than that of the distal clavicular autograft (average ± SD, 3.5 ± 0.6 mm vs 2.1 ± 0.8 mm, respectively). When specimens with osteoarthritis were excluded, this difference decreased to 0.97 mm when compared with the clavicular cartilage ( P = .0026). Conclusion: The distal clavicle autograft can restore a significantly greater glenoid bone deficit than the Latarjet procedure and has the additional benefit of restoring articular cartilage to the glenoid. The articular cartilage thickness of the distal clavicle is within 1.4 mm of that of the native glenoid. Clinical Relevance: The distal clavicular autograft may be a suitable option for reconstruction of instability-related glenoid bone loss. This graft provides a structural osteochondral autograft with a broader radius of reconstruction than that of a coracoid graft, is locally available, has minimal donor site morbidity, is anatomic, and provides articular cartilage.