bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality Improvement Initiative for Assessing Allografts after Lung Transplantation
Authors: Hayes Don , Nicholson Kerri L. , Miller Rebecca , Nance Ashley E. , Kirkby Stephen E. , Parker William , Baker Peter B. 
Published: June 2019

Introduction:
The histologic evaluation of lung allografts after transbronchial biopsy (TBBx) is a key component of the clinical care of lung transplant recipients. With established guidelines on diagnosing allograft rejection, no specific recommendations exist on timeliness to reaching a diagnosis and initiating therapy. A quality improvement initiative focused on 3 key stages of achieving a prompt diagnosis of acute cellular rejection including tissue processing, interpretation, and notification to the treating transplant pulmonologist was initiated to minimize time to treatment onset.

Methods:
We completed a single-center cohort study on all surveillance and clinically indicated TBBx from September 2006 to March 2018. The rapid tissue processing, interpretation, and notification system was instituted in March 2011 with data before this date serving as baseline.

Results:
We enrolled 28 patients who underwent 210 TBBx (1 excluded due to unknown notification date). Thirty-eight TBBx were included at baseline before implementation of the rapid tissue processing and communication system; 171 were included after implementation. Median time to notification following the change was 0 days (interquartile range, 0–1) compared with 1 day (interquartile range, 1–1) before the change (P < 0.001). After the change, same-day notification increased, with 110 (64%) TBBx resulting in same-day notification compared with 0 before (P < 0.001). We initiated treatment of acute cellular rejection on the day of diagnosis for the entire cohort.

Conclusions:
This quality improvement initiative resulted in more efficient analysis of TBBx of allografts in lung transplant recipients and faster communication of results to the clinical team.
Reducing the Cranial CT Rate for Pediatric Minor Head Trauma at Three Community Hospitals
Authors: Smith Alla , Gruskin Karen , Monuteaux Michael C. , Stack Anne M. , Sundberg Melissa , Yim Ramy , Seneski Annie , Becker Theresa 
Published: June 2019

Objective:
Efforts to reduce the rate of computerized cranial tomography (CT) in pediatric patients with minor head trauma (MHT) have focused on academic medical centers. However, community hospitals deliver the majority of pediatric emergency care. We aimed to reduce cranial CT utilization in patients presenting with MHT at 3 community hospital emergency departments (EDs).

Methods:
Multidisciplinary stakeholder teams at each site oversaw the quality improvement effort, which included education about an evidence-based guideline for MHT and individual provider feedback on CT rates. Given the variation in hospital structure, we tailored the specifics of the intervention to each site. We used statistical process control methodology to measure CT rates over time. The primary balancing measure was returned to the ED within 72 hours with clinically important traumatic brain injury.

Results:
We included 3,215 pediatric ED visits for MHT: 1,253 in the baseline period and 1,962 in the intervention period. The CT rate dropped from 18% in the baseline period to 13% in the intervention period, a 28% relative reduction. Pediatric providers saw 72% of the intervention period encounters and drove this reduction. There was no increase in the number of children who returned to their local ED within 72 hours with clinically important traumatic brain injury.

Conclusions:
We safely reduced the proportion of children with MHT who received a cranial CT through a multicenter community ED quality improvement initiative. We did not see an increase in missed clinically important traumatic brain injury.
Implementing Standardized Screening for Adverse Childhood Experiences in a Pediatric Resident Continuity Clinic
Authors: Marsicek Sarah M. , Morrison John M. , Manikonda Neha , O’Halleran Michael , Spoehr-Labutta Zach , Brinn Melissa 
Published: June 2019

Introduction:
Exposure to adversity in childhood has been shown to impact the development of children and increase their risk of poor early childhood mental health and chronic medical conditions in young children, and developing chronic diseases, mental health disorders, and substance abuse disorders as adults. The recognition of adverse childhood experiences (ACEs) and provision of behavioral-based interventions can help children build resilience. We implemented a screening method to help providers better assess patients’ exposure to adversity. Our goal was to increase the screening for ACEs utilizing a standardized ACEs screening tool from 0% to 80% of children presenting for annual well-child visits within 1 year.

Methods:
We implemented a screening tool to determine a child’s exposure to ACEs within our general pediatrics clinic. A variety of interventions, including resident, faculty, and staff-focused educational lectures, simulation, and process changes were performed to increase screening. Also, we surveyed resident physicians and faculty about their experiences with ACEs screening.

Results:
Over 1 year, we screened 1,206 patients for exposure to ACEs and increased screening from 0% to 60%. Provider comfort with discussing abuse with patients and familiarity with resources for children exposed to ACEs did not change significantly.

Conclusions:
Patients can successfully be screened in a resident-led, general pediatric clinic using a standardized ACEs screening tool. Such an approach can successfully identify patients with high-risk ACE scores. Additionally, education on and implementation of the tool may improve provider comfort with screening for ACEs.
Prevention of Pressure Ulcers in a Pediatric Cardiac Intensive Care Unit
Authors: Simsic Janet M. , Dolan Kevin , Howitz Sarah , Peters Stephanie , Gajarski Robert 
Published: June 2019

Background:
Pressure ulcer (PU) is an injury to skin or underlying tissue as a result of pressure or pressure with shear stress. We classify PUs by the level of tissue injury: stage I–IV, unstageable, suspected deep tissue injury. This quality project was aimed to reduce the incidence of PUs > stage II in the cardiothoracic intensive care unit.

Methods:
We reviewed PUs > stage II from March 2010 to December 2017. Interventions included: PU bundle (April 2010, revised January 2013); multidisciplinary huddles for PUs > stage II (October 2011); multidisciplinary weekly skin rounds (March 2010, revised August 2012); unit specific workgroup (October 2012); caregiver input form (December 2012). The PU bundle included diaper barrier cream, pulse oximeter probe rotation, turning schedule, pressure reduction surfaces, heel pressure release, head of the bed elevation.

Results:
Between 2010 and 2014, PUs decreased from 15.7 events per 1,000 patient days to a new baseline of 2.9 events per 1,000 patient days. We have sustained this rate for 3 years. PUs related to immobility decreased from 35 in 2010–2011 to 4 in 2016–2017. PU related to medical devices decreased from 34 in 2010–2011 to 15 in 2016–2017.

Conclusions:
Institution of PU bundle, multidisciplinary weekly skin rounds, and huddles for PUs > stage II reduced PUs related to immobility, allowed for earlier identification of stage II PUs and reduced stage III PUs. Challenges remain in reducing PUs related to medical devices. Importantly, we sustained this improvement over the past 3 years.
Operating Room Codes Redefined: A Highly Reliable Model Integrating the Core Hospital Code Team
Authors: Caruso Thomas J. , Rama Asheen , Knight Lynda J. , Gonzales Ralph , Munshey Farrukh , Darling Curtis , Chen Michael , Sharek Paul J. 
Published: June 2019

Introduction:
Typically, multidisciplinary teams manage cardiac arrests occurring outside of the operating room (OR). This approach results in reduced morbidity. However, arrests that occur in the OR are usually managed by OR personnel alone, missing the benefits of out-of-OR hospital code teams. At our institution, there were multiple pathways to activate codes, each having different respondents, depending on time and day of the week. This improvement initiative aimed to create a reliable intraoperative emergency response system with standardized respondents and predefined roles.

Methods:
A multidisciplinary improvement team led this project at an academic pediatric hospital in California. After simulations performed in the OR (in situ), the team identified a valuable key driver—a consistent activation process that initiated standard respondents, 24 hours a day, 7 days a week. By utilizing core hospital code members routinely available outside of the OR during days, nights, and weekends, respondents were identified to augment OR personnel. Code roles were preassigned. After education, we conducted in situ simulations that included the perioperative and out-of-OR code team members. We administered a knowledge assessment to perioperative staff.

Results:
The knowledge assessment for perioperative staff (n = 52) had an average score of 96%. Review of subsequent OR codes reflects an improved initiation process and management.

Conclusions:
The process for activating the emergency response system and roles for intraoperative code respondents were standardized to ensure a predictable code response, regardless of time or day of the week. Ongoing simulations with perioperative personnel continue to optimize the process.
Learning to evoke complex motor outputs with spatiotemporal neurostimulation using a hierarchical and adaptive optimization algorithm
Authors: Laferriere Samuel , Bonizzato Marco , Dancause Numa , Lajoie Guillaume 
Published: June 2019

AbstractThe development of neurostimulation techniques to evoke motor patterns is an active area of research. It serves as a crucial experimental tool to probe computation in neural circuits, and it has applications in neuroprostheses used to aid recovery of function after stroke or injury. There are two important challenges when designing algorithms to unveil and control neurostimulation-to-motor mappings, thereby linking spatiotemporal patterns of neural stimulation to muscle activation: (1) the exploration of motor maps needs to be fast and efficient (exhaustive search is to be avoided for clinical and experimental reasons) (2) online learning needs to be flexible enough to track ongoing changes in these maps. We propose a stimulation search algorithm to address these issues, and demonstrate its efficacy with experiments in non-human primate models. Our solution is a novel iterative process using Bayesian Optimization via Gaussian Processes on increasingly complex signal spaces. We show that our algorithm can successfully and rapidly learn mappings between complex stimulation patterns and evoked muscle activation patterns, where standard approaches fail. Importantly, we uncover nonlinear circuit-level computations in M1 that would not have been possible to identify using conventional mapping techniques.
Transcranial Pulse Stimulation with Ultrasound in Alzheimer’s disease – A new navigated focal brain therapy
Authors: Beisteiner R. , Matt E. , Fan C. , Baldysiak H. , Schönfeld M. , Philippi Novak T. , Amini A. , Aslan T. , Reinecke R. , Lehrner J. , Weber A. , Reime U. , Goldenstedt C. , Marlinghaus E. , Hallett M. , Lohse-Busch H. 
Published: June 2019

AbstractUltrasound-based brain stimulation techniques offer an exciting potential to modulate the human brain in a highly focal and precisely targeted manner. However, for clinical applications the current techniques have to be further developed. We introduce a new ultrasound stimulation technique, based on single ultrashort ultrasound pulses (transcranial pulse stimulation, TPS) and describe a first navigable clinical TPS system. Feasibility, safety and preliminary (uncontrolled) efficacy data in Alzheimer’s disease (AD) are provided. Simulation data,in vitromeasurements with rat and human skulls/brains and clinical data in 35 AD patients were acquired in a multicentric setting (including CERAD scores and functional MRI). Preclinical results show large safety margins and patient results show high treatment tolerability. Neuropsychological scores improved significantly when tested immediately as well as 1 and 3 months after stimulation and fMRI data displayed significant connectivity increases within the memory network. The results encourage broad neuroscientific application and translation of the new method to clinical therapy and randomized sham-controlled studies.
Arabidopsis Proteome and the Mass Spectral Assay Library
Authors: Zhang Huoming , Liu Pei , Guo Tiannan , Zhao Huayan , Bensaddek Dalila , Aebersold Ruedi , Xiong Liming 
Published: June 2019

AbstractArabidopsis is an important model organism and the first plant with its genome sequenced. Knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics by data-independent acquisition (SWATH/DIA-MS) was recently developed and considered as a high-throughput targetedlike approach for accurate proteome quantitation. In this approach, a high-quality and comprehensive library is a prerequisite. Here, we generated a protein expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups with 1,787 of them being differentially expressed which includes 65 proteins known to respond to abscisic acid stress. Mass spectrometry data are available via ProteomeXchange with identifier PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
Investigating Affective and Motor Improvements with Dance in Parkinson’s Disease
Authors: Ciantar Sarah R. , Bearss Karolina A. , Levkov Gabriella , Bar Rachel J. , DeSouza Joseph F.X. 
Published: June 2019

AbstractBackgroundResearch has supported the notion that dance alleviates motor symptoms for people with Parkinson’s disease (PD) illustrated by observed improvements in gait, balance, and quality of life. However, what remains unclear is whether engaging in weekly dance classes also positively influences nonmotor symptoms of PD, such as affect regulation (mood).ObjectivesTo examine depressive symptoms of participants in a dance program for people with PD, and to extend previous findings on the topics for motor symptoms.MethodsPeople with PD (n=23) and age-matched healthy controls (n=11) between the ages of 58-75 (M=67.91, SD=5.43) participated in a weekly Dance for PD® class. Nonmotor symptoms of PD were assessed using the Geriatric Depression Scale (GDS), administered at three time points over the 1st year of a newly-developed dance program. The Berg Balance Scale (BBS) and the Timed Up and Go (TUG) were also administered at three time points to assess motor function.ResultsLongitudinal mixed methods analysis showed significant improvements in GDS scores, when examining effects of the dance class over the time, with a significant main effect of time (p < 0.01) and condition: pre/post dance class (p < 0.025). Significant improvements were also observed across the motor tests of BBS (p < 0.001) and TUG (p < 0.001) measurements.ConclusionOur findings suggest dance can facilitate positive improvements in both motor and mood related symptoms of PD. These findings show important nonmotor effects of dance as an adjunct treatment for mood that may reduce the burden of this disease.
Longitudinal, Multiparametric MRI Assessment of repetitive mild TBI in rats
Authors: Khan Ahmad Raza , Hansen Brian , Iversen Nina K. , Olesen Jonas L. , Angoa-Perez Mariana , Kuhn Donald M. , Østergaard Leif , Jespersen Sune N. 
Published: June 2019

AbstractRepetitive mild traumatic brain injury (mTBI) has long term health effects and may result in the development of neurodegenerative or neuropsychiatric disorders. Histology shows axonal and dendritic beading, synaptic atrophy, vasodilation and gliosis occuring within hours/days post-mTBI. However, current neuroimaging techniques are unable to detect the early effects of repetitive mTBI. Consequently, mTBI brain scans are normal appearing and inconclusive. Hence, neuroimaging markers capable of detecting subtle microstructural and functional alterations are needed. We present results from longitudinal, multiparametric magnetic resonance imaging (MRI) assessment of repetitive mTBI in rats. We employ advanced in-vivo diffusion MRI (dMRI) to probe brain microstructural alterations, perfusion MRI to assess cerebral blood flow (CBF), close to the injury site, and proton MR spectroscopy to assess metabolic alterations in the ipsilateral cerebral cortex. High resolution anatomical scans were also acquired. In agreement with clinical observations, anatomical scans of rats were normal appearing even after repeated mTBI. Throughout, significance is regarded as p<0.05 post false discovery rate correction. dMRI revealed significant microstructural remodelling in ipsilateral hippocampus (reduced radial kurtosis), may be due to axonal/dendritic beading, demyelination, synaptic atrophy and edema. Consistent with prior reports of reduced cell/fiber density in mTBI, we find significantly increased mean diffusivity in ipsilateral corpus callosum. We also find significantly decreased glutathione (GSH) and increased total Choline (tCho) following second and third mTBI (vs baseline), also reported in clinical mTBI cohorts. Reduced GSH suggests oxidative stress and increase in tCho indicate cell damage/repair. CBF did not change significantly, however, high variability in CBF following the second and third mTBI suggest increased variability in CBF likely due to tissue hypoxia and oxidative stress. Oxidative stress may affect capillary blood flow by disturbing pericyte capillary contraction. Around 40% of pericytes retract after mTBI causing pericyte depletion and white matter dysfunction as suggested by dMRI findings. Multiparametric MRI detects meaningful mTBI-induced alterations otherwise undetectable with conventional MRI. Similar strategies may provide useful information to aid diagnosis of human mTBI.
RobustClone: A robust PCA method of tumor clone and evolution inference from single-cell sequencing data
Authors: Chen Ziwei , Gong Fuzhou , Ma Liang , Wan Lin 
Published: June 2019

AbstractSingle-cell sequencing (SCS) data provide unprecedented insights into intratumoral heterogeneity. With SCS, we can better characterize clonal genotypes and build phylogenetic relationships of tumor cells/clones. However, high technical errors bring much noise into the genetic data, thus limiting the application of evolutionary tools in the large reservoir. To recover the low-dimensional subspace of tumor subpopulations from error-prone SCS data in the presence of corrupted and/or missing elements, we developed an efficient computational framework, termed RobustClone, to recover the true genotypes of subclones based on the low-rank matrix factorization method of extended robust principal component analysis (RPCA) and reconstruct the subclonal evolutionary tree. RobustClone is a model-free method, fast and scalable to large-scale datasets. We conducted a set of systematic evaluations on simulated datasets and demonstrated that RobustClone outperforms state-of-the-art methods, both in accuracy and efficiency. We further validated RobustClone on 2 single-cell SNV and 2 single-cell CNV datasets and demonstrated that RobustClone could recover genotype matrix and infer the subclonal evolution tree accurately under various scenarios. In particular, RobustClone revealed the spatial progression patterns of subclonal evolution on the large-scale 10X Genomics scCNV breast cancer dataset. RobustClone software is available at https://github.com/ucasdp/RobustClone.
Serum-free culture system for spontaneous human mesenchymal stem cell spheroids formation
Authors: Dong Guoyi , Wang Shengpeng , Ge Yuping , Deng Qiuting , Cao Qi , Wang Quanlei , Shang Zhouchun , OuYang Wenjie , Li Jing , Liu Chao , Tang Jie , Zhao Weihua , Gu Ying 
Published: June 2019

AbstractHuman mesenchymal stem cells (hMSCs) are widely used in clinical research because of their multipotential, immunomodulatory, and reparative properties. Previous studies determined that hMSC spheroids from three-dimensional (3D) culture possess higher therapeutic efficacy than conventional hMSCs from monolayer (2D) culture. To date, various 3D culture methods have been developed to form hMSC spheroids, but most of them used culture medium containing fetal bovine serum (FBS), which is not suitable for further clinical use. Here, we demonstrate that dissociated single MSCs seeded in induced pluripotent stems medium (MiPS), adhere loosely to the dish and spontaneously migrate to form spheroids during day 3 to day 6. Through component deletion screening and complementation experiments, the knockout serum replacement (KSR) was identified as necessary and sufficient for hMSC spheroid formation. Transcriptome analysis showed that the overall expression profiles were highly similar between 2D culture with FBS and KSR derived spheroids. Interestingly, genes related to inflammatory response, immune response, and angiogenesis were up-regulated in spheroids at day 6, and qPCR results further validated the increased expression level of related genes, including STC1, CCL7, HGF, IL24, and TGFB3. When spheroids were re-plated in normal FBS medium, cells formed a typical spindle-shaped morphology, and FACS results showed that the recovered cells retained MSC-specific surface markers, such as CD73, CD90, and CD105. In summary, we developed a practical and convenient method to generate hMSC spheroids for clinical research and therapy.
The genomic basis of evolved virus resistance is dependent on environmental resources
Authors: Roberts Katherine , Meaden Sean , Sharpe Stephen , Kay Suzanne , Doyle Toby , Wilson Drew , Bartlett Lewis J. , Paterson Steve , Boots Mike 
Published: June 2019

AbstractParasites impose strong selection on their hosts, but the level of resistance evolved may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource mediated selection are rare, particularly in non-model organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and associated trade-offs, in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole genome sequencing we identify putative mechanisms of resistance that depend on the nutritional environment during selection. We find that the evolution of resistance is specific to diet, with adaptation to a low nutrition diet constraining resistance when challenged with the pathogen on a high nutrition diet. Resistance in a low nutrition environment is negatively correlated with growth rate, consistent with an established trade-off between immunity and development. Whole genome resequencing of the host shows that resistance mechanisms are highly polygenic and suggests evidence for trade-offs at the genetic level. Critically when populations evolve in high resource conditions, resistance is linked to metabolic and immune pathways, however it is more closely associated with cytoskeleton organisation when selected under low nutrition. Our results emphasise the importance of resources on the evolution of resistance.