bluuebunny/crossref_metadata_2025_split huggingface dataset:
Billing and Volunteers Substantially Reduced School-Located Influenza Vaccination Costs, 2 Oregon Counties, 2010-2011
Authors: Patel Suchita A. , Groom Holly C. , Cho Bo-Hyun , Martin Kelly , Moore Robert 
Published: February 2018

Background and Objectives:
After the 2009 pandemic influenza seasons, the financial sustainability of school-located vaccination (SLV) clinics drew much attention. This study estimated and compared the labor costs of SLV clinics and reimbursements for influenza vaccinations for students attending 5 schools in 2 Oregon counties during 2010-2011.

Design/Setting:
Using a biweekly, Web-based survey, staff and volunteers prospectively tracked the time they spent on SLV clinic planning, implementation, and billing. They also tracked claims submitted and reimbursements by payment source.

Main Outcome Measure:
We report labor hours and associated costs for implementing school-based vaccination clinics; number of claims submitted and the reimbursement rate; and total and net costs.

Results:
In county A, 260 doses were administered at a total cost of $5009 and received $3620 in payment. For county B, 165 doses were administered at a cost of $5598 and received $3807 in payments. With billing, the net cost per dose decreased from $19.74 to $8.57 and $38.08 to $16.17, for county A and county B, respectively.

Conclusions:
Reimbursements reduced cost per dose by 48% across SLV clinics across both Oregon counties. Local health departments can bill local health insurers to offset costs for implementing school-based vaccination clinics. Efforts to set up billing processes require dedicated billing staff who can effectively manage claims submission processes with multiple health insurers.
A Patient Safety Toolkit for Family Practices
Authors: Campbell Stephen M. , Bell Brian G. , Marsden Kate , Spencer Rachel , Kadam Umesh , Perryman Katherine , Rodgers Sarah , Litchfield Ian , Reeves David , Chuter Antony , Doos Lucy , Ricci-Cabello Ignacio , Gill Paramjit , Esmail Aneez , Greenfield Sheila , Slight Sarah , Middleton Karen , Barnett Jane , Moore Michael , Valderas Jose M. , Sheikh Aziz , Avery Anthony J. 
Published: February 2018

Objective
Major gaps remain in our understanding of primary care patient safety. We describe a toolkit for measuring patient safety in family practices.

Methods
Six tools were used in 46 practices. These tools were as follows: National Health Service Education for Scotland Trigger Tool, National Health Service Education for Scotland Medicines Reconciliation Tool, Primary Care Safequest, Prescribing Safety Indicators, Patient Reported Experiences and Outcomes of Safety in Primary Care, and Concise Safe Systems Checklist.

Results
Primary Care Safequest showed that most practices had a well-developed safety climate. However, the trigger tool revealed that a quarter of events identified were associated with moderate or substantial harm, with a third originating in primary care and avoidable. Although medicines reconciliation was undertaken within 2 days in more than 70% of cases, necessary discussions with a patient/carer did not always occur. The prescribing safety indicators identified 1435 instances of potentially hazardous prescribing or lack of recommended monitoring (from 92,649 patients). The Concise Safe Systems Checklist found that 25% of staff thought that their practice provided inadequate follow-up for vulnerable patients discharged from hospital and inadequate monitoring of noncollection of prescriptions. Most patients had a positive perception of the safety of their practice although 45% identified at least one safety problem in the past year.

Conclusions
Patient safety is complex and multidimensional. The Patient Safety Toolkit is easy to use and hosted on a single platform with a collection of tools generating practical and actionable information. It enables family practices to identify safety deficits that they can review and change procedures to improve their patient safety across a key sets of patient safety issues.
Characterizing injury severity in nonaccidental trauma: Does Injury Severity Score miss the mark?
Authors: Brown Joshua B. , Gestring Mark L. , Leeper Christine M. , Sperry Jason L. , Peitzman Andrew B. , Billiar Timothy R. , Gaines Barbara A. 
Published: February 2018

BACKGROUND
Children suffering nonaccidental trauma (NAT) are at high risk of death. It is unclear whether markers of injury severity for trauma center/system benchmarking such as Injury Severity Score (ISS) adequately characterize this. Our objective was to evaluate mortality prediction of ISS in children with NAT compared with accidental trauma (AT).

METHODS
Pediatric patients younger than 16 years from the Pennsylvania state trauma registry 2000 to 2013 were included. Logistic regression predicted mortality from ISS for NAT and AT patients. Multilevel logistic regression determined the association between mortality and ISS while adjusting for age, vital signs, and injury pattern in NAT and AT patients. Similar models were performed for head Abbreviated Injury Scale (AIS). Sensitivity analysis examined impaired functional independence at discharge as an alternate outcome.

RESULTS
Fifty thousand five hundred seventy-nine patients were included with 1,866 (3.7%) NAT patients. Nonaccidental trauma patients had a similar rate of mortality at an ISS of 13 as an ISS of 25 for AT patients. Nonaccidental trauma patients also have higher mortality for a given head AIS level (range, 1.2-fold to 5.9-fold higher). Injury Severity Score was a significantly greater predictor of mortality in AT patients (adjusted odds rations [AOR], 1.14; 95% confidence interval [CI], 1.13–1.15; p < 0.01) than NAT patients (AOR, 1.09; 95% CI, 1.07–1.12; p < 0.01) per 1-point ISS increase, while head injury was a significantly greater predictor of mortality in NAT patients (AOR, 3.48; 95% CI, 1.54–8.32; p < 0.01) than AT patients (AOR, 1.21; 95% CI, 0.95–1.45; p = 0.12). Nonaccidental trauma patients had a higher rate of impaired functional independence at any given ISS or head AIS level than AT patients.

CONCLUSION
Nonaccidental trauma patients have higher mortality and impaired function at a given ISS/head AIS than AT patients. Conventional ISS thresholds may underestimate risk and head injury is a more important predictor of mortality in the NAT population. These findings should be considered in system performance improvement and benchmarking efforts that rely on ISS for injury characterization.

LEVEL OF EVIDENCE
Epidemiologic study, level III.
A novel, minimally invasive approach to assure hemostasis for intercostal bleeding after trauma
Authors: Park Habeeba , Glaser Jacob , Florecki Katherine , Schmoekel Nathan , DuBose Joseph , Stein Deborah , Scalea Thomas 
Published: February 2018

ABSTRACT
Intercostal artery injury can cause large hemothoraces. While many patients with intercostal artery injury present hemodynamically unstable and require emergent thoracotomy for hemostasis, some tamponade spontaneously. They may rebleed later, however, and cause recurrent hemothorax or retained hemothorax. Video-assisted thoracic surgery (VATS) is an effective way to evacuate retained hemothorax. However, assessing and ligating intercostal artery injury during VATS can be difficult, and often, open thoracotomy is pursued. Even with open surgery, ligation of the intercostal artery can be a challenge. We present a minimally invasive method of definitive intercostal artery ligation during VATS or open thoracotomy.
Single-Nucleotide-Resolution Computing and Memory in Living Cells
Authors: Farzadfard Fahim , Gharaei Nava , Higashikuni Yasutomi , Jung Giyoung , Cao Jicong , Lu Timothy K. 
Published: February 2018

AbstractComputing and memory in living cells are central to encoding next-generation therapies and studying in situ biology, but existing strategies have limited encoding capacity and are challenging to scale. To overcome this bottleneck, we developed a highly scalable, robust and compact platform for encoding logic and memory operations in living bacterial and human cells. This platform, named DOMINO for DNA-based Ordered Memory and Iteration Network Operator, converts DNA in living cells into an addressable, readable, and writable computation and storage medium via a single-nucleotide resolution read-write head that enables dynamic and highly efficient DNA manipulation. We demonstrate that the order and combination of DNA writing events can be programmed by biological cues and multiple molecular recorders can be coordinated to encode a wide range of order-independent, sequential, and temporal logic and memory operations. Furthermore, we show that these operators can be used to perform both digital and analog computation, and record signaling dynamics and cellular states in a long-term, autonomous, and minimally disruptive fashion. Finally, we show that the platform can be functionalized with gene regulatory modules and interfaced with cellular circuits to continuously monitor cellular phenotypes and engineer gene circuits with artificial learning capacities. We envision that highly scalable, compact, and modular DOMINO operators will lay the foundation for building robust and sophisticated synthetic gene circuits for numerous biotechnological and biomedical applications.One Sentence SummaryA programmable read-write head with single-nucleotide-resolution for genomic DNA enables robust and scalable computing and memory operations in living cells.
Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach
Authors: Renaut Sébastien , Guerra Davide , Hoeh Walter R. , Stewart Donald T. , Bogan Arthur E. , Ghiselli Fabrizio , Milani Liliana , Passamonti Marco , Breton Sophie 
Published: February 2018

AbstractFreshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of “N” nucleotides), representing 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.
Coordinate based meta-analysis of whole-brain voxel-based morphometry studies does not show evidence of grey matter loss specific to PTSD
Authors: Tench Christopher R. , Tanasescu Radu , Jethwa Ketan D. , Constantinescu Cris S. 
Published: February 2018

AbstractNeuroimaging studies have detected structural alteration in post-traumatic stress disorder (PTSD), but findings are inconsistent. This might be explained by heterogeneity between subjects with PTSD in terms of common comorbidities such as depressive and anxiety disorders and also in traumatic experience. Despite this, coordinate based meta-analysis (CBMA) has been used to try and identify localised grey matter changes, and does suggest some PTSD specific pathology. However, there are multiple technical issues that make the meta-analytic evidence questionable, warranting a re-evaluation.A literature search for voxel-based morphometry studies was performed. Only whole-brain studies using subjects with a current diagnosis of PTSD, and having a comparison group of either healthy or trauma exposed controls, were included. Twenty one voxel-based morphometry studies met the inclusion criteria. CBMA was performed to identify altered grey matter (GM) structures.Using a novel coordinate based random effect size meta-analysis, no grey matter structure was identified as being consistently altered in PTSD compared to controls. This was also verified using the activation likelihood estimate algorithm.There is no evidence, from CBMA, of consistent localised grey matter changes specific to PTSD. Inconsistency may reflect true heterogeneity in PTSD pathology or methodological issues with imaging and/or analysis, limiting the detection of PTSD specific pathology.
Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions inAcinetobacter baumanniiATCC 17978
Authors: Adams Felise G. , Stroeher Uwe H. , Hassan Karl A. , Marri Shashikanth , Brown Melissa H. 
Published: February 2018

AbstractIn recent years, effective treatment of infections caused byAcinetobacter baumanniihas become challenging due to the ability of the bacterium to acquire or up-regulate antimicrobial resistance determinants. Two component signal transduction systems are known to regulate expression of virulence factors including multidrug efflux pumps. Here, we investigated the role of the AdeRS two component signal transduction system in regulating the AdeAB efflux system, determined whether AdeA and/or AdeB can individually confer antimicrobial resistance, and explored the interplay between pentamidine resistance and growth conditions inA. baumanniiATCC 17978. Results identified that deletion ofadeRSaffected resistance towards chlorhexidine and 4’,6-diamidino-2-phenylindole dihydrochloride, two previously defined AdeABC substrates, and also identified an 8-fold decrease in resistance to pentamidine. Examination of ΔadeA, ΔadeBand ΔadeABcells augmented results seen for ΔadeRSand identified a set of dicationic AdeAB substrates. RNA-sequencing of ΔadeRSrevealed transcription of 290 genes were ≥2-fold altered compared to the wildtype. Pentamidine shock significantly increasedadeAexpression in the wildtype, but decreased it in ΔadeRS, implying that AdeRS activatesadeABtranscription in ATCC 17978. Investigation under multiple growth conditions, including the use of Biolog phenotypic microarrays, revealed resistance to pentamidine in ATCC 17978 and mutants could be altered by bioavailability of iron or utilization of different carbon sources. In conclusion, the results of this study provide evidence that AdeAB in ATCC 17978 can confer intrinsic resistance to a subset of dicationic compounds and in particular, resistance to pentamidine can be significantly altered depending on the growth conditions.
GenoGAM 2.0: Scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes
Authors: Stricker Georg , Galinier Mathilde , Gagneur Julien 
Published: February 2018

AbstractGenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirements of its current implementation prohibit its application to gigabase-scale genomes such as mammalian genomes.Here we present GenoGAM 2.0 a scalable and efficient implementation that is 2-3 orders of magnitude faster than the previous version. This is achieved by exploiting the sparsity of the model using the SuperLU direct solver for parameter fitting, and sparse Cholesky factorization together with the sparse inverse subset algorithm for computing standard errors. Furthermore the HDF5 library is employed to store data efficiently on hard drive, reducing memory footprint while keeping I/O low. Whole-genome fits for human ChIP-seq datasets (ca. 300 million parameters) could be obtained in less than 9 hours on a standard 60-core server. GenoGAM 2.0 is implemented as an open source R package and currently available on GitHub. A Bioconductor release of the new version is in preparation.We have vastly improved the performance of the GenoGAM framework, opening up its application to all types of organisms. Moreover, our algorithmic improvements for fitting large GAMs could be of interest to the statistical community beyond the genomics field.
Live cell monitoring of double strand breaks inS. cerevisiae
Authors: Waterman David P. , Lee Cheng-Sheng , Tsabar Michael , Zhou Felix , Eapen Vinay V. , Mazzella Allison , Haber James E. 
Published: February 2018

AbstractWe have used two different live-cell fluorescent protein markers to monitor the formation and localization of double-strand breaks (DSBs) in budding yeast. Using GFP derivatives of the Rad51 recombination protein or the Ddc2 checkpoint protein, we find that cells with three site-specific DSBs, on different chromosomes, usually display 2 or 3 foci that coalesce and dissociate. Rad51-GFP, by itself, is unable to repair DSBs by homologous recombination in mitotic cells, but is able to form foci and allow repair when heterozygous with a wild type Rad51 protein. The kinetics of disappearance of Rad51-GFP foci parallels the completion of DSB repair. However, in meiosis, Rad51-GFP is proficient when homozygous. Using Ddc2-GFP, we conclude that co-localization of foci following 3 DSBs does not represent formation of a homologous recombination "repair center," as the same distribution of Ddc2-GFP foci was found in the presence or absence of the Rad52 protein. The maintenance of separate DSB foci and much of their dynamics depend on functional microtubules, as addition of nocodazole resulted in a greater population of cells displaying a single focus.Author SummaryDouble strand breaks (DSBs) pose the greatest threat to the fidelity of an organism’s genome. While much work has been done on the mechanisms of DSB repair, the arrangement and interaction of multiple DSBs within a single cell remain unclear. Using two live-cell fluorescent DSB markers, we show that cells with 3 site-specific DSBs usually form 2 or 3 foci what can coalesce into fewer foci but also dissociate. The aggregation of DSBs into a single focus does not depend on the Rad52 recombination protein, suggesting that there is no “repair center” for homologous recombination. DSB foci are highly dynamic and their dynamic nature is dependent on microtubules.
Modeling brain dynamics in brain tumor patients using The Virtual Brain
Authors: Aerts Hannelore , Schirner Michael , Jeurissen Ben , Van Roost Dirk , Achten Rik , Ritter Petra , Marinazzo Daniele 
Published: February 2018

AbstractPresurgical planning for brain tumor resection aims at delineating eloquent tissue in the vicinity of the lesion to spare during surgery. To this end, non-invasive neuroimaging techniques such as functional MRI and diffusion weighted imaging fiber tracking are currently employed. However, taking into account this information is often still insufficient, as the complex non-linear dynamics of the brain impede straightforward prediction of functional outcome after surgical intervention. Large-scale brain network modeling carries the potential to bridge this gap by integrating neuroimaging data with biophysically based models to predict collective brain dynamics.As a first step in this direction, an appropriate computational model has to be selected, after which suitable model parameter values have to be determined. To this end, we simulated large-scale brain dynamics in 25 human brain tumor patients and 11 human control participants using The Virtual Brain, an open-source neuroinformatics platform. Local and global model parameters of the Reduced Wong-Wang model were individually optimized and compared between brain tumor patients and control subjects. In addition, the relationship between model parameters and structural network topology and cognitive performance was assessed.Results showed (1) significantly improved prediction accuracy of individual functional connectivity when using individually optimized model parameters; (2) local model parameters can differentiate between regions directly affected by a tumor, regions distant from a tumor, and regions in a healthy brain; and (3) interesting associations between individually optimized model parameters and structural network topology and cognitive performance.
Distinct co-modulation rules of synaptic and voltage-gated currents coordinates interactions of multiple neuromodulators
Authors: Li Xinping , Bucher Dirk , Nadim Farzan 
Published: February 2018

AbstractDifferent neuromodulators usually activate distinct receptors but can have overlapping targets. Consequently, circuit output depends on neuromodulator interactions at shared targets, a poorly understood process. We explored quantitative rules of co-modulation of two principal targets: voltage-gated and synaptic ionic currents. In the stomatogastric ganglion of the crab Cancer borealis, the neuropeptides proctolin and CCAP modulate synapses of the pyloric circuit, and activate a voltage-gated current (IMI) in multiple neurons. We examined the validity of a simple dose-dependent quantitative rule that co-modulation by proctolin and CCAP is predicted by the linear sum of the individual effects of each modulator, up to saturation. We found that this rule is valid for co-modulation of synapses, but not for the activation of IMI, where co-modulation was sublinear. Given the evolutionary conservation of neuromodulator receptors and signaling pathways, such distinct rules for co-modulation of different targets are likely to be common across neuronal circuits.