bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paediatric Glaucoma in Scotland
Authors: Beck Daniel , Galea Martin , Loo Cheng Yi , Schmoll Conrad , Burgess Frederick R. , Montgomery Donald , Tatham Andrew J 
Published: December 2019

Abstract
Background
The primary aim was to estimate the incidence of primary and secondary childhood glaucoma in Scotland over a 2-year period. The secondary aim was to gauge the confidence and experience of ophthalmologists in Scotland in managing these patients.
Methods
A 7 question electronic survey was distributed to all consultant members of the Scottish Paediatric Club and Scottish Glaucoma Club. Respondents were asked to report the number of cases and types of childhood glaucoma they had managed in the last 2 years. Respondents were also asked about experience and confidence in a range of glaucoma procedures, number of patients requiring referral to specialist centres and interest in the development of a centre of excellence in Scotland.
Results
The survey returned a 56% response rate, reporting 85 new cases of paediatric glaucoma in Scotland over the preceding 2 years. 11 (12.9%) had primary glaucoma and 74 (87.1%) had secondary glaucoma. The most common subtype of secondary glaucoma was uveitic glaucoma (n=29). None of the respondents declared confidence or experience in trabeculotomy or goniotomy procedures. 11 children required referral to a specialist unit outside Scotland. 85.7% of respondents felt Scotland would benefit from a specialist unit for paediatric glaucoma.
Conclusions
This survey reflects an appetite for a specialist service for paediatric glaucoma in Scotland. However, further consideration is needed to determine if there is sufficient patient load to maintain such a service.
Exploring and analysing single cell multi-omics data with VDJView
Authors: Samir Jerome , Rizzetto Simone , Gupta Money , Luciani Fabio 
Published: December 2019

AbstractBackground Single cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information.Results We developed VDJView, which permits the simultaneous or independent analysis and visualisation of gene expression, immune receptors, and clinical metadata of both T and B cells. This tool is implemented as an easy-to-use R shiny web-application, which integrates numerous gene expression and TCR analysis tools, and accepts data from plate-based sorted or high-throughput single cell platforms. We utilised VDJView to analyse several 10X scRNA-seq datasets, including a recent dataset of 150,000 CD8+ T cells with available gene expression, TCR sequences, quantification of 15 surface proteins, and 44 antigen specificities (across viruses, cancer, and self-antigens). We performed quality control, filtering of tetramer non-specific cells, clustering, random sampling and hypothesis testing to discover antigen specific gene signatures which were associated with immune cell differentiation states and clonal expansion across the pathogen specific T cells. We also analysed 563 single cells (plate-based sorted) obtained from 11 subjects, revealing clonally expanded T and B cells across primary cancer tissues and metastatic lymph-node. These immune cells clustered with distinct gene signatures according to the breast cancer molecular subtype. VDJView has been tested in lab meetings and peer-to-peer discussions, showing effective data generation and discussion without the need to consult bioinformaticians.Conclusions VDJView enables researchers without profound bioinformatics skills to analyse immune scRNA-seq data, integrating and visualising this with clonality and metadata profiles, thus accelerating the process of hypothesis testing, data interpretation and discovery of cellular heterogeneity. VDJView is freely available at https://bitbucket.org/kirbyvisp/vdjview .
1-1-8 one-step sevoflurane wash-in scheme for low-flow anesthesia: simple, rapid, and predictable induction
Authors: Tribuddharat Sirirat , Sathitkarnmanee Thepakorn , Vattanasiriporn Naruemon , Thananun Maneerat , Nonlhaopol Duangthida , Somdee Wilawan 
Published: December 2019

Abstract
Background Sevoflurane is suitable for low-flow anesthesia (LFA). LFA needs a wash-in phase. The reported sevoflurane wash-in schemes lack simplicity, target coverage, and applicability. We proposed a one-step 1-1-8 wash-in scheme for sevoflurane LFA to be used with both N 2 O and Air. The objective of our study was to identify time for achieving each level of alveolar concentration of sevoflurane (F A S) from 1% to 3.5% in both contexts.Methods We recruited 199 adults requiring general anesthesia with endotracheal intubation and controlled ventilation—102 in group N 2 O and 97 in group Air. After induction and intubation, a wash-in was started using a fresh gas flow of O 2 :N 2 O or O 2 :Air at 1:1 L·min -1 plus sevoflurane 8%. The ventilation was controlled to maintain end-tidal CO 2 of 30-35 mmHg.Results The rising patterns of F A S and inspired concentration of sevoflurane (F I S) are similar, running parallel between the groups. The F A S/F I S ratio increased from 0.46 to 0.72 within 260 sec in group N 2 O and from 0.42 to 0.69 within 286 sec in group Air. The respective time to achieve an F A S of 1%, 1.5%, 2%, 2.5%, 3%, and 3.5% was 1, 1.5, 2, 3, 3.5, and 4.5 min in group N 2 O and 1, 1.5, 2, 3, 4, and 5 min in group Air. The heart rate and blood pressure of both groups significantly increased initially then gradually decreased as F A S increased.Conclusions The 1-1-8 wash-in scheme for sevoflurane LFA has many advantages, including simplicity, coverage, swiftness, safety, economy, and that it can be used with both N 2 O and Air. A respective F A S of 1%, 1.5%, 2%, 2.5%, 3%, and 3.5% when used with N 2 O and Air can be expected at 1, 1.5, 2, 3, 3.5, and 4.5 min and 1, 1.5, 2, 3, 4, and 5 min. This scheme may be applied for sevoflurane LFA in situations where an anesthetic gas analyzer is unavailable.
The effect of comorbidities for the prognosis of community-acquired pneumonia: an epidemiologic study using a hospital surveillance in Japan
Authors: Nguyen Mai Thi Ngoc , Saito Nobuyuki , Wagatsuma Yukiko 
Published: December 2019

Abstract
Objective Pneumonia is a common but serious illness that continues to present significant morbidity and mortality. Although the effect of severity at admission on outcome has been well reported, the role of comorbidity is still not widely understood. The Charlson Comorbidity Index measures comorbidity with a well-established history of predicting long-term outcome but its utility in pneumonia prognosis is still limited. Here, we use the Charlson Comorbidity Index and hospital surveillance data to investigate associations between comorbidities and in-hospital mortality due to community-acquired pneumonia.Results Among the 535 eligible adult patients (69.0% male, median [IQR] age, 79 [70-84] years), 100 (18.7%) acquired severe to extremely severe pneumonia. The median [IQR] CCI was 1[1-3]. Malignancy (129 of 535, 24.1%), chronic pulmonary diseases (113 of 535, 21.1%) and congestive heart failure (103 of 535, 19.3%) were frequent. Higher Charlson Comorbidity Index scores were associated with higher risk of in-hospital mortality (OR 1.28; 95% CI 1.07-1.53). These results support the inclusion of comorbid burden in predicting community-acquired pneumonia outcome.
Can introvoxel incoherent motion MRI be used to differentiate patients with placenta accreta spectrum disorders?
Authors: Lu Tao , Pu Hong , Li Kuide , Mei Jie , Huang Meng-wei , Wang Shao-yu 
Published: December 2019

Abstract
Objective Background The incidence of PAS disorders increased rapidly in recent years, and introvoxel incoherent motion (IVIM) MRI has been applied in the assessment of placenta. The study aims to investigate whether the parameters from IVIM can be used to differentiate patients with PAS disorders complicating placenta previa and secondly to differentiate different categories of PAS disorders. Methods The study participants were comprised of 99 patients with placenta previa, including 16 patients with placenta accreta, 51 patients with increta, 8 patients with percreta and 24 patients without PAS disorders between 28+0 and 39+6 weeks. IVIM MRI was performed on a 1.5T scanner. Perfusion fraction (f), pseudodiffusion coefficient (D*) and standard diffusion coefficient (D) were calculated. Results Women with PAS disorders had a higher perfusion fraction (p=0.019) than women without the disease. Multiple comparisons showed perfusion fraction in patients without PAS disorders was significantly lower than in patients with placenta accreta and percreta(P=0.018 and 0.033 respectively), but was not lower than in patients with increta(p=1). Conclusion Patients with placenta accreta and percreta differed in placental perfusion fraction from women with increta and without PAS disorders.
Diagnostic potential of ultrasound in carpal tunnel syndrome with different etiologies: correlation of sonographic median nerve measures with electrodiagnostic severity.
Authors: Elnady Basant , Rageh Elsayed M , Ekhouly Tohamy H. , Fathy Sabry M. , Alshaar Mohamed , Fouda El Saeed , Attar Mohammed , Abdelaal Ahmed M. , Tantawi Ahmed El , Algethami Mohammed M , Bong David Andrew 
Published: December 2019

Abstract
Background: Carpal tunnel syndrome (CTS) is the commonest entrapment neuropathy. The aim of this study was to assess the accuracy and validity of high resolution musculoskeletal ultrasound (US) in the diagnosis of CTS in the Saudi population. Methods: Sixty patients were diagnosed clinically to have CTS involving 89 wrists that were confirmed by neurophysiologic studies. Each affected wrist was characterized as idiopathic or associated with either diabetes mellitus or hypothyroidism and were assigned a severity grade based on results of neurophysiologic studies. Seventy-six healthy wrists from fifty age, sex and BMI matched healthy subjects were included in the control group . High resolution ultrasound (US) was performed to assess median nerve cross sectional area distal (CSAd) at the entry to the carpal tunnel and proximally (CSAp) at the level of pronator quadratus muscle with a further calculation of their difference (ΔCSA) and their mean average or CSAd+CSAp/2 (CSApd) . Results: There was a significant difference between both groups regarding mean ±SD of CSAd, CSAp, ∆CSA, and CSApd (p = 0.0001). A positive significant correlation was also found between the CSAd, ∆ CSA and the CSApd measurements with neurophysiologic severity grade of CTS (P=0.001). A ∆CSA threshold of 2.5 mm 2 showed the highest sensitivity and specificity to diagnose CTS in Saudis. Conclusion High resolution ultrasound is a valid and accurate diagnostic modality in carpal tunnel syndrome and correlated to CTS severity. A ∆CSA greater than 2.5 mm 2 is considered a valid diagnostic value for CTS in our Saudi population. CTS in our patients with diabetes tend to have greater median nerve US measurement values.
Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance
Authors: Tadmor-Levi Roni , Doron-Faigenboim Adi , Marcos-Haddad Jenny , Petit Jules , Hulata Gideon , Forlenza Maria , Wiegertjes Geert F. , David Lior 
Published: December 2019

Abstract
Background Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp ( Cyprinus carpio ), one of the most farmed fish species worldwide. Genetically disease resistant strains are highly sought after as a sustainable solution to this problem. To study the genetic basis and cellular pathways underlying disease resistance, RNA-Seq was used to characterize transcriptional responses of susceptible and resistant fish at day 4 after CyHV-3 infection. Results In susceptible fish, over four times more differentially expressed genes were up-regulated between day 0 and 4 compared to resistant fish. Susceptible and resistant fish responded distinctively to infection as only 55 (9%) of the up-regulated genes were shared by these two fish types. Susceptible fish elicited a typical anti-viral response, involving interferon and interferon responsive genes, earlier than resistant fish did. Furthermore, chemokine profiles indicated that the two fish types elicited different cellular immunity responses. A comparative phylogenetic approach assisted in chemokine copies annotation pointing to different orthologous copies common to bony-fishes and even carp-specific paralogs that were differentially regulated and contributed to the different response of these two fish types. Susceptible fish up-regulated more ccl19 chemokines, which attract T-cells and macrophages, the anti-viral role of which is established, whereas resistant fish up-regulated more cxcl8/il8 chemokines, which attract neutrophils, the antiviral role of which is unfamiliar. Conclusions Taken together, by pointing out transcriptional differences between susceptible and resistant fish in response to CyHV-3 infection, this study unraveled possible genes and pathways that take part in disease resistance mechanisms in fish and thus, enhances our understanding of fish immunogenetics and supports the development of sustainable and safe aquaculture.
Comparative physiological and biochemical mechanisms of salt tolerance in five contrasting highland quinoa cultivars
Authors: Cai Zhiquan , Gao Qi 
Published: December 2019

Abstract
Background: Chenopodium quinoa Willd., a halophytic crop, shows great variability among different genotypesin response to salt. To investigate the salinitytolerance mechanisms, five contrasting quinoa cultivars belonging to highland ecotype were compared for their seed germination (under 0, 100 and 400 mM NaCl) and seedling’s responses under five salinity levels (0, 100, 200, 300 and 400 mM NaCl). Results: Substantial variations were found in plant size (biomass) and overall salinity tolerance (plant biomass in salt treatment as % of control) among the different quinoa cultivars. Plant salinity tolerance was negatively associated with plant size, especially at lower salinity levels (<300 mM NaCl), but salt tolerance between seed germination and seedling growth is was not closely correlated. Except for shoot/root ratio, all measured plant traits responded to salt in a genotype-specific way. Salt stress resulted in decreased plant height, leaf area, root length, and root/shoot ratio in each cultivar. With increasing salinity levels, leaf superoxide dismutase (SOD) activity and lipid peroxidation generally increased, but catalase (CAT) and peroxidase (POD) activities showed non-linear patterns. Organic solutes (soluble sugar, proline and protein) accumulated in leaves, whereas inorganic ion (Na + and K + )increased but K + /Na + decreased in both leaves and roots. Across different salinity levels and cultivars, without close relationships with antioxidant enzyme activities (SOD, POD, or CAT), salinity tolerance was significantly negatively correlated with leaf organic solute and malondialdehyde contents in leaves and inorganic ion contents in leaves or roots ( not except for root K + content), but positively correlated with K + /Na + ratio in leaves or roots. Conclusion: Our results establish indicate ed that leaf osmoregulation, K + retention, Na + exclusion, and ion homeostasis are the main physiological mechanisms conferring salinity tolerance of these cultivars, rather than the regulations of leaf antioxidative ability.As an index of salinity tolerance, K + /Na + ratio in leaves or roots can be used for the selective breeding of highland quinoa cultivars.
Two-way Messaging Therapy for Depression and Anxiety: Longitudinal Response Trajectories
Authors: Hull Thomas Derrick , Malgaroli Matteo , Connolly Philippa , Feuerstein Seth , Simon Naomi 
Published: December 2019

Abstract
Background: Telemedicine is a strategy for overcoming barriers to access evidence-based psychotherapy. Digital modalities that operate outside session-based treatment formats, such as ongoing two-way messaging, may further address these challenges. However, no study to date has established suitability criteria for this medium. Methods: A large outpatient sample (n = 10,718) engaged in daily messaging with licensed clinicians from a telemedicine provider. Patients consisted of individuals from urban and rural settings in all 50 states of the US, who signed to a telemedicine provider. Using a longitudinal design, symptoms changes were observed during a 12 week treatment course. Symptoms were assessed from baseline every three weeks using the Patient Health Questionnaire (PHQ-9) for depression, and the Generalized Anxiety Disorder (GAD-7) for anxiety. Demographics and engagement metrics, such as word count for both patients and therapists, were also assessed. Growth mixture modeling was used to tease symptoms trajectories, and identify predictors of treatment response. Results: Two subpopulations had GAD-7 and PHQ-9 remission outcomes (Recovery and Acute Recovery, 30.7% of patients), while two others showed amelioration of symptoms (Depression and Anxiety Improvement, 36.9% of patients). Two subpopulations experienced no changes in symptoms (Chronic and Elevated Chronic, 32.4% of patients). Higher use of written communication, patient characteristics, and engagement metrics reliably distinguished patients with the greatest level of remission (Recovery and Acute Recovery groups). Conclusions: Remission of depression and anxiety symptoms was observed during delivery of psychotherapy through messaging. Improvements rate were consistent with face-to-face therapy, suggesting the suitability of two-way messaging psychotherapy delivery. Characteristics of improving patients were identified and could be used for treatment recommendation. These findings suggest the opportunity for further research, to directly compare messaging delivery with a control group of treatment as usual.
HIV Status Disclosure and its associated factors among Children on Antiretroviral Therapy in West Shoa Zone, Ethiopia, 2019: A Mixed method cross-sectional study
Authors: Shallo Seifadn Ahmed , Tassew Mesfin 
Published: December 2019

Abstract
Background Evidences from previous studies claim that informing children about their HIV status has long term positive implications in the HIV disease management, children's quality of life and ART drug adherence. However, in many parts of the Sub-Saharan African Countries, the HIV status disclosure among children reaches from 0 to 69.2%. Since the issue of disclosure is complex and highly influenced by socio-cultural characters and perception of the community towards HIV disease, it is important to investigate the up to date evidence which will help in designing contextualized approaches for disclosure. The objective of the current study was to assess the HIV status disclosure and its associated factors among children on ART in West Shoa Zone, Ethiopia.Methods Institutional based quantitative cross-sectional study supplemented by qualitative was conducted from February to April /2019 among 247 caregivers and or their children.Results The mean age of the children was 11.11±SD2.8, and 43.6%, (95% CI: 37, 50.9) of the children were fully disclosed. The average age at disclosure was 11 ±SD2.12. The main reasons for the disclosure were for drug adherence and better self-care, while underage was the commonest reason for nondisclosure. Compared to the age (10-15) years, the child in the age (6-9) was 97% [AOR: 0.027, 95% CI: 0.003, 0.22, P<0.001] less likely to be disclosed. Female children were 2.7 times more likely to be disclosed compared to males children [AOR: 2.73, 95% CI: 1.24, 6, P<0.013].Conclusion The current finding reveals that the HIV status disclosure is generally low, and the decision to disclose or not to do so is affected by many factors like child age, and child sex. This will affect directly or indirectly the child drug adherence, treatment outcome and also disease transmission.
The integration preference of Sleeping Beauty at non-TA site is related to the transposon end sequences
Authors: Zhou Yiting , Ma Guangwei , Yang Jiawen , Guo Yabin 
Published: December 2019

Abstract
Background: Sleeping Beauty (SB) transposon had been thought to strictly integrate into TA dinucleotides. Recently, we found that SB also integrates into non-TA sites at a lower frequency. Here we performed further study on the non-TA integration of SB. Results: 1) SB can integrate into non-TA sites in HEK293T cells as well as in mouse cell lines. 2) Both the hyperactive transposase SB100X and the traditional SB11 catalyze integrations at non-TA sites. 3) The consensus sequence of the non-TA target sites only occur at the opposite side of the sequenced junction between transposon end and the genomic sequences, indicating that the integrations at non-TA sites are mainly aberrant integrations. 4) The consensus sequence of the non-TA target sites is corresponding to the transposon end sequence. When the transposon end sequence is mutated, the consensus sequences changed too. Conclusion: The interaction between the SB transposon end and genomic DNA may be involved in the target site selection of the SB integrations at non-TA sites.
Identifying cases of chronic pain using health administrative data: A validation study
Authors: Foley Heather E , Knight John C , Ploughman Michelle , Asghari Shabnam , Audas Rick 
Published: December 2019

Abstract
Background: Chronic pain is a pervasive and challenging public health issue. Prevalence estimates vary widely, both globally (2-54%) and in Canada (6.5-44%). Most estimates are derived from surveys, which are expensive and labour intensive. Health administrative data is a potential easily-accessed, low-cost method to obtain epidemiological and cost estimates of chronic pain, but its validity as a source to ascertain cases of this complex and multi-faceted condition is unknown. The purpose of this study was to derive and validate an algorithm to identify cases of chronic pain using health administrative data.Methods: A reference standard was developed and applied to the electronic medical records data of a general population sample participating in the Canadian Primary Care Sentinel Surveillance Network. Preliminary chronic pain algorithms were then created and refined through health administrative data analysis of four populations with known chronic pain diagnoses. Classification performance of the chronic pain administrative data algorithms was compared to that of the reference standard, and statistical tests of selection accuracy (sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratio positive, likelihood ratio negative, diagnostic odds ratio, Kappa agreement, and area under the Receiver Operating Characteristic curve) were calculated. Results: The optimal algorithm to ascertain cases of chronic pain from health administrative data was a combination of one chronic pain clinic procedure code OR five physician claims with a pain-related diagnostic code in five years with more than 183 days separating at least two claims. The sensitivity was 0.703 (0.684-0.721 95% confidence interval), the specificity was 0.668 (0.657-0.679 95% confidence interval), and the positive predictive value was 0.408(0.398-0.418 95% confidence interval). The Chronic Pain Algorithm identified 37.6% of a Newfoundland and Labrador provincial cohort. Conclusions: Health administrative data is a valid source for information on chronic pain in Canada. The optimal chronic pain algorithm can be used to determine epidemiology and health care utilization statistics on people seeking physician care for chronic pain, and to evaluate cost effectiveness of any change to policy or health service delivery.