bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Refractive Measures of Three Autorefractors in Children and Adolescents
Authors: Xiong Shuyu , Lv Minzhi , Zou Haidong , Zhu Jianfeng , Lu Lina , Zhang Bo , Deng Junjie , Yao Chunxia , He Xiangui , Xu Xun
Published: August 2017

SIGNIFICANCE

Our study found a good agreement between three autorefractors. Not only will readers benefit as they can now compare data measured with either device in different studies but the three devices can be used in the same study to generate one pool of data, which can be analyzed together.

PURPOSE

The present study aims to evaluate the agreement of three commonly used autorefractors in children and adolescents, and the potential for their interchangeable application in a large-scale study.

METHODS

Participants from seven schools were enrolled using cluster sampling. Refractive errors were measured using the following three autorefractors under cycloplegic conditions in random sequence: Topcon KR-8900, Nidek ARK-510A, and Huvitz HRK-7000A. Refractive errors were compared in terms of spherical equivalent refraction (SER), cylinder power, and the J
0 and J
45 by repeated-measures analysis of variance (RM-ANOVA) and Bland-Altman 95% limits of agreement (95% LoA).

RESULTS

A total of 2072 participants aged from 4 to 18 years were included. The mean ± SD and 95% LoA of the differences in SER between Topcon and Nidek, Topcon and Huvitz, and Nidek and Huvitz were 0.01 ± 0.24D (−0.46 to 0.48), −0.06 ± 0.31D (−0.66 to 0.54), and −0.07 ± 0.26D (−0.58 to 0.44), and those for the differences in cylinder power were −0.07 ± 0.26D (−0.57 to 0.44), 0.01 ± 0.32D (−0.63 to 0.64), and 0.07 ± 0.28D (−0.48 to 0.62), respectively (RM-ANOVA, P < .001). Further, the mean differences in J
0 and J
45 between each refractor pair ranged from −0.03 to 0.01, and the 95% LoA were −0.78 to 0.74, −0.79 to 0.74, and −0.73 to 0.72 for J
0 and −0.86 to 0.87, −0.86 to 0.88, and −0.83 to 0.84 for J
45, respectively.

CONCLUSIONS

Our study will allow for use of these three autorefractors interchangeably in large screening studies.
Primary Renal Sarcomas With BCOR-CCNB3 Gene Fusion
Authors: Argani Pedram , Kao Yu-Chien , Zhang Lei , Bacchi Carlos , Matoso Andres , Alaggio Rita , Epstein Jonathan I. , Antonescu Cristina R.
Published: August 2017

We report 2 primary renal sarcomas demonstrating BCOR-CCNB3 gene fusions that have recently been identified in undifferentiated round cell sarcomas of bone and soft tissue. These neoplasms occurred in male children aged 11 and 12 years, and both were cystic as a result of entrapment and dilatation of native renal tubules. Both cases were composed of variably cellular bland spindle cells with fine chromatin set in myxoid stroma and separated by a branching capillary vasculature. Both neoplasms demonstrated immunoreactivity for BCOR, cyclin D1, TLE1, and SATB2 in the spindle neoplastic cells and negativity in the prominent capillary vasculature. One case was extensively cystic and had hypocellular areas that simulated cystic nephroma; this neoplasm recurred 3 years later as a solid, highly cellular spindle cell sarcoma in the abdominal cavity. The morphology and immunoprofile of these renal neoplasms was compared with a control group of other sarcomas with BCOR genetic abnormalities, including clear cell sarcoma of the kidney (CCSK), infantile undifferentiated round cell sarcomas of soft tissue/primitive myxoid mesenchymal tumor of infancy, and bone/soft tissue sarcomas with BCOR-CCNB3 gene fusion; along with primary renal synovial sarcoma. Our findings show that the renal sarcomas with BCOR-CCNB3 gene fusion overlap with CCSK. These results are in keeping with a “BCOR-alteration family” of renal and extrarenal neoplasms which includes CCSK and undifferentiated round cell sarcomas of soft tissue/primitive myxoid mesenchymal tumor of infancy (which typically harbor BCOR internal tandem duplication), and BCOR-CCNB3 sarcomas, all of which are primarily driven by BCOR overexpression and have overlapping (but not identical) clinicopathologic features.
Similar Metabolic, Innate Immunity, and Adipokine Profiles in Adult and Pediatric Sepsis Versus Systemic Inflammatory Response Syndrome—A Pilot Study
Authors: Tavladaki Theonymfi , Spanaki Anna Maria , Dimitriou Helen , Kondili Efmorfia , Choulaki Christianna , Georgopoulos Dimitris , Briassoulis George
Published: August 2017

Objectives:

To examine whether the septic profiles of heat shock protein 72, heat shock protein 90α, resistin, adiponectin, oxygen consumption, CO2 production, energy expenditure, and metabolic pattern, along with illness severity, nutritional, and inflammatory indices, differ between adult and pediatric patients compared with systemic inflammatory response syndrome and healthy controls. To evaluate whether these biomolecules may discriminate sepsis from systemic inflammatory response syndrome in adult and pediatric patients.

Design:

Prospective cohort study.

Setting:

University ICU and PICU.

Patients:

Seventy-eight adults (sepsis/23; systemic inflammatory response syndrome/23; healthy controls/33), 67 children (sepsis/18; systemic inflammatory response syndrome/23; controls/27), mechanically ventilated.

Interventions:

None.

Measurements and Main Results:

Flow cytometry determined mean fluorescence intensity for monocyte or neutrophil heat shock protein expression. Resistin, adiponectin, and extracellular heat shock proteins were measured using enzyme-linked immunosorbent assay; energy expenditure by E-COVX (GE Healthcare). Genomic DNA was extracted with PureLink Genomic DNA kit (Invitrogen, Carlsbad, CA) to detect heat shock protein 72 single nucleotide polymorphisms. Similarly, in adult and pediatric patients, Acute Physiology and Chronic Evaluation-II/Acute Physiology and Pediatric Risk of Mortality-III, Simplified Acute Physiology Score-III, C-reactive protein, lactate, and resistin were higher and myocardial contractility, monocyte heat shock protein 72, oxygen consumption, CO2 production, energy expenditure, metabolic pattern, glucose, and albumin lower in sepsis compared with systemic inflammatory response syndrome or controls (p < 0.05). For discriminating sepsis from systemic inflammatory response syndrome, resistin, extracellular heat shock protein 90α, and lactate achieved a receiver operating characteristic curve greater than 0.80 in children and greater than 0.75 in adults (p < 0.05). In both, adults and children, genotype heat shock protein 72 analysis did not disclose any diagnosis or mortality group differences regarding either rs6457452 or rs1061581 haplotypes.

Conclusions:

Sepsis presents with similar profiles in adult and pediatric patients, characterized by enhanced inflammatory hormonal response and by repressed innate immunity, metabolism, and myocardial contractility. These features early distinguish sepsis from systemic inflammatory response syndrome across all age groups.
Enteral Nutrition Practices in Critically Ill Children Requiring Noninvasive Positive Pressure Ventilation*
Authors: Leroue Matthew K. , Good Ryan J. , Skillman Heather E. , Czaja Angela S.
Published: August 2017

Objectives:

Evaluate the practice of providing enteral nutrition in critically ill children requiring noninvasive positive pressure ventilation.

Design:

Retrospective cohort study.

Setting:

PICU within a quaternary care children’s hospital.

Patients:

PICU patients older than 30 days requiring noninvasive positive pressure ventilation for greater than or equal to 24 hours from August 2014 to June 2015. Invasive mechanical ventilation prior to noninvasive positive pressure ventilation and inability to receive enteral nutrition at baseline were additional exclusionary criteria.

Interventions:

None.

Measurements and Main Results:

The primary outcome was enteral nutrition initiation within 24 hours of admission. Secondary outcomes included time to goal enteral nutrition rate, adequacy of nutrition, adverse events (pneumonia not present at admission, intubation after enteral nutrition initiation, feeding tube misplacement), and lengths of noninvasive positive pressure ventilation and PICU stay. Among those included (n = 562), the median age was 2 years (interquartile range, 39 d to 6.8 yr), 54% had at least one chronic condition, and 43% had malnutrition at baseline. The most common primary diagnosis was bronchiolitis/viral pneumonia. The median length of time on noninvasive positive pressure ventilation was 2 days (interquartile range, 2.0–4.0). Most (83%) required continuous positive airway pressure or bi-level support during their PICU course. Sixty-four percent started enteral nutrition within 24 hours, with 72% achieving goal enteral nutrition rate within 72 hours. Forty-nine percent and 44% received an adequate cumulative calorie and protein intake, respectively, during their PICU admission. Oral feeding was the most common delivery method. On multivariable analysis, use of bi-level noninvasive positive pressure ventilation (odds ratio, 0.40; 95% CI, 0.25–0.63) and continuous dexmedetomidine (odds ratio, 0.59; 95% CI, 0.35–0.97) were independently associated with decreased likelihood of early enteral nutrition. Twelve percent of patients had at least one adverse event.

Conclusions:

A majority of patients requiring noninvasive positive pressure ventilation received enteral nutrition within 24 hours. However, less than half achieved caloric and protein goals during their PICU admission. Further investigation is warranted to determine the safety and effectiveness of early enteral nutrition in this population.
Computed Tomography Use Plateaus Among Children With Emergency Visits for Abdominal Pain
Authors: Fahimi Jahan , Kornblith Aaron E. , Kanzaria Hemal , Herring Andrew , Wang Ralph C.
Published: August 2017

Objectives

Abdominal pain is a common pediatric complaint to emergency departments (EDs), and clinicians often rely on imaging for diagnosis. Studies have demonstrated an increase in computed tomography (CT) in this population. Following emphasis on radiation reduction by researchers and organizations, this study evaluates recent national trends in CT use among pediatric patients presenting to EDs with abdominal pain.

Methods

This is a cross-sectional analysis of ED patients 18 years or younger with chief complaint of abdominal pain in the National Hospital Ambulatory Medical Care Survey from 2008 to 2011. Outcomes include annual proportions of visits with x-ray, ultrasound, or CT, as well as diagnosis of appendicitis and hospital admission.

Results

Of 32,304 ED visits, 2120 (6.6%) were for abdominal pain. Proportions of visits using CT, ultrasound, and plain x-ray were 16.0%, 10.5%, and 23.4%, respectively. For all outcome measures, including imaging, hospital admission, and diagnosis of appendicitis, there was no change from 2008 to 2011. Considering previous data, there was a significant rise in ultrasound use from 5.4% (95% confidence interval, 2.4%–8.4%) in 1998 to 12.1% (95% confidence interval, 9.4%–13.7%) in 2011. Multivariate analysis of CT use found the strongest predictor to be increasing age. Females, black children, and those with Medicaid insurance had lower odds of having a CT.

Conclusions

In contrast to the earlier dramatic increase in CT use for pediatric patients with abdominal pain, CT remained constant between 2008 and 2011. There was no associated change in the rate of diagnosis of appendicitis or hospitalization; however, ultrasound is increasing.
Comparison of Spot Urine Protein to Creatinine Ratio to 24-Hour Proteinuria to Identify Important Change Over Time in Proteinuria in Lupus
Authors: Medina-Rosas Jorge , Su Jiandong , Cook Richard J. , Sabapathy Arthy , Touma Zahi
Published: August 2017

Objectives

The aim of this study was to determine whether spot urine protein-to-creatinine ratio (PCR) accurately measures the change in proteinuria compared with 24-hour proteinuria (24H-P).

Methods

This was a retrospective analysis on patients’ paired visits and paired urine samples for PCR and 24H-P. Patients with both abnormal 24H-P (>0.5 g/d) and PCR (>0.05 g/mmol) or both normal 24H-P (≤0.5 g/d) and PCR (≤0.05 g/mmol) at baseline visit were identified.

The first follow-up visit with partial recovery (50% decrease in proteinuria) or complete recovery (≤0.5 g/d) was identified for those with abnormal baseline 24H-P, and new proteinuria (>0.5 g/d) was identified for those with normal 24H-P. Twenty-four-hour urine collection and PCR end-point frequencies were compared. Twenty-four-hour urine collection results were converted to 24H-PCR. Twenty-four-hour PCR and PCR were utilized to measure the magnitude of change (by standardized response mean [SRM]) in patients who achieved the end points.

Results

Of 230 patients, at baseline, 95 patients had abnormal and 109 had normal 24H-P and PCR. On follow-up, 57 achieved partial recovery, and 53 achieved complete recovery by 24H-P. Standardized response mean was −1.03 and −1.10 for 24H-PCR and PCR, respectively. By PCR, 53 patients had partial recovery, and 27 had complete recovery. Standardized response mean was −1.25 and −0.86 by 24H-PCR and PCR, respectively.

For new proteinuria, 28 patients were identified by 24H-P and 21 by PCR. Twenty-four-hour PCR SRM was 0.80, and PCR SRM was 0.68.

Conclusions

Protein-to-creatinine ratio does not have sufficient accuracy compared with 24H-P for improvement and worsening to be used in lieu of 24H-P.
Noninvasive Derivation of Fractional Flow Reserve From Coronary Computed Tomographic Angiography
Authors: Benton Stewart M. , Tesche Christian , De Cecco Carlo N. , Duguay Taylor M. , Schoepf U. Joseph , Bayer Richard R.
Published: August 2017

Coronary computed tomographic angiography (CCTA) has evolved as a rapid and highly sensitive method for the exclusion of obstructive coronary artery disease. Unfortunately, as it pertains to moderate and severe lesions, the ability to discriminate between those that are hemodynamically significant and those that are nonobstructive is lacking. Consequently, this deficiency can result in a significant number of unnecessary referrals for invasive angiography that yields nonobstructive results. Fractional flow reserve (FFR), which assesses the hemodynamic significance of a specific lesion, when performed during invasive angiography, results in improved patient outcomes compared with visual stenosis assessment alone. Through the application of computational analytic methods to CT-derived anatomic coronary models, noninvasive calculation of FFR has become possible. This allows for the improved ability to differentiate between nonobstructive coronary lesions and those that are truly hemodynamically significant. Currently, HeartFlow FFRCT is the only FDA-approved and commercially available CCTA-derived FFR (CT-FFR) platform. By reducing the number of invasive procedures performed for nonobstructive disease, CT-derived FFR has the ability to lower health care expenditures and become the true gatekeeper to invasive angiography.
Strategies for Reducing Population Surgical Costs in Medicare
Authors: Nathan Hari , Thumma Jyothi R. , Norton Edward C. , Dimick Justin B.
Published: August 2017

Objective:

We sought to assess hospital cost variation for elective inpatient surgical procedures within small geographic areas.

Summary Background Data:

Previous studies have documented cost variation for inpatient surgical procedures on a national basis, suggesting opportunities for savings. Cost variation within small geographic areas is more relevant to policymakers, providers, and patients, but it has not been studied.

Methods:

Using Medicare payment data, we identified elderly patients undergoing 1 of 7 elective inpatient surgical procedures during 2010–2012. We calculated 30-day surgical episode costs including payments for the index hospitalization, readmission, physician services, and post-acute care. Using hierarchical regression models, we identified hospitals with significantly higher average costs than the least expensive hospitals in their metropolitan statistical areas.

Results:

The proportion of patients undergoing surgery at the lowest-cost hospitals in their metropolitan statistical areas ranged from 10% for hip replacement to 25% for coronary artery bypass grafting. In contrast, the proportion of patients undergoing surgery at significantly higher-cost hospitals ranged from 5.0% for bariatric surgery to 64% for hip replacement. These high-cost hospitals had higher complication and readmission rates than their lowest-cost peers. Surgery at high-cost hospitals resulted in Medicare expenditures that were $4427 to $10,417 higher than those at the lowest-cost hospitals, increasing episode costs by 25% to 47% per case.

Conclusions:

Significant excess expenditures are incurred due to care at hospitals with substantially higher average costs than their nearby peers. This finding highlights the potential for substantial savings without the need to refer patients over long distances. Some of the procedures studied may represent appropriate targets for future Medicare bundled payment initiatives.
Faculty Development for the Operating Room
Authors: Gardner Aimee K. , Timberlake Matthew D. , Dunkin Brian J.
Published: August 2017

Objective:

We describe a half-day faculty development course designed to equip surgical educators with evidence-based teaching frameworks shown to promote learning in the operating room (OR). We hypothesize that participating faculty will deliver improved instruction as perceived by residents.

Methods:

Residents anonymously rated faculty teaching behaviors among whom they had recently worked in the OR (minimum 3 cases in preceding 6 months) using the Briefing - Intraoperative teaching - Debriefing Assessment Tool (BIDAT; 1 = never, 5 = always). Faculty then attended a half-day course. The curriculum was based on the “briefing-intraoperative teaching-debriefing” framework. Discussion and practice centered on goal setting, performance-enhancing instruction, dual task interference, and feedback. After the course, residents again evaluated the faculty. Paired-samples and independent-samples t tests were used to analyze pre and post course changes and differences between groups, respectively.

Results:

Nineteen faculty completed the course. Associate professors (N = 4) demonstrated improved briefing (4.32 ± 0.48 → 4.76 ± 0.45, P < 0.01), debriefing (4.30 ± 0.29 → 4.77 ± 0.43, P < 0.01), and total teaching (4.38 ± 0.78 → 4.79 ± 0.39, P < 0.05). No significant changes were observed among assistant (N = 9) or full professors (N = 6). All 3 faculty members who served as course co-instructors, regardless of rank, improved significantly in briefing (4.42 ± 0.22 → 4.98 ± 0.29, P < 0.05), debriefing (4.27 ± 0.23 → 4.98 ± 0.29, P < 0.04), and total teaching (4.37 ± 0.21 → 4.99 ± 0.02, P < 0.05). Faculty with baseline teaching scores in the bottom quartile improved teaching behaviors in all phases of instruction (P < 0.05). Teaching scores over the same period did not change among faculty who did not attend.

Conclusions:

A half-day course aimed at enhancing intraoperative instruction can contribute to resident-perceived improvement in structured teaching behavior among participating faculty. Initiatives directed at intraoperative instruction might be best targeted towards midlevel faculty with established technical expertise who are motivated to expand teaching efforts and those who have low levels of baseline teaching scores.
Perioperative Use of Erythromycin Reduces Cognitive Decline After Coronary Artery Bypass Grafting Surgery: A Pilot Study
Authors: Thomaidou Evanthia , Argiriadou Helena , Vretzakis Georgios , Megari Kalliopi , Taskos Nikolaos , Chatzigeorgiou Georgios , Anastasiadis Kyriakos
Published: August 2017

Objectives

Adverse neurologic outcome can be a debilitating complication after cardiac surgery. The aim of this study was to investigate the potential neuroprotective action of erythromycin, a well known antibiotic agent, regarding postoperative cognitive decline in patients undergoing cardiac surgery.

Methods

Forty patients scheduled for elective coronary artery bypass grafting surgery were prospectively randomly assigned in 2 groups: the erythromycin group (n = 19) who received erythromycin at a dose of 25 mg/kg before and after surgery and the control group (n = 21) who did not receive it. All patients were monitored with near-infrared spectroscopy during the operation. Interleukin (IL) 1 and IL-6 as inflammatory markers and tau protein as a marker of brain injury were measured before and after surgery. Neurocognitive assessment was performed before surgery, on the day of discharge, and at 3 months postoperatively.

Results

Both groups were comparable in terms of demographic and clinical data. Patients who took erythromycin presented with significantly better cognitive performance before discharge and 3 months after surgery. No significant differences between the 2 groups referring to IL-1 and IL-6 values were detected. Tau serum values were lower in the erythromycin group after surgery.

Conclusions

Erythromycin administration attenuates cerebral damage and postoperative cognitive decline after coronary artery bypass grafting surgery.

Trial registration

The study was retrospectively registered at ClinicalTrials.gov (NCT01274754). Study start day: November 2008.
A dinosaur missing-link?
Chilesaurus
and the early evolution of ornithischian dinosaurs
Authors: Baron Matthew G. , Barrett Paul M.
Published: August 2017

The enigmatic dinosaur taxon
Chilesaurus diegosuarezi
was originally described as a tetanuran theropod, but this species possesses a highly unusual combination of features that could provide evidence of alternative phylogenetic positions within the clade. In order to test the relationships of
Chilesaurus
, we added it to a new dataset of early dinosaurs and other dinosauromorphs. Our analyses recover
Chilesaurus
in a novel position, as the earliest diverging member of Ornithischia, rather than a tetanuran theropod. The basal position of
Chilesaurus
within the clade and its suite of anatomical characters suggest that it might represent a ‘transitional’ taxon, bridging the morphological gap between Theropoda and Ornithischia, thereby offering potential insights into the earliest stages of ornithischian evolution, which were previously obscure. For example, our results suggest that pubic retroversion occurred prior to some of the craniodental and postcranial modifications that previously diagnosed the clade (e.g. the presence of a predentary bone and ossified tendons).
Adaptive compliant structures for flow regulation
Authors: Arena Gaetano , M. J. Groh Rainer , Brinkmeyer Alex , Theunissen Raf , M. Weaver Paul , Pirrera Alberto
Published: August 2017

This paper introduces conceptual design principles for a novel class of adaptive structures that provide both flow regulation and control. While of general applicability, these design principles, which revolve around the idea of using the instabilities and elastically nonlinear behaviour of post-buckled panels, are exemplified through a case study: the design of a shape-adaptive air inlet. The inlet comprises a deformable post-buckled member that changes shape depending on the pressure field applied by the surrounding fluid, thereby regulating the inlet aperture. By tailoring the stress field in the post-buckled state and the geometry of the initial, stress-free configuration, the deformable section can snap through to close or open the inlet completely. Owing to its inherent ability to change shape in response to external stimuli—i.e. the aerodynamic loads imposed by different operating conditions—the inlet does not have to rely on linkages and mechanisms for actuation, unlike conventional flow-controlling devices.
Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor
Authors: Hamouche W. , Maurini C. , Vidoli S. , Vincenti A.
Published: August 2017

We have designed and tested experimentally a morphing structure consisting of a neutrally stable thin cylindrical shell driven by a multi-parameter piezoelectric actuation. The shell is obtained by plastically deforming an initially flat copper disc, so as to induce large isotropic and almost uniform inelastic curvatures. Following the plastic deformation, in a perfectly isotropic system, the shell is theoretically neutrally stable, having a continuous set of stable cylindrical shapes corresponding to the rotation of the axis of maximal curvature. Small imperfections render the actual structure bistable, giving preferred orientations. A three-parameter piezoelectric actuation, exerted through micro-fibre-composite actuators, allows us to add a small perturbation to the plastic inelastic curvature and to control the direction of maximal curvature. This actuation law is designed through a geometrical analogy based on a fully nonlinear inextensible uniform-curvature shell model. We report on the fabrication, identification and experimental testing of a prototype and demonstrate the effectiveness of the piezoelectric actuators in controlling its shape. The resulting motion is an apparent rotation of the shell, controlled by the voltages as in a ‘gear-less motor’, which is, in reality, a precession of the axis of principal curvature.
Unsteady solute dispersion in small blood vessels using a two-phase Casson model
Authors: Rana Jyotirmoy , Murthy P. V. S. N.
Published: August 2017

This study explores the transport of a solute in an unsteady blood flow in small arteries with and without absorption at the wall. The Casson fluid model is suitable for blood flow in small vessels. Owing to the aggregation of red cells in the central region of the small vessels, a two-phase model is considered in this investigation. Using the generalized dispersion model (Sankarasubramanian & Gill 1973
Proc. R. Soc. Lond. A
333
, 115–132. (doi:10.1098/rspa.1973.0051)), the convection, dispersion and mean concentration of the solute are analysed at all times in small arteries of different radii. The effects of the yield stress, wall absorption, the amplitude of the fluctuating pressure gradient component, the peripheral layer thickness, the Womersley frequency parameter, the Schmidt number and the Peclet number on the dispersion process are discussed. A comparative study of solute dispersion among single- and two-phase fluid models is presented. For small vessels, a significant difference between these models is observed during the solute dispersion; however, this difference becomes insignificant for large vessels. The mean concentration of solute reduces with increasing radius of the vessels. The present investigation is more realistic for understanding the transportation process of drugs in blood flow in small arteries using the non-Newtonian fluid model.
Curatr: a web application for creating, curating, and sharing a mass spectral library
Authors: Palmer Andrew , Phapale Prasad , Fay Dominik , Alexandrov Theodore
Published: August 2017

Motivation

Identification from metabolomics mass spectrometry experiments requires comparison of fragmentation spectra from experimental samples to spectra from analytical standards. As the quality of identification depends directly on the quality of the reference spectra, manual curation is routine during the selection of reference spectra to include in a spectral library. Whilst building our own in-house spectral library we realised that there is currently no vendor neutral open access tool for for facilitating manual curation of spectra from raw LC-MS data into a custom spectral library.

Results

We developed a web applicationcuratrfor the rapid generation of high quality mass spectral fragmentation libraries for liquid-chromatography mass spectrometry analysis. Curatr handles datasets from single or multiplexed standards, automatically extracting chromatographic profiles and potential fragmentation spectra for multiple adducts. These are presented through an intuitive interface for manual curation before being documented in a custom spectral library. Searchable molecular information and the providence of each standard is stored along with metadata on the experimental protocol. Curatr support the export of spectral libraries in several standard formats for easy use with third party software or submission to community databases, maximising the return on investment for these costly measurements. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library which is publicly available athttp://curatr.mcf.embl.de.

Availability

The source code is freely available athttp://github.com/alexandrovteam/curatr/along with example data.

Supplementary information

A step-by step user manual is available in the supplementary information
Quantifying the thermostability landscape separating plant sesquiterpene synthase orthologs using Maximum Entropy
Authors: Nartey Charisse M. , Aljadeff Johnatan , Fernandez Irma , Laurendon Caroline , Koo Hyun Jo , O’Maille Paul E. , Sharpee Tatyana O. , Noel Joseph P.
Published: August 2017

As global temperatures rise due to climate change, crops are becoming increasingly vulnerable to failure. We tested the accessibility of thermodynamic phenotypic diversity within limited positional changes using 29=512 mutants of a terpene synthase (TPS), Tobacco 5-epi-Aristolchene synthase. First, we measured the thermal unfolding curves of each mutant and found that mutations shifted the Tms both higher and lower, including a cohort of mutants that failed to fold. The low correlation coefficient between the Tms of these mutants and the proportions of each terpene product output by the enzymes revealed that thermostability and product output are independent traits. Maximum Noise Entropy analyses were used to analyze the impact of the 9 mutational positions on thermostability, revealing that three of these positions were mainly responsible for the trait of increased Tm. These positions form a functional network as measured by the nonlinearity of their combined effects on thermostability. Unexpectedly, the strongly destabilizing positions combine nonlinearly to ameliorate each other’s deleterious effects resulting in a synergistic dampening. Taken together, our study shows the high potential for specialized metabolic enzyme engineering but also reveals a complex interconnected system of amino acids that will continue to evade perfect predictability.
PrPSc-induced conformational changes and strain-specific structures of PrPScrevealed by Disulfide-crosslink scanning
Authors: Taguchi Yuzuru , Nishida Noriyuki , Schatzl Hermann S.
Published: August 2017

There exist many phenotypically-varied prion strains, like viruses, despite the absence of conventional genetic material which codes the phenotypic information. As prion is composed solely of the pathological isoform (PrPSc) of prion protein (PrP), the strain-specific traits are hypothesized to be enciphered in the structural details of PrPSc. Identification of the structures of PrPScis therefore vital for the understanding of prion biology, though they remain unidentified due to the incompatibility of PrPScwith conventional high-resolution structural analyses. Based on our previous hypothesis that the region between the first and the second α-helix (H1∼H2) and the distal region of the third helix (Ctrm) of the cellular isoform of PrP (PrPC) have important roles for efficient interactions with PrPSc, we created series of mutant PrPs with two cysteine substitutions (C;C-PrP) which were systematically designed to form an intramolecular disulfide crosslink between H1∼H2 and Ctrm and assessed their conformational changes by prions: Specifically, a cysteine substitution in H1∼H2 from 165 to 169 was combined with cysteine-scanning along Ctrm from 220 to 229. C;C-PrPs with the crosslinks were expressed normally with the similar glycosylation patterns and subcellular localization as the wild-type PrP albeit with varied expression levels. Interestingly, some of the C;C-PrPs converted to the protease-resistant isoforms in the N2a cells persistently infected with 22L prion strain, whereas the same mutants did not convert in the cells infected with another prion strain Fukuoka1, indicating that local structures of PrPScin these regions vary among prion strains and contribute to prion-strain diversity. Moreover, patterns of the crosslinks of the convertible C;C-PrPs implied drastic changes in positional relations of H1∼H2 and Ctrm in the PrPSc-induced conformational changes by 22L prion. Thus, disulfide-crosslink scanning is a useful approach for investigation of strain-specific structures of PrPSc, and would be applicable to other types of amyloids as well.
A global envelope test to detect early and late bursts of trait evolution
Authors: Murrell D. J.
Published: August 2017

The joint analysis of species’ evolutionary relatedness and their morphological evolution has offered much promise in understanding the processes that underpin the generation of biological diversity. Disparity through time (DTT) is a popular method that estimates the relative trait disparity within and between subclades at each time point, and compares this to the null hypothesis that trait values follow an uncorrelated random walk along the time calibrated phylogenetic tree. A simulation envelope is normally created by calculating, at every time point, the 95% minimum and 95% maximum disparity values from multiple simulations of the null model on the phylogenetic tree. The null hypothesis is rejected whenever the empirical DTT curve falls outside of this envelope, and these time periods may then be linked to events that may have sparked non-random trait evolution. However, this method of envelope construction leads to multiple testing and a poor, uncontrolled, false positive rate. As a consequence it cannot be recommended. A recently developed method in spatial statistics is introduced that constructs a confidence envelope by giving each DTT curve a single ranking value based upon its most extreme disparity value. This method avoids the pitfalls of multiple testing whilst retaining a visual interpretation. Results using simulated data show this new test has desirable type 1 properties and is at least as powerful in correctly rejecting the null hypothesis as the morphological disparity index and node height test that lack a visual interpretation. Three example datasets are reanalyzed to show how the new test may lead to different inferences being drawn. Overall the results suggest the new rank envelope test should be used in null model testing for DTT analyses, and that there is no need to combine the envelope test with other tests such as has been done previously. Moreover, the rank envelope method can easily be adopted into recently developed posterior predictive simulation methods. More generally, the rank envelope test should be adopted when-ever a null model produces a vector of correlated values and the user wants to determine where the empirical data is different to the null model.
Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla
Authors: Becraft Eric D. , Woyke Tanja , Jarett Jessica , Ivanova Natalia , Vitorino Filipa Godoy , Poulton Nicole , Brown Julia M. , Brown Joseph , Lau C.Y.M. , Onstott Tullis , Eisen Jonathan A. , Moser Duane , Stepanauskas Ramunas
Published: August 2017

Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the “Candidate phylum SPAM” represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66%-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual SPAM cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior metagenomic studies. Based on these observations, we propose renaming SPAM to “Candidate phylum Solagigasbacteria”. Current evidence suggests that Solagigasbacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers and the deep subsurface, with no reports from marine environments to date.
Modeling the emergence of antibiotic resistance in the environment: an analytical solution for the minimum selection concentration
Authors: Greenfield Ben K. , Shaked Shanna , Marrs Carl F. , Nelson Patrick , Raxter Ian , Xi Chuanwu , McKone Thomas E. , Jolliet Olivier
Published: August 2017

Environmental antibiotic risk management requires an understanding of how subinhibitory antibiotic concentrations contribute to the spread of resistance. We develop a simple model of competition between sensitive and resistant bacterial strains to predict the minimum selection concentration (MSC), the lowest level of antibiotic at which resistant bacteria are selected. We present an analytical solution for the MSC based on the routinely measured minimum inhibitory concentration (MIC) and the selection coefficient (sc) that expresses fitness differences between strains. We calibrated the model by optimizing the shape of the bacterial growth dose–response curve to antibiotic or metal exposure (the Hill coefficient, κ) to fit previously published experimental growth rate difference data. The model fit varied among nine compound-taxa combinations examined, but predicted the experimentally observed MSC/MIC ratio well (R2≥ 0.95). The shape of the antibiotic response curve varied among compounds (0.7 ≤ κ ≤ 10.5), with the steepest curve for the aminoglycosides streptomycin and kanamycin. The model was sensitive to this antibiotic response curve shape and to the sc, indicating the importance of fitness differences between strains for determining the MSC. The MSC can be more than one order of magnitude lower than the MIC, typically by a factor scκ. This study provides an initial quantitative depiction and a framework for a research agenda to examine the growing evidence of selection for resistant bacteria communities at low environmental antibiotic concentrations.
A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Authors: Demircioğlu Deniz , Kindermans Martin , Nandi Tannistha , Cukuroglu Engin , Calabrese Claudia , Fonseca Nuno A. , Kahles Andre , Lehmann Kjong , Stegle Oliver , Brazma Alvis , Brooks Angela N. , Rätsch Gunnar , Tan Patrick , Göke Jonathan ,   on behalf of the PCAWG Transcriptome Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Published: August 2017

Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. While the role of promoters as driver elements in cancer has been recognized, the contribution of alternative promoters to regulation of the cancer transcriptome remains largely unexplored. Here we infer active promoters using RNA-Seq data from 1,188 cancer samples with matched whole genome sequencing data. We find that alternative promoters are a major contributor to context-specific regulation of isoform expression and that alternative promoters are frequently deregulated in cancer, affecting known cancer-genes and novel candidates. Our study suggests that a highly dynamic landscape of active promoters shapes the cancer transcriptome, opening many opportunities to further explore the interplay of regulatory mechanism and noncoding somatic mutations with transcriptional aberrations in cancer.
Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
Authors: Kirstahler Philipp , Bjerrum Søren Solborg , Friis-Møller Alice , Cour Morten la , Aarestrup Frank M. , Westh Henrik , Pamp Sünje Johanna
Published: August 2017

Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy, and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: i) human hosts, ii) ambiguousness/contaminants in public microbial reference genomes, and iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism than was determined in cultivation‐ and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management.
Interactions between species introduce spurious associations in microbiome studies
Authors: Menon Rajita , Ramanan Vivek , Korolev Kirill S.
Published: August 2017

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease.
Discovery and whole genome sequencing of a human clinical isolate of the novel speciesKlebsiella quasivariicolasp. nov
Authors: Wesley Long S. , Linson Sarah E. , Saavedra Matthew Ojeda , Cantu Concepcion , Davis James J. , Brettin Thomas , Olsen Randall J.
Published: August 2017

Originally thought to be a single species,Klebsiella pneumoniaehas been divided into three distinct species:K. pneumoniae,K. quasipneumoniaeandK. variicola. In a recent study of 1,777 extended-spectrum beta-lactamase (ESBL)-producingKlebsiellastrains recovered from human infections in Houston, we discovered one strain (KPN1705) causing a wound infection that was phylogenetically distinct from all currently recognizedKlebsiellaspecies. Whole genome sequencing of strain KPN1705 revealed that it was single locus variant of the multilocus sequence type ST-1155. This sequence type was reported only once previously. To further investigate the phylogeny of these two organisms, we sequenced the genome of strain KPN1705 to closure and compared its genetic features toKlebsiellareference strains. Results demonstrated strain KPN1705 extensively shares core gene content, antimicrobial resistance genes, and plasmids withK. pneumoniae,K. quasipneumoniaeandK. variicola. Since strain KPN1705 and the previously reported novel strain are phylogenetically most closely related toK. variicola,we propose the nameK. quasivariicolasp. nov.
ProphET, Prophage Estimation Tool: a standalone prophage sequence prediction tool with self-updating reference database
Authors: Reis-Cunha João L. , Bartholomeu Daniella C. , Earl Ashlee M. , Birren Bruce W. , Cerqueira Gustavo C.
Published: August 2017

Prophages are a significant force in prokaryote evolution. The remaining sequences of a bacteriophage integration event are known for altering gene expression, enabling creative destruction of the bacterial genome and to induce pathogenicity by harboring and transposing virulence and antibiotic resistance factors. In the light of the dreadful expansion of antibiotic resistance bacteriophages have gathered renewed interest from the scientific community and public health decision makers as a promising long forgotten alternative to control bacterial infections. Cataloging the repertoire of prophages and their integration sites is an important initial step in the understanding of bacteriophages either as tool or as a threat. In this work, we present ProphET (Prophage Estimation Tool), a standalone application without the limitations of their web based counterparts and which identifies prophages in bacterial genomes with higher precision than similar applications.
The antibody repertoire of colorectal cancer
Authors: Cha Seong Won , Bonissone Stefano , Na Seungjin , Pevzner Pavel A. , Bafna Vineet
Published: August 2017

Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search. We introduce a novel proteogenomic approach, AbScan, to identify these highly variable antibody peptides, by developing a customized antibody database construction method using RNA-seq reads aligned to immunoglobulin (Ig) genes. AbScan starts by filtering transcript (RNA-seq) reads that match the template for Ig genes. The retained reads are used to construct a repertoire graph using the 'split' de Bruijn graph: a graph structure that improves upon the standard de Bruijn graph to capture the high diversity of Ig genes in a compact manner. AbScan corrects for sequencing errors, and converts the graph to a format suitable for searching with MS/MS search tools. We used AbScan to create an antibody database from 90 RNA-seq colorectal tumor samples. Next, we used proteogenomics analysis to search MS/MS spectra of matched colorectal samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) against the AbScan generated database. AbScan identified 1,940 distinct antibody peptides. Correlating with previously identified Single Amino-Acid Variants (SAAVs) in the tumor samples, we identified 163 pairs (antibody peptide, SAAV) with significant co-occurrence pattern in the 90 samples. The presence of co-expressed antibody and mutated peptides was correlated with survival time of the individuals. Our results suggest that AbScan (https://github.com/csw407/AbScan.git) is an effective tool for a proteomic exploration of the immune response in cancers.