bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristics and Outcomes of Pediatric Patients Supported With Ventricular Assist Device—A Multi-Institutional Analysis*
Authors: Puri Kriti , Anders Marc M. , Tume Sebastian C. , Cabrera Antonio G. , Heinle Jeffrey S. , Causey Jamie C. , Wang Yunfei , Moffett Brady S. , Shekerdemian Lara S.
Published: June 2019

Objectives:

The use of ventricular assist devices for pediatric patients with heart failure is increasing, but is associated with significant morbidity and mortality. Our objectives were to describe the admission outcomes and resource utilization of pediatric patients supported with ventricular assist devices, utilizing a multicenter database.

Data Sources:

Pediatric Health Information System database (comprising 49 nonprofit children’s hospitals).

Study Selection:

Retrospective cohort analysis of the database from January 2006 to September 2015 for all admissions less than or equal to 21 years old with ventricular assist device implantation.

Data Extraction:

The primary outcome was hospital mortality. The secondary outcomes were hospital length of stay and adjusted cost.

Data Synthesis:

We analyzed 744 ventricular assist device implantations (740 patients), 422 (57%) males, and 363 (49%) non-Hispanic white. Median age at admission was 5.9 years (interquartile range, 0.9–13.5 yr), and median length of stay was 69 days (interquartile range, 36–122 d). The overall hospital mortality was 188 (25%), whereas 395 (53%) were transplanted and 141 (19%) were discharged on ventricular assist device. Extracorporeal membrane oxygenation was used, in addition to ventricular assist device, in 340 (46%). The majority of ventricular assist device implantations (453, 61%) were from 2011 to 2015 (compared to 2006–2010). More patients discharged on ventricular assist device from 2011 to 2015 (23% vs 13% in 2006–2010; p = 0.001). There was no difference in median age, mortality, length of stay, or adjusted costs between these time periods. On multivariable analysis, underlying congenital heart disease, renal failure, liver congestion, sepsis, cerebrovascular accident, and extracorporeal membrane oxygenation were associated with hospital mortality. Sepsis and ventricular assist device replacement/repair were associated with higher adjusted cost and longer length of stay.

Conclusions:

The pediatric ventricular assist device experience continues to grow, with a significant increase in the number of patients undergoing ventricular assist device implantation and a higher proportion being discharged from hospital on ventricular assist device support in recent years. Underlying congenital heart disease, renal failure, sepsis, cerebrovascular accident, and extracorporeal membrane oxygenation are significantly associated with hospital mortality.
Painful Foot Disorders in the Geriatric Population
Authors: Oh-Park Mooyeon , Kirschner Jonathan , Abdelshahed Dena , Kim Dennis D.J.
Published: June 2019

Painful foot disorders are highly prevalent among older adults causing a significant impact on mobility, function, and risk of falls. Despite its significance, foot pain is often interpreted as a normal part of aging and relatively ignored by health care providers as well as by the older people themselves. Accurate diagnosis of the cause of foot pain is possible for most cases via clinical evaluation without a costly workup. Clinicians should consider, not only musculoskeletal pathologies but also vascular and neurological disorders in older patients with foot pain. Fortunately, most patients improve with physiatric, nonoperative interventions involving biomechanical analysis, function-oriented rehabilitation programs and therapeutic exercise, the use of proper footwear and orthoses, and selected percutaneous interventions, as indicated. In this review, we discuss the physiologic changes of the aging foot relevant to foot pain, the impact of painful foot disorders on function and other key outcomes, and principles of diagnosis and intervention. We also briefly describe painful foot disorders of the older people commonly encountered in a physiatric practice.
Application of Blood Oxygenation Level–Dependent Magnetic Resonance Imaging and Intravoxel Incoherent Motion to Assess Bilateral Renal Pathophysiological Processes Induced by Iodixanol Renal Artery First-Pass in Rabbit Model
Authors: Wang Zhiqiang , Ren Ke
Published: June 2019

Background

Noninvasive blood oxygen level–dependent imaging and intravoxel incoherent motion sequences were used to assess bilateral renal oxygenation, hemodynamics, and proton diffusion in iodixanol renal artery first-pass in rabbit model.

Methods

Forty-two rabbits were divided into 2 groups. Saline and iodixanol (1 g iodine/kg, left renal artery) were administered. Magnetic resonance imaging scans were acquired longitudinally at 24 hours prior to and 1, 24, 48, and 72 hours after administration to assess apparent diffusion coefficient, pure molecular diffusion (D), perfusion-related diffusion (D*), volume fraction (f), and relative spin-spin relaxation rate (R2*) values, respectively. The experiment evaluated serum creatinine, histological, and hypoxia-inducible factor 1α immunoexpression.

Results

During 1 to 48 hours, the values of D, f, and D* significantly decreased (P < 0.05), but R2* values significantly increased (P < 0.05) in cortex, outer medulla, and inner medulla after administration of iodixanol through left renal artery, which showed in the 72 hours. The change of the left kidney is noteworthy. Significant negative correlations were observed between apparent diffusion coefficient, D, f, and R2* in cortex, outer medulla, and inner medulla (all P < 0.001, r = −0.635–0.697).

Conclusions

The first-pass effect of the contrast agent significantly reduces ipsilateral renal perfusion and renal oxygenation, and noninvasive monitoring can be performed by using blood oxygen level–dependent magnetic resonance imaging and intravoxel incoherent motion.
Coronary Artery Anomalies and Associated Radiologic Findings
Authors: Saade Charbel , Fakhredin Rayan Bou , El Achkar Bassam , Ghieh Diamond , Mayat Ahmad , Abchee Antoine , Refaat Marwan , Ismail Hussein , El-Rayess Hebah , Karout Lina , El Merhi Fadi
Published: June 2019

Coronary anomalies occur in about 1% of the general population and in severe cases can lead to sudden cardiac death. Coronary computed tomography angiography and magnetic resonance imaging have been deemed appropriate for the evaluation of coronary anomalies by accurately allowing the noninvasive depiction of coronary artery anomalies of origin, course, and termination. The aim of this article is to describe and illustrate a comprehensive array for the classification of coronary artery anomalies.
Radionuclide Therapy With 177Lu-PSMA in a Case of Metastatic Adenoid Cystic Carcinoma of the Parotid
Authors: Has Simsek Duygu , Kuyumcu Serkan , Agaoglu Fulya Yaman , Unal Seher Nilgun
Published: June 2019

In vivo prostate-specific membrane antigen (PSMA) overexpression creates an opportunity for PSMA-directed theranostic approach in adenoid cystic carcinoma of the parotid. Herein, we illustrate a patient with metastatic PSMA-directed theranostic approach in adenoid cystic carcinoma of the parotid who had intense PSMA uptake on metastatic lesions, followed by radionuclide therapy with 177Lu-PSMA.
99mTc-MIBI Embolus in the Late Phase of a Parathyroid Scan
Authors: Savvopoulos Christos , Geijer Håkan
Published: June 2019

We report a case of a transient focal MIBI uptake in the late, 90 minutes postinjection phase of a parathyroid scintigraphy in which SPECT/CT imaging proved valuable in delineating the nature of this incidental finding.
Robotic Thyroidectomy Decreases Postoperative Pain Compared With Conventional Thyroidectomy
Authors: Kim Min Kyoung , Kang Hyun , Choi Geun Joo , Kang Kyung Ho
Published: June 2019

Background:

This retrospective study compared postoperative pain between patients undergoing open thyroidectomy (OT) and bilateral axillo-breast approach (BABA) robotic thyroidectomy (RT).

Materials and Methods:

We analyzed the electronic medical records of 1269 patients who underwent OT or RT at Chung-Ang University Hospital between January 1, 2010 and April 30, 2016. On the basis of the surgical procedure performed, patients were categorized into an OT (n=1128) and a BABA RT (BRT) group (n=141). On the basis of covariates, patients in these groups were matched using propensity score matching (n=86 in each group).

Results:

After propensity score matching, no intergroup differences were observed in the covariates. The visual analogue scale scores for pain on postoperative day 0 were lower in the BRT than in the OT group (2.57±0.95 vs. 2.28±0.95, P=0.040). However, no statistically significant differences were observed in the use of rescue analgesics, the numerical rating scale score for nausea, and the use of rescue antiemetics.

Conclusions:

Pain on postoperative day 0 was lesser in the BRT than in the OT group. Similarly, the severity of nausea was lesser in the BRT group, despite longer operation time and broad dissection performed for docking the robotic arms.
Systematic review of oxygenation and clinical outcomes to inform oxygen targets in critically ill trauma patients
Authors: Douin David J. , Schauer Steven G. , Anderson Erin L. , Jones Jacqueline , DeSanto Kristen , Cunningham Cord W. , Bebarta Vikhyat S. , Ginde Adit A.
Published: June 2019

BACKGROUND

Oxygen therapy is frequently administered to critically ill trauma patients to avoid hypoxia, but optimal oxygenation strategies are not clear.

METHODS

We conducted a systematic review of oxygen targets and clinical outcomes in trauma and critically ill patients. We searched Ovid MEDLINE, Cochrane Library, Embase, and Web of Science Core Collection from 1946 through 2017. Our initial search yielded 14,774 articles with 209 remaining after abstract review. We reviewed full text articles of human subjects with conditions of interest, an oxygen exposure or measurement, and clinical outcomes, narrowing the review to 43 articles. We assessed article quality using Grading of Recommendation, Assessment, Development, and Evaluation (GRADE) criteria.

RESULTS

Of the 43 final studies meeting inclusions criteria, 17 focused on trauma and 26 studies focused on medical and/or surgical critical illness without trauma specifically. Four trauma studies supported lower oxygenation/normoxia, two supported higher oxygenation, and 11 supported neither normoxia nor higher oxygenation (five neutral and six supported avoidance of hypoxia). Fifteen critical illness studies supported lower oxygenation/normoxia, one supported higher oxygenation, and 10 supported neither normoxia nor higher oxygenation (nine neutral and one supported avoidance of hypoxia). We identified seven randomized controlled trials (four high quality, three moderate quality). Of the high-quality randomized controlled trials (none trauma-related), one supported lower oxygenation/normoxia and three were neutral. Of the moderate-quality randomized controlled trials (one trauma-related), one supported higher oxygenation, one was neutral, and one supported avoidance of hypoxia.

CONCLUSION

We identified few trauma-specific studies beyond traumatic brain injury; none were high quality. Extrapolating primarily from nontrauma critical illness, reduced oxygen administration targeting normoxia in critically ill trauma patients may result in better or equivalent clinical outcomes. Additional trauma-specific trials are needed to determine the optimal oxygen strategy in critically injured patients.

LEVEL OF EVIDENCE

Systematic review, level IV.
An Engineered Cas-Transposon System for Programmable and Precise DNA Transpositions
Authors: Chen Sway P. , Wang Harris H.
Published: June 2019

Efficient targeted insertion of heterologous DNA into a genome remains a challenge in genome engineering. Recombinases that can introduce kilobase-sized DNA constructs require pre-existing recombination sites to be present in the genome and are difficult to reprogram to other loci. Genome insertion using current CRISPR-Cas methods relies on host DNA repair machinery, which is generally inefficient. Here, we describe a Cas-Transposon (CasTn) system for genomic insertions that uses a transposase fused to a catalytically-dead dCas9 nuclease to mediate programmable, site-specific transposition. CasTn combines the power of the Himar1 transposase, which inserts multi-kb DNA transposons into TA dinucleotides by a cut-and-paste mechanism, and the targeting capability of Cas9, which uses guide-RNAs to bind to specific DNA sequences. Usingin vitroassays, we demonstrated that Himar-dCas9 proteins increased the frequency of transposon insertions at a single targeted TA dinucleotide by >300-fold compared to an untargeted transposase, and that site-specific transposition is dependent on target choice while robust to log-fold variations in protein and DNA concentrations. We then showed that Himar-dCas9 mediates site-specific transposition into a target plasmid inE. coli. This work provides CasTn as a new method for host-independent, programmable, targeted DNA insertions to expand the genomic engineering toolbox.
Analysis of Nucleotide Pools in Bacteria Using HPLC-MS in HILIC Mode
Authors: Zborníková Eva , Knejzlík Zdeněk , Hauryliuk Vasili , Krásný Libor , Rejman Dominik
Published: June 2019

Nucleotides, nucleosides and their derivatives are present in cells at varying concentrations that rapidly change with the nutritional, and energetic status of the cell. Knowledge of the concentration dynamics of these molecules is instrumental for understanding their regulatory effects. Determination of these concentrations is challenging due to the inherent instability of these molecules and, despite many decades of research, the reported values differ widely. Here, we present a comprehensive and easy-to-use approach to determine intracellular concentrations of >25 target molecular species. The approach uses rapid filtration and cold acidic extraction followed by high performance liquid chromatography (HPLC) in the hydrophilic interaction liquid chromatography (HILIC) mode using zwitterionic columns coupled with UV and MS detectors. The method reliably detects and quantifies all the analytes expected to be observed in the bacterial cell and paves the way for future studies correlating their concentrations with biological effects.
Accurate denoising of single-cell RNA-Seq data using unbiased principal component analysis
Authors: Wagner Florian , Barkley Dalia , Yanai Itai
Published: June 2019

Single-cell RNA-Seq measurements are commonly affected by high levels of technical noise, posing challenges for data analysis and visualization. A diverse array of methods has been proposed to computationally remove noise by sharing information across similar cells or genes, however their respective accuracies have been difficult to establish. Here, we propose a simple denoising strategy based on principal component analysis (PCA). We show that while PCA performed on raw data is biased towards highly expressed genes, this bias can be mitigated with a cell aggregation step, allowing the recovery of denoised expression values for both highly and lowly expressed genes. We benchmark our resulting ENHANCE algorithm and three previously described methods on simulated data that closely mimic real datasets, showing that ENHANCE provides the best overall denoising accuracy, recovering modules of co-expressed genes and cell subpopulations. Implementations of our algorithm are available at https://github.com/yanailab/enhance.
Whole-genome sequencing of 128 camels across Asia provides insights into origin and migration of domestic Bactrian camels
Authors: Ming Liang , Yuan Liyun , Yi Li , Ding Guohui , Hasi Surong , Chen Gangliang , Jambl Tuyatsetseg , Hedayat-Evright Nemat , Batmunkh Mijiddorj , Badmaevna Garyaeva Khongr , Gan-Erdene Tudeviin , Batskh TS , Zhang Wenbin , Zulipikaer Azhati , Hosblig  , Erdemt  , Natyrov Arkady , Mamay Prmanshayev , Narenbatu  , Meng Gendalai , Narangerel Choijilsuren , Khongorzul Orgodol , He Jing , Hai Le , Lin Weili , Sirendalai  , Sarentuya  , Aiyisi  , Li Yixue , Wang Zhen , Jirimutu
Published: June 2019

The domestic Bactrian camels were treated as the principal means of locomotion between the eastern and western cultures in history. To address the question of their origin, we performed whole-genome sequencing of 128 camels across Asia, including representative populations of domestic Bactrian camels from the Mongolian Plateau to the Caspian Sea, as well as the extant wild Bactrian camels and dromedaries. The domestic and wild Bactrian camels showed remarkable genetic divergence since they were split from dromedaries, confirming they were separated species. The wild Bactrian camels made also little contribution to the ancestry of domestic ones. Among the domestic Bactrian camels, those from Iran exhibited the largest genetic distance from others, and were the first population to separate in the phylogeny. Although evident admixture was observed between domestic Bactrian camels and dromedaries living around the Caspian Sea, the large genetic distance and basal position of Iranian Bactrian camels could not be explained by introgression alone. Taken together, our study favored the Iranian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where the native wild Bactrian camels inhabited. This study illustrated the complex genomic landscape of migration underlying domestication in Bactrian camels.
Comparative metagenome-assembled genome analysis ofLachnovaginosumgenomospecies, formerly known as BVAB1
Authors: Holm Johanna B. , France Michael , Ma Bing , Robinson Courtney K. , McComb Elias , Brotman Rebecca M. , Ravel Jacques
Published: June 2019

Bacterial Vaginosis Associated Bacteria 1 (BVAB1) is an uncultured bacterial species found in the human vagina that belongs to the familyLachnospiraceaewithin the orderClostridiales, and as its name suggests, is often associated with bacterial vaginosis (BV). In reproductive health, BV is of concern due to its associated risk for HIV,Chlamydia trachomatis, andNeisseria gonorrhoeaeacquisition as well as preterm birth. BVAB1 has been shown to be associated with BV persistence after metronidazole treatment and increased vaginal inflammation, and to confer a higher risk of puerperal infections. To date, no genome of BVAB1 is available, which has made it difficult to understand its disease-associated features. We present here a comparative analysis of seven metagenome-assembled genomes (MAGs) of BVAB1, derived from the cervicovaginal lavages of seven separate women. One metagenome was sequenced with long-read technology on a PacBio Sequel II instrument while the others were sequenced using the Illumina HiSeq platform. The MAGs were 1.5-1.7 Mb long, encoding an average of 1,499 genes and had >98% average nucleotide identity to each other. CheckM-estimated genome completion was 98.2%. We propose to rename BVAB1 toLachnovaginosumgenomospecies based on a phylogenetic analysis, and provide genomic evidence that this species may metabolize D-lactate, produce trimethylamine (the chemical responsible for BV-associated odor), and be motile. These MAGs will be a valuable resource and will contribute to our understanding of the heterogenous etiologies of bacterial vaginosis.
Brain Network Mechanisms of General Intelligence
Authors: Sripada Chandra , Angstadt Mike , Rutherford Saige , Taxali Aman
Published: June 2019

We identify novel mechanisms of general intelligence involving activation patterns of large-scale brain networks. During hard, cognitively demanding tasks, the fronto-parietal network differentially activates relative to the default mode network, creating greater “separation” between the networks, while during easy tasks, network separation is reduced. In 920 adults in the Human Connectome Project dataset, we demonstrate that these network separation patterns across hard and easy task conditions are strongly associated with general intelligence, accounting for 21% of the variance in intelligence scores across individuals. Moreover, we identify the presence of a crossover relationship in which FPN-DMN separation profiles that strongly predict higher intelligence in hard task conditions reverse direction and strongly predict lower intelligence in easy conditions, helping to resolve conflicting findings in the literature. We further clarify key properties of FPN-DMN separation: It is a mediator, and not just a marker, of general intelligence, and FPN-DMN separation profiles during the task state can be reliably predicted from connectivity patterns during rest. We demonstrate the robustness of our results by replicating them in a second task and in an independent large sample of youth. Overall, our results establish FPN-DMN separation as a major locus of individual differences in general intelligence, and raise intriguing new questions about how FPN-DMN separation is regulated in different cognitive tasks, across the lifespan, and in health and disease.
Multiscale activity imaging in mammary gland reveals how oxytocin enables lactation
Authors: Stevenson Alexander J. , Vanwalleghem Gilles , Stewart Teneale A. , Condon Nicholas D. , Lloyd-Lewis Bethan , Marino Natascia , Putney James W. , Scott Ethan K. , Ewing Adam D. , Davis Felicity M.
Published: June 2019

The mammary epithelium is indispensable for the continued survival of more than 5000 mammalian species. For some, the volume of milk ejected in a single day exceeds their entire blood volume. Here, we unveil the spatiotemporal properties of physiological signals that orchestrate milk ejection. Using quantitative, multidimensional imaging of mammary cell ensembles, we reveal how stimulus evoked Ca2+oscillations couple to contractions in basal epithelial cells. Moreover, we show that Ca2+-dependent contractions generate the requisite force to physically deform the innermost layer of luminal cells, compelling them to discharge the fluid that they produced and housed. Through the collective action of thousands of these biological positive displacement pumps, each linked to a contractile ductal network, milk is delivered into the mouth of the dependent neonate, seconds after the command.

Significance Statement

The mammary gland is functional for only a brief period of a female’s lifetime—if at all. During this time, it operates not for the survival of the individual, but for the survival of her species. Here, we visualize the nature of alveolar contractions in the functionally-mature mammary gland, revealing how specialized epithelial cells, which possess the ability to behave like smooth muscle cells, undergo Ca2+-dependent contractions. We demonstrate that individual oscillators can be electrically coupled to achieve global synchrony, a phenomenon that has not yet been observed in the mammary gland. By imaging activity across scales, we provide a window into the organization, dynamics and role of epithelial Ca2+oscillations in the organ principally responsible for sustaining neonatal life in mammals.
A mechanistic model for the negative binomial distribution of single-cell mRNA counts
Authors: Amrhein Lisa , Harsha Kumar , Fuchs Christiane
Published: June 2019

Several tools analyze the outcome of single-cell RNA-seq experiments, and they often assume a probability distribution for the observed sequencing counts. It is an open question of which is the most appropriate discrete distribution, not only in terms of model estimation, but also regarding interpretability, complexity and biological plausibility of inherent assumptions. To address the question of interpretability, we investigate mechanistic transcription and degradation models underlying commonly used discrete probability distributions. Known bottom-up approaches infer steady-state probability distributions such as Poisson or Poisson-beta distributions from different underlying transcription-degradation models. By turning this procedure upside down, we show how to infer a corresponding biological model from a given probability distribution, here the negative binomial distribution. Realistic mechanistic models underlying this distributional assumption are unknown so far. Our results indicate that the negative binomial distribution arises as steady-state distribution from a mechanistic model that produces mRNA molecules in bursts. We empirically show that it provides a convenient trade-off between computational complexity and biological simplicity.

Graphical Abstract
Exogenous application of KNO3 elevates the salinity tolerance of Stevia rebaudiana through ion homeostasis mechanism
Authors: Mahajan Mitali , Sharma Surbhi , Kumar Pawan , Pal Probir Kumar
Published: June 2019

Though relatively little is understood of adaptation, physiological and metabolic changes of Stevia rebaudiana under exposure to salinity stress, it is hypothesized that exogenous application of potassium (K+) could elevates the salinity tolerance through ions homeostasis. Thus, an experiment was conducted with twenty treatment combinations comprising four salinity levels (irrigation with normal water as control and three level of NaCl at 40, 80 and 120 mM) and five different concentrations of KNO3 (0.0, 2.5, 5.0, 7.5, and 10.0 g L−1). Dry leaf yield was not negatively affected with mild salinity (40 mM). However, the detrimental effects were observed at moderate and higher salinity levels (80 and 120 mM). The uptakes of K+, Ca2+, and N were significantly reduced at higher salinity level, whereas accumulations of Na+ and Cl− ions in plant tissues were substantially increased. Proline content in leaf was also increased significantly (P≤0.05) in response to salt stress. Among the foliar application, KNO3 at 5.0 gL−1 registered significantly (P≤0.05) higher dry leaf yield compared with control. Exogenous application of K+ under moderate salinity stress maintained ion balance in cytosol, particularly K: Na. Thus, the salinity tolerance of stevia can be elevated to some extent through exogenous application of K+.

Highlight

The detrimental effects of moderate and higher salinity levels on growth and dry leaf yield of stevia were observed. However, tolerance level can be elevated through exogenous application of KNO3.
Alignment and mapping methodology influence transcript abundance estimation
Authors: Srivastava Avi , Malik Laraib , Sarkar Hirak , Zakeri Mohsen , Almodaresi Fatemeh , Soneson Charlotte , Love Michael I. , Kingsford Carl , Patro Rob
Published: June 2019

Background

The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy.

Results

We investigate the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis. We observe that, even when the quantification model itself is held fixed, the effect of choosing a different alignment methodology, or aligning reads using different parameters, on quantification estimates can sometimes be large, and can affect downstream differential expression analyses as well. These effects can go unnoticed when assessment is focused too heavily on simulated data, where the alignment task is often simpler than in experimentally-acquired samples. We also introduce a new alignment methodology, called selective alignment, to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment.

Conclusion

We observe that, on experimental datasets, the performance of lightweight mapping and alignment-based approaches varies significantly and highlight some of the underlying factors. We show this variation both in terms of quantification and downstream differential expression analysis. In all comparisons, we also show the improved performance of our proposed selective alignment method and suggest best practices for performing RNA-seq quantification.
Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline
Authors: Ou Shujun , Su Weija , Liao Yi , Chougule Kapeel , Ware Doreen , Peterson Thomas , Jiang Ning , Hirsch Candice N. , Hufford Matthew B.
Published: June 2019

Sequencing technology and assembly algorithms have matured to the point that high-qualityde novoassembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and allow for annotation of TEs. There are numerous methods for each class of elements with unknown relative performance metrics. We benchmarked existing programs based on a curated library of rice TEs. Using the most robust programs, we created a comprehensive pipeline called Extensivede-novoTE Annotator (EDTA) that produces a condensed TE library for annotations of structurally intact and fragmented elements. EDTA is open-source and freely available:https://github.com/oushujun/EDTA.
Enhancing virtual bronchoscopy with intra-operative data using a multi-objective GAN
Authors: Gil D. , Esteban-Lansaque A. , Borras A. , Sánchez C.
Published: June 2019

This manuscript has been withdrawn by bioRxiv due to upload of an incorrect version of the manuscript by the authors. Therefore, this manuscript should not be cited as reference for this project.
3D-printed moulds for image-guided surgical biopsies: an open source computational platform
Authors: Crispin-Ortuzar Mireia , Gehrung Marcel , Ursprung Stephan , Gill Andrew B , Warren Anne Y , Beer Lucian , Gallagher Ferdia A , Mitchell Thomas J , Mendichovszky Iosif A , Priest Andrew N , Stewart Grant D , Sala Evis , Markowetz Florian
Published: June 2019

PURPOSE

Spatial heterogeneity of tumours is a major challenge in precision oncology. The relationship between molecular and imaging heterogeneity is still poorly understood, as it relies on the accurate co-registration of medical images and tissue biopsies. tumour moulds can guide the localization of biopsies, but their creation is time consuming, technologically challenging, and difficult to interface with routine clinical practice. These hurdles have so far hindered the progress in the area of multiscale integration of tumour heterogeneity data.

METHODS

We have developed an open source computational framework to automatically produce patient-specific 3D-printed moulds that can be used in the clinical setting. Our approach achieves accurate co-registration of sampling location between tissue and imaging, and integrates seamlessly with clinical, imaging and pathology workflows.

RESULTS

We applied our framework to patients with renal cancer undergoing radical nephrectomy. We created personalised moulds for five patients, obtaining Dice similarity coefficients between imaging and tissue sections ranging from 0.86 to 0.93 for tumour regions, and between 0.70 and 0.76 for healthy kidney. The framework required minimal manual intervention, producing the final mould design in just minutes, while automatically taking into account clinical considerations such as a preference for specific cutting planes.

CONCLUSION

Our work provides a robust and automated interface between imaging and tissue samples, enabling the development of clinical studies to probe tumour heterogeneity on multiple spatial scales.
Random Scanning Mutagenesis
Authors: Forloni Matteo , Liu Alex Y. , Wajapeyee Narendra
Published: June 2019

In vitro oligonucleotide and polymerase chain reaction (PCR)-based mutagenesis is generally used for altering the nucleotide sequence of genes to study their functional importance and the products they encode. A thorough approach to this problem is to systematically change each successive amino acid residue in the protein to alanine (i.e., alanine-scanning mutagenesis) or to a limited number of alternative amino acids. Although these strategies can provide useful information, it is sometimes desirable to test a broader spectrum of amino acid changes at the targeted positions. “Random scanning mutagenesis” was developed to examine the functional importance of individual amino acid residues in the conserved structural motif of human immunodeficiency virus (HIV) reverse transcriptase, and this protocol is adapted from that method. This strategy is an oligonucleotide-based method for generating all 19 possible replacements at individual amino acid sites within a protein.
A systematic review of fidelity measurements in complex interventions for people with intellectual disabilities and behaviours that challenge
Authors: Paulauskaite Laura , Hassiotis Angela , Ali Afia
Published: June 2019

Purpose

Fidelity data in clinical trials are not only necessary for appraising the internal and external validity, but also could provide useful insights how to improve the application of an intervention in everyday settings. The purpose of this paper is to understand the current literature of fidelity measurements in complex interventions for people with intellectual disabilities (ID) and behaviours that challenge.

Design/methodology/approach

The electronic databases MEDLINE, Embase, PsycINFO, Web of Science and CINAHL Plus were searched for studies published between 1990 to 2017 that have mentioned fidelity in randomised controlled trials of complex interventions for people with ID and behaviours that challenge based on positive behaviour support or applied behaviour analysis principles. The authors also searched the grey literature and reference lists.

Findings

Five randomised controlled trials were included in the review. The authors found variable and inconsistent fidelity measurements reported in the studies. The most frequently provided fidelity elements found in four out of five studies were adherence of implementation, dose and some aspects of quality of delivery.

Research limitations/implications

Research recommendations for a standardised approach of measuring fidelity in such studies are suggested.

Originality/value

The first review of such type that confirms the paucity of research measuring fidelity in complex interventions in this population.
Effects of two fibers used separately and in combination on physico-chemical, textural, nutritional and sensory properties of beef fresh sausage
Authors: Ben Slima Sirine , Ktari Naourez , Triki Mehdi , Trabelsi Imen , Moussa Hafedh , Makni Skandar , Abdeslam Asehraou , Herrero Ana Maria , Jiménez-Colmenero Francisco , Ruiz-Capillas Claudia , Ben Salah Riadh
Published: June 2019

Purpose

The purpose of this paper is to investigate the influence of different dietary fibers on color, nutritional, physico-chemical, sensory and textural properties of fresh sausage.

Design/methodology/approach

This study was undertaken to determine the effects of partial beef meat substitution (15, 10.5 and 6 percent) at different combinations: barley beta-glucan concentrate (BBC at 1 percent) alone, carrot fiber (ID809 at 1 percent) alone and a mixture of both fibers (BBC and ID809 at 0.5 percent of each), on the quality of fresh sausage.

Findings

Results revealed that the supplementation of dietary fibers generally decreased protein contents and increased moisture. Color parameters were significantly affected by the addition of dietary fibers. Meat substitution with dietary fibers tended toward red coloration, which enhanced sensory properties of fresh sausages, especially general acceptability. Fresh sausages formulated with a mixture of dietary fibers recorded good firmness. Indeed, it increased extrusion force values and provided a greater hardness at sensory level. This manuscript reports that beef sausage formulated with a mixture of BBC and ID809 and reduced beef meat rate improved acceptability to consumer.

Originality/value

The paper approaches a new subject that may be relevant to functional food. There are few research works to evaluate consumer preferences of new product developments and to achieve healthier and more economic fresh sausages formulated with a mixture of two fibers after reducing beef meat content.
Underage drinking as a natural part of growing up: a UK study of parental beliefs
Authors: Fulton Emily , Baines Darrin , Bartle Naomi
Published: June 2019

Purpose

Parental beliefs about underage drinking are known to influence the drinking behaviours of their children. The purpose of this paper is to explore parental beliefs about their own child drinking alcohol and young people in general, in order to ascertain whether there is a need to target such beliefs in the design of public health interventions.

Design/methodology/approach

Parents of 11–18 year olds attending one of nine schools in the Midlands of England, UK were invited to take part. Participants completed a newly designed 40-item questionnaire measuring parental beliefs about the impact and causes of underage drinking; talking to their child about alcohol; and how much and how often they thought their child consumed alcohol.

Findings

In total, 185 parents took part in the study, reporting on their eldest child aged 18 or under. The majority of parents agreed that underage drinking is detrimental to child health and wellbeing. However, over 60 per cent believed that alcohol consumption is a “natural part of growing up”, and stronger agreement with this belief was associated with higher parental reports of alcohol consumption in their children.

Social implications

The majority of parents recognised the risks and negative effects of alcohol; however, many also believe it is a natural part of growing up. Parents may hold conflicting beliefs about underage drinking, which could impact on the drinking beliefs and behaviours of their children.

Originality/value

Public health interventions may need to counter the common parental belief that underage drinking is a normal part of growing up and therefore to be expected. Clear messages about the impact parent beliefs and behaviour have on young people drinking, to ensure parents recognise that messages are aimed at themselves, and not just “other parents” are imperative.
How much of library digital content is checked out but never used?
Authors: Lieu Angela , Zhao Dangzhi
Published: June 2019

Purpose

This paper aims to identify patterns, trends and potential implications related to post-checkout non-usage (material that is checked out by a user, but subsequently never opened and/or downloaded) of library digital content.

Design/methodology/approach

A large urban Canadian public library’s data (2013-2017) from Rakuten OverDrive was analyzed. Pending items (items that are checked out, but neither opened nor downloaded) were compared with total checkouts to determine post-checkout non-usage rates.

Findings

Checkouts and overall rates of post-checkout non-usage of e-books and e-audiobooks have risen significantly and consistently. Juvenile and non-fiction e-books demonstrate higher post-checkout non-usage rates than adult and fiction e-books, respectively. The library spends up to US$10,700 per year on metered access e-books that are never opened by users. This number has grown significantly over the years.

Originality/value

E-materials in libraries have been growing rapidly, but their current lending models are still largely a direct application of concepts in traditional library services that have developed based on physical materials, such as checkouts, due dates, renewals, holds and wait times. However, e-materials do not have the limitation of physical materials that prevents other users from accessing a checked-out item, which makes many of the traditional concepts no longer applicable. New concepts and lending models should be developed that allow users to access any library e-materials at any time, and are financially functional and sustainable for both libraries and e-content providers.
Information protection behaviors: morality and organizational criticality
Authors: Lankton Nancy K. , Stivason Charles , Gurung Anil
Published: June 2019

Purpose

Organizational insiders play a critical role in protecting sensitive information. Prior research finds that moral beliefs influence compliance decisions. Yet, it is less clear what factors influence moral beliefs and the conditions under which those factors have stronger/weaker effects. Using an ethical decision-making model and value congruence theory, this study aims to investigate how moral intensity and organizational criticality influence moral beliefs and intentions to perform information protection behaviors.

Design/methodology/approach

The hypotheses were tested using a scenario-based survey of 216 organizational insiders. Two of the scenarios depict low criticality information security protection behaviors and two depict high criticality behaviors.

Findings

A major finding is that users rely more on perceived social consensus and magnitude of consequences when organizational criticality is low and on temporal immediacy and proximity when criticality is high. In addition, the moral intensity dimensions explain more variance in moral beliefs when organizational criticality is low.

Research limitations/implications

The study is limited by its sample, which is organizational insiders at a mid-size university. It is also limited in that it only examined four of the six moral intensity dimensions.

Practical implications

The findings can guide management about which moral intensity dimensions are more important to focus on when remediating tone at the top and other leadership weaknesses relating to information security.

Originality/value

This study adds value by investigating the separate dimensions of moral intensity on information protection behaviors. It also is the first to examine moral intensity under conditions of low and high organizational criticality.
Service-delivery success and failure under the sharing economy
Authors: Furunes Trude , Mkono Muchazondida
Published: June 2019

Purpose

Informed by the role and script theory, this paper aims to explore workforce and customer experiences related to service delivery under the sharing economy. The study is expedient as the sharing economy spreads its disruptive innovation across the hospitality industry.

Design/methodology/approach

This paper applies a qualitative approach, sourcing online data from virtual platforms.

Findings

The results indicate both positive and negative experiences for customers and the workforce, and the paper highlights the challenges of fragmented service delivery as a result of service delivery mediated through mobile applications.

Practical implications

Food delivery mediated through mobile applications is likely to expand as more households are lured by its convenience. This change has implications for both restaurants and the workforce.

Originality/value

Although a growing number of studies analyse the impact of the sharing economy on the hospitality industry, much of the focus has been on accommodation, and the impact and implications for the food-service segment has not been thoroughly investigated yet.
Self-verification striving and employee outcomes
Authors: Kim Tae-Yeol , Gilbreath Brad , David Emily M. , Kim Sang-Pyo
Published: June 2019

Purpose

The purpose of this paper is to test whether self-verification striving serves as an individual difference antecedent of emotional labor and explore whether various emotional labor tactics acted as mediating mechanisms through which self-verification striving relates to employee outcomes.

Design/methodology/approach

The sample used in this paper consisted of supervisor–subordinate dyads working in six hotels in South Korea and used multi-level analyses and the Monte Carlo method to test the research hypotheses presented in this paper.

Findings

Self-verification striving was positively and directly related to job performance as well as two out of three forms of emotional labor (i.e. the expression of naturally felt emotions and deep acting). Self-verification striving also indirectly related to job satisfaction through the expression of naturally felt emotions and indirectly related to job performance through deep acting.

Practical implications

The findings of this paper suggest that organizations should consider self-verification striving as an employment selection criterion and provide training programs to help their customer service employees engage in appropriate types of emotional labor.

Originality/value

This paper is the first to explore the underlying mechanisms through which self-verification striving relates to employee outcomes. It also empirically bolsters the notion that expressing naturally felt emotions is an important means of authentic self-expression that positively contributes to job satisfaction. Further, the authors found that self-verification striving positively relates to job performance partially through deep acting. Moreover, they have shown that self-verification striving, as an individual differences variable, is an antecedent of different types of emotional labor.
Management of traditional retail markets in the UK: comparative case studies
Authors: Hoang Dong , Barnes Cathy , Munroe Olga
Published: June 2019

Purpose

The purpose of this paper is to examine the current state of the management of traditional retail markets (TRM) in the UK. TRM are indoor and outdoor markets located in town and city centres across the UK, selling food, household goods, clothing and the like.

Design/methodology/approach

The paper employs a comparative analysis approach of multiple cases using an analytical framework drawn from place management and retail business management literature. The study investigates 11 retail markets in the UK, including 7 run by Local Councils, 2 privately run and 2 operated by Charity Trusts.

Findings

The paper identifies the management challenges of TRM lying at the intersect between its private-like business entity and the management overseen by local authorities, whose roles and functions are mainly on delivering public services. Although some council markets struggle, it remains a popular model for TRM because it offers social space and inclusion which other types of markets lack. The study also highlights that the environment within which TRM operate, such as policy, infrastructure, business and entrepreneurial aspects play an important role in influencing the performance of the markets.

Originality/value

The paper contributes to the retail literature’s conceptual and empirical understanding of TRM management – the area which has been mostly neglected and under-researched. It offers an integrated analytical framework, including four dimensions of policy, infrastructure, business and entrepreneurial environment to advance the current limited understanding of this traditional form of retailing and sheds light on future research in this area.
Foreign market learning: an integrative model of its antecedents, processes and outcomes
Authors: Nordin Fredrik , Lindbergh Jessica
Published: June 2019

Purpose

The purpose of this paper is to offer an integrative model of foreign market learning, including different learning processes, antecedents and outcomes.

Design/methodology/approach

The paper makes a critical review of the relevant literature, drawing on a keywords-based search of three major databases and a range of other published work for a broader perspective on the subject.

Findings

The resulting integrative model shows in a number of ways how companies can learn and benefit from differences in foreign markets and what results this can lead to.

Research limitations/implications

The sample of subject-specific contributions to the literature may have been insufficient, and a wider selection of keywords to identify them might have captured a richer variety of concepts and opinions.

Originality/value

The integrative model contributes to the literature on foreign market learning and innovation and serves as a basis for future studies and current management strategy.