bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality Improvement Interventions across a Network of Pediatric Hematology–Oncology Clinics
Authors: Morgan Jennifer , Deyo Jeffrey , Cox Jennifer , Fasipe Francisca , Mohamed Ashraf , Russo Carolyn 
Published: June 2019

Introduction:
Achieving improvement in quality among different institutions is challenging. Immunocompromised children with febrile neutropenia are at high risk of severe infection. Pediatric hematology–oncology patients frequently experience central line–associated bloodstream infections (CLABSIs) associated with implanted catheters. A network of 8 pediatric hematology–oncology clinics affiliated with St. Jude Children’s Research Hospital launched 2 initiatives designed to reduce the incidence of infections and improve infection treatment.

Methods:
We reviewed the timing of antibiotic administration for immunocompromised patients with a fever before and after a quality improvement intervention tailored to each affiliate clinic. We also reviewed the frequency of CLABSIs before and after implementing a central line care bundle for implanted catheters in ambulatory patients.

Results:
Across the affiliate clinic network, the timing of antibiotic administration improved from the preintervention period (23% of patients received antibiotics within 60 min of registration) to 53% and 73%, in successive postintervention periods. Implementing a central line bundle for implanted catheters was associated with increased compliance and a trend toward increased time between CLABSIs.

Conclusion:
We describe an approach to quality improvement utilizing a system of monitoring with annual clinical audits, development of joint quality improvement initiatives, ongoing education, and focused training of staff for effecting change that improves patient healthcare across multiple institutions.
Encouraging Resident Adverse Event Reporting: A Qualitative Study of Suggestions from the Front Lines
Authors: Szymusiak John , Walk Thomas J. , Benson Maggie , Hamm Megan , Zickmund Susan , Gonzaga Alda Maria , Bump Gregory M. 
Published: June 2019

Introduction:
Little is known about what motivates residents to report adverse events. The goals of the qualitative study were to: (1) better understand facilitators to residents’ event reporting and (2) identify effective interventions that encourage residents to report.

Methods:
The authors conducted focus groups of upper-level residents from 4 training programs (2 internal medicine, a pediatric, and a combined medicine-pediatric) who rotated at 3 institutions within a large healthcare system in 2016. Quantitative data on reporting experience were gathered. Focus groups were audio recorded and transcribed. Two coders reviewed transcripts using the editing approach and organized codes into themes.

Results:
Sixty-four residents participated in 8 focus groups. Residents were universally exposed to reportable events and knew how to report. Residents’ reporting behavior varied by site according to local culture, with residents filing more reports at the pediatric hospital compared to other sites, but all groups expressed similar general views about facilitators to reporting. Facilitators included familiarity with the investigation process, reporting via telephone, and routine safety educational sessions with safety administrators. Residents identified specific interventions that encouraged reporting at the pediatric hospital, including incorporating an attending physician review of events into sign-out and training on error disclosure.

Conclusions:
This study provides insight into what motivates resident event reporting and describes concrete interventions to increase reporting. Our findings are consistent with the Theoretical Domains Framework of behavioral change. These strategies could prove successful at other pediatric hospitals to build a culture that values reporting and prepares residents as patient safety champions.
Quality Initiative to Reduce Cardiac CT Angiography Radiation Exposure in Patients with Congenital Heart Disease
Authors: Ali Fatima , Rizvi Arjumand , Ahmad Huzaifa , McGonagill Phillip , Khan Muneeb , Krishnamurthy Rajesh , Jamil Zafar , Nadeem Naila , Yousuf Mohammad , Hasan Babar 
Published: June 2019

Background:
The use of cardiac computed tomography angiography (CCTA) as a complementary diagnostic modality to echocardiography in patients with congenital heart diseases (CHDs) is expanding in low- and middle-income countries. The adoption of As Low As Reasonably Achievable techniques is not widespread, resulting in significant unintended radiation exposure, especially in children. Simple quality improvement measures geared toward reducing radiation dose can have a impact on patient safety in resource-limited centers in low- and middle-income countries.

Objectives:
To determine how a quality improvement initiative can reduce radiation exposure during CCTA in patients with CHD.

Methods:
We designed a key driver -based quality initiative to reduce radiation dose during CCTA for CHD using protocol optimization, communication, and training and implementation as the drivers for intervention. Preintervention variables (radiation exposure, scanning protocols, and image quality) were collected from September 2012 to July 2016 and compared with variables in the postimplementation phase (February 2017 to July 2017). We compared quantitative and categorical variables using the chi-square test. Linear regression analysis was used to evaluate the effect of various factors on radiation dose.

Results:
We documented a reduction in the effective dose in the postintervention versus preintervention phase (mean, 2.0 versus 21 mSv, P < 0.0001, respectively). Linear regression showed that the optimal organizational levels are associated with the same reduction in radiation. This finding shows that the time factor translates a combination of organizational and technical factors that contributed to the reduction in radiations.

Conclusions:
Our project showed a reduction in CCTA-associated radiation exposure.
Predicting the Prognosis of Non-Small Cell Lung Cancer by Integrating Microarray and Clinical Data with Deep Learning
Authors: Lai Yu-Heng , Chen Wei-Ning , Hsu Te-Cheng , Lin Che , Tsao Yu , Wu Semon 
Published: June 2019

AbstractNon-small cell lung cancer (NSCLC) is one of the most common lung cancers worldwide. Accurate prognostic stratification of NSCLC can become an important clinical reference when designing therapeutic strategies for cancer patients. With this clinical application in mind, we developed a deep neural network (DNN) combining heterogeneous data sources of gene expression and clinical data to accurately predict the prognosis of NSCLC patients. Based on microarray data from a cohort set (614 patients), seven well-known NSCLC markers were used to group patients into marker- and marker+ subgroups. Using a systems biology approach, prognosis relevance values (PRV) were then calculated to select eight additional novel prognostic gene markers. Gene markers along with clinical data were then used to develop an integrative DNN via bimodal learning to predict the 5-year survival rate of NSCLC patients with tremendously high accuracy (AUC: 0.8163, accuracy: 75.44%), which is superior to all other existing methods based on AUC. Using the capability of deep learning, we believe that our predicted cancer prognosis can be a promising index helping oncologists and physicians develop personalized therapy and build the foundation of precision medicine in the future.
Fluoxetine-induced dematuration of hippocampal neurons and adult cortical neurogenesis in the common marmoset
Authors: Ohira Koji , Hagihara Hideo , Miwa Miki , Nakamura Katsuki , Miyakawa Tsuyoshi 
Published: June 2019

AbstractThe selective serotonin reuptake inhibitor fluoxetine (FLX) is widely used to treat depression and anxiety disorders. Chronic FLX treatment reportedly induces cellular responses in the brain, including increased adult hippocampal and cortical neurogenesis and reversal of neuron maturation in the hippocampus, amygdala, and cortex. However, because most previous studies have used rodent models, it remains unclear whether these FLX-induced changes occur in the primate brain. To evaluate the effects of FLX in the primate brain, we used immunohistological methods to assess neurogenesis and the expression of neuronal maturity markers following chronic FLX treatment (3 mg/kg/day for 4 weeks) in adult marmosets (n = 3 per group). We found increased expression of doublecortin and calretinin, markers of immature neurons, in the hippocampal dentate gyrus of FLX-treated marmosets. Further, FLX treatment reduced parvalbumin expression and the number of neurons with perineuronal nets, which indicate mature fast-spiking interneurons, in the hippocampus, but not in the amygdala or cerebral cortex. We also found that FLX treatment increased the generation of cortical interneurons; however, significant up-regulation of adult hippocampal neurogenesis was not observed in FLX-treated marmosets. These results suggest that dematuration of hippocampal neurons and increased cortical neurogenesis may play roles in FLX-induced effects and/or side effects. Our results are consistent with those of previous studies showing hippocampal dematuration and increased cortical neurogenesis in FLX-treated rodents. In contrast, FLX did not affect hippocampal neurogenesis or dematuration of interneurons in the amygdala and cerebral cortex.
A data-driven approach to optimising the encoding for multi-shell diffusion MRI with application to neonatal imaging
Authors: Tournier J-Donald , Christiaens Daan , Hutter Jana , Price Anthony N. , Cordero-Grande Lucilio , Hughes Emer , Bastiani Matteo , Sotiropoulos Stamatios N. , Smith Stephen M. , Rueckert Daniel , Counsell Serena J. , Edwards A. David , Hajnal Joseph V. 
Published: June 2019

AbstractDiffusion MRI has the potential to provide important information about the connectivity and microstructure of the human brain during normal and abnormal development, non-invasively and in vivo. Recent developments in MRI hardware and reconstruction methods now permit the acquisition of large amounts of data within relatively short scan times. This makes it possible to acquire more informative multi-shell data, with diffusion-sensitisation applied along many directions over multiple b-value shells. Such schemes are characterised by the number of shells acquired, and the specific b-value and number of directions sampled for each shell. However, there is currently no clear consensus as to how to optimise these parameters. In this work, we propose a means of optimising multi-shell acquisition schemes by estimating the information content of the diffusion MRI signal, and optimising the acquisition parameters for sensitivity to the observed effects, in a manner agnostic to any particular diffusion analysis method that might subsequently be applied to the data. This method was used to design the acquisition scheme for the neonatal diffusion MRI sequence used in the developing Human Connectome Project, which aims to acquire high quality data and make it freely available to the research community. The final protocol selected by the algorithm, and currently in use within the dHCP, consists of b = 0, 400, 1000, 2600 s/mm2 with 20, 64, 88 & 128 DW directions per shell respectively.HighlightsA data driven method is presented to design multi-shell diffusion MRI acquisition schemes (b-values and no. directions).This method optimises the multi-shell scheme for maximum sensitivity to the information content in the signal.When applied in neonates, the data suggest that a b=0 + 3 shell strategy is appropriate
Visual dynamics cues in learning complex physical interactions
Authors: Hasson Christopher J. , Jalili Paneed F. 
Published: June 2019

ABSTRACTThis study investigated the role of visual dynamics cues (VDCs) in learning to interact with a complex physical system. Manual gait training was used as an exemplary case, as it requires therapists to control the non-trivial locomotor dynamics of patients. A virtual analog was developed that allowed naïve subjects to manipulate the leg of a virtual stroke survivor (a virtual patient; VP) walking on a treadmill using a small robotic manipulandum. The task was to make the VP’s leg pass through early, mid, and late swing gait targets. One group of subjects (n = 17) started practice seeing the VP’s affected thigh and shank (i.e., VDCs); a second control group (n = 16) only saw the point-of-contact (VP ankle). It was hypothesized that, if seeing the VP’s leg provides beneficial dynamics information, the VDC group would have better task performance and generalization than controls. Results were not supportive. Both groups had similar task performance, and for the late swing gait target, a decrement in manipulative accuracy was observed when VDCs were removed in a generalization task. This suggests that when learning to manipulate complex dynamics, VDCs can create a dependency that negatively affects generalization if the visual context is changed.
Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth
Authors: Everson Todd M. , Vives-Usano Marta , Seyve Emie , Cardenas Andres , Lacasaña Marina , Craig Jeffrey M. , Lesseur Corina , Baker Emily R. , Fernandez-Jimenez Nora , Heude Barbara , Perron Patrice , Gónzalez-Alzaga Beatriz , Halliday Jane , Deyssenroth Maya A. , Karagas Margaret R. , Íñiguez Carmen , Bouchard Luigi , Carmona-Sáez Pedro , Loke Yuk J. , Hao Ke , Belmonte Thalia , Charles Marie A. , Martorell-Marugán Jordi , Muggli Evelyne , Chen Jia , Fernández Mariana F. , Tost Jorg , Gómez-Martín Antonio , London Stephanie J. , Sunyer Jordi , Marsit Carmen J. , Lepeule Johanna , Hivert Marie-France , Bustamante Mariona 
Published: June 2019

AbstractMaternal smoking during pregnancy (MSDP) contributes to poor birth outcomes, in part through disrupted placental functions, which may be reflected in the placental epigenome. We meta-analyzed the associations between MSDP and placental DNA methylation (DNAm) and between DNAm and birth outcomes within the Pregnancy And Childhood Epigenetics (PACE) consortium (7 studies, N=1700, 344 with any MSDP). We identified 1224 CpGs that were associated with MSDP, of which 341 associated with birth outcomes and 141 associated with gene expression. Only 6 of these CpGs were consistent with the findings from a prior meta-analysis of cord blood DNAm, demonstrating substantial tissue-specific responses to MSDP. The placental MSDP associated CpGs were enriched for growth-factor signaling, hormone activity, inflammation, and vascularization, which play important roles in placental function. We demonstrate links between placental DNAm, MSDP and poor birth outcomes, which may better inform the mechanisms through which MSDP impacts placental function and fetal growth.
Integrated Identification of Disease Specific Pathways Using Multi-omics data
Authors: Lu Yingzhou , Chang Yi-Tan , Hoffman Eric P. , Yu Guoqiang , Herrington David M. , Clarke Robert , Wu Chiung-Ting , Chen Lulu , Wang Yue 
Published: June 2019

AbstractMotivationIdentification of biological pathways plays a central role in understanding both human health and diseases. Although much work has previously been done to explore the biological pathways by using single omics data, little effort has been reported using multi-omics data integration, mainly due to methodological and technological limitations. Compared to single omics data, multi-omics data will help identifying disease specific functional pathways with both higher sensitivity and specificity, thus gaining more comprehensive insights into the molecular architecture of disease processes.ResultsIn this paper, we propose two computational approaches that integrate multi-omics data and identify disease-specific biological pathways with high sensitivity and specificity. Applying our methods to an experimental multi-omics data dataset on muscular dystrophy subtypes, we identified disease-specific pathways of high biological plausibility. The developed methodology will likely have a broad impact on improving the molecular characterization of many common diseases.Contactyuewang@vt.eduSupplementary informationSupplementary information attached.
Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis
Authors: Schubert Ryan D. , Hawes Isobel , Ramachandran Prashanth S. , Ramesh Akshaya , Crawford Emily D. , Pak John E. , Wu Wesley , Cheung Carly K. , O’Donovan Brian D. , Tato Cristina M. , Lyden Amy , Tan Michelle , Sit Rene , Sowa Gavin , Sample Hannah A. , Zorn Kelsey C. , Banerji Debarko , Khan Lillian M. , Bove Riley , Hauser Stephen L. , Gelfand Amy A. , Johnson-Kerner Bethany , Nash Kendall , Krishnamoorthy Kalpathy S. , Chitnis Tanuja , Ding Joy Z. , McMillan Hugh J. , Chiu Charles Y. , Briggs Benjamin , Glaser Carol A. , Yen Cynthia , Chu Victoria , Wadford Debra A. , Dominguez Samuel R. , Ng Terry Fei Fan , Marine Rachel L. , Lopez Adriana S. , Nix W. Allan , Soldatos Ariane , Gorman Mark P. , Benson Leslie , Messacar Kevin , Konopka-Anstadt Jennifer L. , Oberste M. Steven , DeRisi Joseph L. , Wilson Michael R. 
Published: June 2019

AbstractBackgroundSince 2014, the United States has experienced a biennial spike in pediatric acute flaccid myelitis (AFM). Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF) and only inconsistently identified from the respiratory tract, serum, or stool.MethodsWe interrogated CSF from children with AFM (n=42) and pediatric controls with other neurologic diseases (OND) (n=58). Samples were incubated with T7 bacteriophage expressing 481,966 sixty-two amino acid peptides with a fourteen amino acid overlap tiled across all known vertebrate virus and arbovirus genomes, an adaption of the VirScan method. Antibody-bound phage were deep sequenced to quantify enriched peptides with normalized counts expressed as reads per hundred thousand (rpK). EV antibody findings were confirmed with ELISA using whole viral protein 1 (VP1) from contemporary enterovirus (EV) A71 and D68 strains. Separately, metagenomic next-generation sequencing (mNGS) of CSF RNA, both unbiased and with targeted enrichment for EVs, was performed.ResultsThe most significantly enriched viral family by VirScan of CSF in AFM versus OND controls wasPicornaviridae(mean rpK 11,266 versus mean rpK 950, p-adjusted < 0.001, Wilcoxon signed-rank test with Bonferroni adjustment). EnrichedPicornaviridaepeptides belonged almost entirely to the genusEnterovirus.The mean EV VP1 ELISA signal in AFM (mean OD 0.51) was significantly higher than OND controls (mean OD 0.08, p-value < 0.001, Mann-Whitney test). mNGS did not detect additional enterovirus RNA in CSF.ConclusionDespite the rare detection of EV RNA in the CNS of patients with AFM, a pan-viral serologic assay identified high levels of CSF EV antibodies in AFM CSF compared to CSF from OND controls. These results provide further evidence for a causal role of non-polio enteroviruses in AFM.
Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics
Authors: Zhong Huanzi , Ren Huahui , Lu Yan , Fang Chao , Hou Guixue , Yang Ziyi , Chen Bing , Yang Fangming , Zhao Yue , Shi Zhun , Zhou Baojin , Wu Jiegen , Zou Hua , Zi Jin , Chen Jiayu , Bao Xiao , Hu Yihe , Gao Yan , Zhang Jun , Xu Xun , Hou Yong , Yang Huanming , Wang Jian , Liu Siqi , Jia Huijue , Madsen Lise , Brix Susanne , Liu Fang , Kristiansen Karsten , Li Junhua 
Published: June 2019

AbstractBackgroundThe gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development.MethodWe used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naïve type 2 diabetic (TN-T2D, n=77), pre-diabetic (Pre-DM, n=80), and normal glucose tolerant (NGT, n=97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naïve T2D individuals to elucidate possible host-microbial interplays characterising different disease stages.FindingsWe observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups, such as reduced faecal level of antimicrobial peptides and pancreatic enzymes in TN-T2D.InterpretationOur findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and emphasize the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host.FundingNational Key Research and Development Program of China, No. 2017YFC0909703, Shenzhen Municipal Government of China, No. JCYJ20170817145809215, and National Natural Science Foundation of China, No. 31601073.
Next generation taxonomy: integrating traditional species description with the holobiont concept and genomic approaches - The in-depth characterization of a novelEuplotesspecies as a case study
Authors: Serra Valentina , Gammuto Leandro , Nitla Venkatamahesh , Castelli Michele , Lanzoni Olivia , Sassera Davide , Bandi Claudio , Sandeep Bhagavatula Venkata , Verni Franco , Modeo Letizia , Petroni Giulio 
Published: June 2019

AbstractIn 1991 Margulis defined holobionts as the assemblage of “two or more organisms, members of different species” which remain associate “throughout a significant portion of the life history”. In recent times, holobionts have been described among many and far-related groups of living beings, such as plants, algae, insects, corals, and even humans. These studies have arisen an increasing interest in different contexts but, to our knowledge, the holobiont concept has not been applied in taxonomy. Here we propose a new approach to modern taxonomy, aimed to integrate the holobiont concept and genomic and bioinformatic analyses with the classical/morphological tools traditionally used in taxonomy. The inclusion of symbiont morphology, and of mitochondrial and symbiont genomes will allow the discipline to move toward what could become the “next generation taxonomy”. As an example of this new paradigm in the characterization of holobionts, we herein provide the taxonomic description of the ciliate protistEuplotes vanleeuwenhoekisp. nov. (Euplotia, Ciliophora) and its bacterial endosymbiont “CandidatusPinguicoccus supinus” gen. nov., sp. nov. (Opitutae, Verrucomicrobia). Interestingly, we found that this endosymbiont has an extremely reduced genome (~163 Kbp), which is suggestive of a high integration with the host and represents the first case of such an extreme reduction inVerrucomicrobia, and the first case in a protist host.