bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of a diesel engine calibration for operating with a residual glycerol-derived biofuel
Authors: Lapuerta Magín , Ramos Ángel , Rubio Sara , Estévez Carles
Published: December 2019

The new European directive for the promotion of renewable energy mandates an increase in the share of advanced and waste-based biofuels in the transport sector. In this study, an advanced glycerol-derived biofuel was used as a component of a ternary blend, denoted as o·bio®. This blend included 27.4 %v/v of fatty acid glycerol formal ester, 69.6 %v/v of fatty acid methyl ester and 3 %v/v of acetals obtained as a by-product of the fatty acid glycerol formal ester production process (which were proved to improve cold-flow properties). Finally, o·bio® was blended with diesel fuel at a content of 20 %v/v. Two operating conditions based on usual driving modes were selected, where the engine calibration could be re-optimized after the change of fuel, corresponding to vehicle velocities of 50 and 70 km/h. Since the main effect of the blend used is to reduce particulate matter emissions, exhaust gas recirculation was increased and injection was delayed, so that the initial benefits in particulate matter emissions could be re-distributed into benefits in both particulate matter and nitrogen oxides (NOx) emissions. From a combined analysis of the particulate matter–NOx trade-off and trying to limit the negative effect of delaying injection on fuel consumption, the final proposal was to set an additional 6% exhaust gas recirculation at 50 km/h and an additional 3% exhaust gas recirculation at 70 km/h, while delaying injection 2 °CA after top dead center at both vehicle operating conditions with respect to the original calibration. The use of the blend along with the optimization of the engine calibration is expected to reduce particulate matter and NOx emissions by around 50% with a vehicle speed condition of 50 km/h and to reduce particulate matter and NOx emissions by around 30% and 40% at 70 km/h with respect to diesel fuel emissions.
‘This isn’t a movie . . . it’s a tourism ad for Australia’: The Dundee campaign and the semiotics of audiovisual tourism promotion
Authors: Leotta Alfio
Published: December 2019

This article proposes a theorization of audiovisual media promotion as a distinct media field. Despite their omnipresence, very few scholars have examined the aesthetic, thematic and institutional characteristics of tourism films, commercials and promotional videos. The field of tourism audiovisual promotion poses a significant conceptual challenge as it consists of a vast array of diverse media texts and aesthetic forms. Such vast aesthetic differences, along with the different promotional potential associated with each of these forms, complicate any straightforward definition of this media field. This article will use the analysis of a recent case study – the Dundee campaign launched by Tourism Australia in 2018 – to develop a theorization of audiovisual tourism promotion. In particular, it will argue that the meaning and function of tourism audiovisual promotional texts are determined by a ‘discursive framework’ which, in turn, is informed by converging textual and contextual factors.
Staying in the middle or avoiding extremes? A test of the effect of rating scale length in advertising research with Chinese consumers
Authors: Li Cong , Yoon Gunwoo , Petit John
Published: December 2019

Given the rapid growth of many Asian economies in recent years, Asian advertising research is attracting increasing attention. However, systematic examinations of how to move this body of research forward from both theoretical and methodological perspectives are lacking. This study discusses a method-related issue in Asian advertising research, specifically focusing on the rating scale length used in measuring consumer attitude and behavioral intention. The experiment examines whether using different rating scale lengths (i.e., 1–3, 1–5, 1–7, and 1–9) will produce inconsistent research results due to the influence of Confucianism on East Asian consumers’ response style. Based on the experimental findings, a theoretical discussion of how to consider the cultural impact on measurement in an East Asian advertising context is provided.
Comparing STEM Majors by Examining the Relationship Between Student Perceptions of Campus Climate and Classroom Engagement
Authors: Victorino Christine , Denson Nida , Ing Marsha , Nylund-Gibson Karen
Published: December 2019

This study built upon research examining the effects of diversity in STEM (science, technology, engineering, and mathematics) fields and higher education by investigating the relationship between student perceptions of campus diversity and classroom engagement for first- and second-year Latinx and White students at two structurally diverse institutions. Findings suggested that perceptions of campus climate have a positive and significant relationship with classroom engagement—which is an important indicator of overall grade point average.
Safely traversing venous sinus stenosis: The "Cobra" technique
Authors: Schwarz Justin , Santillan Alejandro , Patsalides Athos
Published: December 2019

Venous sinus stenting is an accepted and minimally invasive treatment for idiopathic intracranial hypertension associated with significant venous sinus stenosis. There is inherent difficulty in navigating past the region of venous stenosis in order to safely deliver and deploy a stent. We have developed the “Cobra” technique, which allows for the safe and efficient navigation past regions of high-grade venous sinus stenosis.
Designing and evaluating dose-escalation studies made easy: The MoDEsT web app
Authors: Pallmann Philip , Wan Fang , Mander Adrian P , Wheeler Graham M , Yap Christina , Clive Sally , Hampson Lisa V , Jaki Thomas
Published: December 2019

Background/aims:

Dose-escalation studies are essential in the early stages of developing novel treatments, when the aim is to find a safe dose for administration in humans. Despite their great importance, many dose-escalation studies use study designs based on heuristic algorithms with well-documented drawbacks. Bayesian decision procedures provide a design alternative that is conceptually simple and methodologically sound, but very rarely used in practice, at least in part due to their perceived statistical complexity. There are currently very few easily accessible software implementations that would facilitate their application.

Methods:

We have created MoDEsT, a free and easy-to-use web application for designing and conducting single-agent dose-escalation studies with a binary toxicity endpoint, where the objective is to estimate the maximum tolerated dose. MoDEsT uses a well-established Bayesian decision procedure based on logistic regression. The software has a user-friendly point-and-click interface, makes changes visible in real time, and automatically generates a range of graphs, tables, and reports. It is aimed at clinicians as well as statisticians with limited expertise in model-based dose-escalation designs, and does not require any statistical programming skills to evaluate the operating characteristics of, or implement, the Bayesian dose-escalation design.

Results:

MoDEsT comes in two parts: a ‘Design’ module to explore design options and simulate their operating characteristics, and a ‘Conduct’ module to guide the dose-finding process throughout the study. We illustrate the practical use of both modules with data from a real phase I study in terminal cancer.

Conclusion:

Enabling both methodologists and clinicians to understand and apply model-based study designs with ease is a key factor towards their routine use in early-phase studies. We hope that MoDEsT will enable incorporation of Bayesian decision procedures for dose escalation at the earliest stage of clinical trial design, thus increasing their use in early-phase trials.
Revolting families: The Catalan ‘opt out’ movement and practices of resistance against Standard Assessment Test (SAT). Some exploratory research
Authors: Collet-Sabé Jordi , Ball Stephen J
Published: December 2019

Neoliberal policy technologies are spreading across the globe. Most go unrecognised and unopposed, but in some cases, they have provoked reactions and movements that reject or resist them. In this article we focus on one such movement of resistance, consisting of a network of families (the ‘opt out’ movement) that is boycotting the Standard Assessment Tests of primary education in Catalonia. We draw on exploratory research based on in-depth interviews with six of these families, as well as a review of articles, websites and documents produced by or about the movement. The participation of these families is examined in the light of Foucault’s notion of resistance in two different respects: resistance as a ‘tactical reversal’ and refusal as an ‘aesthetics of existence’. We begin with an outline of the global ideological context in which the Standard Assessment Tests are set, and then examine the background to the opt out movement’s resistance to the Standard Assessment Tests in Catalonia. This is followed by a Foucauldian analysis of this resistance, and then a description of the methodology used and the families interviewed. We make no significant empirical claims in the paper but rather seek to theorise certain paradoxes and tensions in relation to opting out and end with some remarks on the significance of the movement.
The Utility of Computed Tomography and Intrathecal Fluorescein in the Management of Cerebrospinal Fluid Leak
Authors: Flynn John P. , Pavelonis Anna , Ledbetter Luke , Bhalla Vidur , Alvi Sameer A. , Chiu Alexander G. , Villwock Jennifer
Published: December 2019

Background

Intrathecal fluorescein (IF) has become a common tool for localization of cerebrospinal fluid (CSF) leak, but despite frequent use, IF lacks Food and Drug Administration approval. The diagnostic ability of high-resolution computed tomography (HRCT) has increased over several decades. Subspecialized rhinology training within otolaryngology has, similarly, allowed for dedicated skull base surgeons to become more adept at CSF leak localization.

Objectives

To evaluate the utility of HRCT and IF in CSF leak localization. To identify certain patient populations in which IF has added utility. To analyze the ability of fellowship-trained neuroradiologist and rhinologist to localize CSF leak sites.

Methods

Data were collected from a single, tertiary care academic institution. Patients admitted for CSF leak between 2003 and 2016 were included. Diagnostic yield of preoperative imaging and IF for identification of leak site was analyzed. Fellowship-trained neuroradiologist and rhinologist performed retrospective review of CT imaging and identified CSF leak sites.

Results

One hundred and two patients underwent CSF leak repair. Skull base defects were preoperatively localized to exact sinus on imaging report in 67% of patients. Preoperative imaging stratified by CT slice thickness of 0.625 mm identified leak site in 88.9% of cases. Blinded retrospective review by a neuroradiologist and rhinologist was able to localize the CSF leak to the correct or adjacent sinus in >80% of cases. IF was useful for intraoperative localization in 73% of cases. When preoperative imaging failed at leak site localization, IF was able to correctly identify leak site in 75% of cases.

Conclusions

The diagnostic yield of IF and CT imaging was equivalent, with each modality localizing leak site approximately two-thirds of the time. CT imaging with 0.625 mm slice thickness proved more efficacious in identification of skull base defects. IF demonstrated increased utility in instances where preoperative imaging has failed at leak site identification.
MRI depiction of fetal brain abnormalities
Authors: Pfeifer Cory M , Willard Scott D , Cornejo Patricia
Published: December 2019

Intracranial abnormalities are commonly suspected findings on antenatal ultrasound that require evaluation by magnetic resonance imaging. This review depicts multiple abnormalities imaged as a means to guide clinicians in proper diagnosis.
A Set of Time-and-Frequency-Localized Short-Duration Speech-Like Stimuli for Assessing Hearing-Aid Performance via Cortical Auditory-Evoked Potentials
Authors: Stone Michael A. , Visram Anisa , Harte James M. , Munro Kevin J.
Published: December 2019

Short-duration speech-like stimuli, for example, excised from running speech, can be used in the clinical setting to assess the integrity of the human auditory pathway at the level of the cortex. Modeling of the cochlear response to these stimuli demonstrated an imprecision in the location of the spectrotemporal energy, giving rise to uncertainty as to what and when of a stimulus caused any evoked electrophysiological response. This article reports the development and assessment of four short-duration, limited-bandwidth stimuli centered at low, mid, mid-high, and high frequencies, suitable for free-field delivery and, in addition, reproduction via hearing aids. The durations were determined by the British Society of Audiology recommended procedure for measuring Cortical Auditory-Evoked Potentials. The levels and bandwidths were chosen via a computational model to produce uniform cochlear excitation over a width exceeding that likely in a worst-case hearing-impaired listener. These parameters produce robustness against errors in insertion gains, and variation in frequency responses, due to transducer imperfections, room modes, and age-related variation in meatal resonances. The parameter choice predicts large spectral separation between adjacent stimuli on the cochlea. Analysis of the signals processed by examples of recent digital hearing aids mostly show similar levels of gain applied to each stimulus, independent of whether the stimulus was presented in isolation, bursts, continuous, or embedded in continuous speech. These stimuli seem to be suitable for measuring hearing-aided Cortical Auditory-Evoked Potentials and have the potential to be of benefit in the clinical setting.
“We Really Help, Taking Care of Each Other”: Older Homeless Adults as Caregivers
Authors: Rosenwohl-Mack Sarah , Kushel Margot , Ramsey Claire , Handley Margaret , Knight Kelly R.
Published: December 2019

Objectives:

Many older homeless adults maintain contact with family. We conducted a qualitative study examining the role of family caregiving for older homeless adults.

Method:

We conducted semi-structured qualitative interviews with a sample of 46 homeless participants who reported spending at least one night with a housed family member in the prior 6 months.

Results:

A total of 13 of 46 older adult participants provided caregiving. Themes included (a) the death of the care recipient led to the participant’s homelessness; (b) feeling a duty to act as caregivers; (c) providing care in exchange for housing; (d) caregivers’ ability to stay was tenuous; (e) providing care conflicted with the caregiver’s needs; and (f) resentment when family was ungrateful.

Discussion:

In a sample of older homeless adults in contact with family, many provided caregiving for housed family. For some, caregiving precipitated homelessness; for others, caregiving provided temporary respite from homelessness, and for others, caregiving continued during homelessness.
Connexin-43 is a promising target for pulmonary hypertension due to hypoxaemic lung disease
Authors: Bouvard Claire , Genet Nafiisha , Phan Carole , Rode Baptiste , Thuillet Raphaël , Tu Ly , Robillard Paul , Campagnac Marilyne , Soleti Raffaella , Dumas De La Roque Eric , Delcambre Frédéric , Cronier Laurent , Parpaite Thibaud , Maurat Elise , Berger Patrick , Savineau Jean-Pierre , Marthan Roger , Guignabert Christophe , Freund-Michel Véronique , Guibert Christelle
Published: December 2019

The mechanisms underlying pulmonary hypertension (PH) are complex and multifactorial, and involve different cell types that are interconnected through gap junctional channels. Although connexin (Cx)-43 is the most abundant gap junction protein in the heart and lungs, and critically governs intercellular signalling communication, its contribution to PH remains unknown. The focus of the present study is thus to evaluate Cx43 as a potential new target in PH.

Expressions of Cx37, Cx40 and Cx43 were studied in lung specimens from patients with idiopathic pulmonary arterial hypertension (IPAH) or PH associated with chronic hypoxaemic lung diseases (chronic hypoxia-induced pulmonary hypertension (CH-PH)). Heterozygous Cx43 knockdown CD1 (Cx43+/−) and wild-type littermate (Cx43+/+) mice at 12 weeks of age were randomly divided into two groups, one of which was maintained in room air and the other exposed to hypoxia (10% oxygen) for 3 weeks. We evaluated pulmonary haemodynamics, remodelling processes in cardiac tissues and pulmonary arteries (PAs), lung inflammation and PA vasoreactivity.

Cx43 levels were increased in PAs from CH-PH patients and decreased in PAs from IPAH patients; however, no difference in Cx37 or Cx40 levels was noted. Upon hypoxia treatment, the Cx43+/−mice were partially protected against CH-PH when compared to Cx43+/+mice, with reduced pulmonary arterial muscularisation and inflammatory infiltration. Interestingly, the adaptive changes in cardiac remodelling in Cx43+/−mice were not affected. PA contraction due to endothelin-1 (ET-1) was increased in Cx43+/−mice under normoxic and hypoxic conditions.

Taken together, these results indicate that targeting Cx43 may have beneficial therapeutic effects in PH without affecting compensatory cardiac hypertrophy.
The effect of HIV-associated tuberculosis, tuberculosis-IRIS and prednisone on lung function
Authors: Stek Cari , Allwood Brian , Du Bruyn Elsa , Buyze Jozefien , Schutz Charlotte , Thienemann Friedrich , Lombard Adele , Wilkinson Robert J. , Meintjes Graeme , Lynen Lutgarde
Published: December 2019

Residual pulmonary impairment is common after treatment for tuberculosis (TB). Lung function data in patients with HIV-associated TB are scarce, especially in the context of paradoxical TB-associated immune reconstitution inflammatory syndrome (TB-IRIS) and prophylactic prednisone. We aimed to determine the prevalence of lung function abnormalities in patients with HIV-associated TB and CD4 counts ≤100 cells·μL−1and assess the effect of prophylactic prednisone and the development of paradoxical TB-IRIS on pulmonary impairment.

We performed spirometry, 6-min walk test (6MWT) and chest radiography at baseline (week 0) and at weeks 4, 12 and 28 in participants of the PredART trial, which evaluated a 28-day course of prednisone to prevent TB-IRIS in patients with HIV-associated TB commencing antiretroviral therapy.

153 participants underwent spirometry and/or 6MWT at one or more time points. Abnormal spirometry measurements were present in 66% of participants at week 0 and 50% at week 28; low forced vital capacity was the commonest abnormality. Chest radiographs showed little or no abnormalities in the majority of participants. Prednisone use resulted in a 42 m greater 6-min walk distance and a 4.9% higher percentage of predicted forced expiratory volume in 1 s at week 4; these differences were no longer significantly different from week 12 onwards. TB-IRIS did not significantly impair lung function outcome.

Residual pulmonary impairment is common in HIV-associated TB. In patients with low CD4 counts, neither prophylactic prednisone as used in our study nor the development of TB-IRIS significantly affected week-28 pulmonary outcome.
The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases
Authors: Zhao Zhongming , Dai Yulin , Zhang Chi , Mathé Ewy , Wei Lai , Wang Kai
Published: December 2019

Between June 9–11, 2019, the International Conference on Intelligent Biology and Medicine (ICIBM 2019) was held in Columbus, Ohio, USA. The conference included 12 scientific sessions, five tutorials or workshops, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics in bioinformatics, medical informatics, systems biology and intelligent computing. Here, we describe 13 high quality research articles selected for publishing in BMC Bioinformatics.
Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge
Authors: Eicher Tara , Patt Andrew , Kautto Esko , Machiraju Raghu , Mathé Ewy , Zhang Yan
Published: December 2019

Background

Proteomic measurements, which closely reflect phenotypes, provide insights into gene expression regulations and mechanisms underlying altered phenotypes. Further, integration of data on proteome and transcriptome levels can validate gene signatures associated with a phenotype. However, proteomic data is not as abundant as genomic data, and it is thus beneficial to use genomic features to predict protein abundances when matching proteomic samples or measurements within samples are lacking.

Results

We evaluate and compare four data-driven models for prediction of proteomic data from mRNA measured in breast and ovarian cancers using the 2017 DREAM Proteogenomics Challenge data. Our results show that Bayesian network, random forests, LASSO, and fuzzy logic approaches can predict protein abundance levels with median ground truth-predicted correlation values between 0.2 and 0.5. However, the most accurately predicted proteins differ considerably between approaches.

Conclusions

In addition to benchmarking aforementioned machine learning approaches for predicting protein levels from transcript levels, we discuss challenges and potential solutions in state-of-the-art proteogenomic analyses.
A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships
Authors: Kim Suyeon , Thapa Ishwor , Zhang Ling , Ali Hesham
Published: December 2019

Background

Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to have significant impact on their host environment. For example, variants in gut microbiomes have been reported to be associated with several chronic conditions, such as inflammatory disease and irritable bowel syndrome. However, how microbial bacteria contribute to pathogenesis still remains unclear and major research questions in this domain remain unanswered.

Methods

We propose a split graph model to represent the composition and interactions of a given microbiome. We used metagenomes from Korean populations in this study. The dataset consists of three different types of samples, viz. mucosal tissue and stool from Crohn’s disease patients and stool from healthy individuals. We use the split graph model to analyze the impact of microbial compositions on various host phenotypes. Utilizing the graph model, we have developed a pipeline that integrates genomic information and pathway analysis to characterize both critical informative components of inter-bacterial correlations and associations between bacterial taxa and various metabolic pathways.

Results

The obtained results highlight the importance of the microbial communities and their inter-relationships and show how these microbial structures are correlated with Crohn’s disease. We show that there are significant positive associations between detected taxonomic biomarkers as well as multiple functional modules in the split graph of mucosal tissue samples from CD patients. Bacteria Moraxellaceae and Pseudomonadaceae were detected as taxonomic biomarkers in CD groups. Higher abundance of these bacteria have been reported in previous study and several metabolic pathways associated with these bacteria were characterized in CD samples.

Conclusions

The proposed pipeline provides a new way to approach the analysis of complex microbiomes. The results obtained from this study show great potential in unraveling mechansims in complex biological systems to understand how various components in such complex environments are associated with critical biological functions.
Identification of lung cancer gene markers through kernel maximum mean discrepancy and information entropy
Authors: Zhao Zhixun , Peng Hui , Zhang Xiaocai , Zheng Yi , Chen Fang , Fang Liang , Li Jinyan
Published: December 2019

Background

The early diagnosis of lung cancer has been a critical problem in clinical practice for a long time and identifying differentially expressed gene as disease marker is a promising solution. However, the most existing gene differential expression analysis (DEA) methods have two main drawbacks: First, these methods are based on fixed statistical hypotheses and not always effective; Second, these methods can not identify a certain expression level boundary when there is no obvious expression level gap between control and experiment groups.

Methods

This paper proposed a novel approach to identify marker genes and gene expression level boundary for lung cancer. By calculating a kernel maximum mean discrepancy, our method can evaluate the expression differences between normal, normal adjacent to tumor (NAT) and tumor samples. For the potential marker genes, the expression level boundaries among different groups are defined with the information entropy method.

Results

Compared with two conventional methods t-test and fold change, the top average ranked genes selected by our method can achieve better performance under all metrics in the 10-fold cross-validation. Then GO and KEGG enrichment analysis are conducted to explore the biological function of the top 100 ranked genes. At last, we choose the top 10 average ranked genes as lung cancer markers and their expression boundaries are calculated and reported.

Conclusion

The proposed approach is effective to identify gene markers for lung cancer diagnosis. It is not only more accurate than conventional DEA methods but also provides a reliable method to identify the gene expression level boundaries.
Finding prognostic gene pairs for cancer from patient-specific gene networks
Authors: Park Byungkyu , Lee Wook , Park Inhee , Han Kyungsook
Published: December 2019

Background

Molecular characterization of individual cancer patients is important because cancer is a complex and heterogeneous disease with many possible genetic and environmental causes. Many studies have been conducted to identify diagnostic or prognostic gene signatures for cancer from gene expression profiles. However, some gene signatures may fail to serve as diagnostic or prognostic biomarkers and gene signatures may not be found in gene expression profiles.

Methods

In this study, we developed a general method for constructing patient-specific gene correlation networks and for identifying prognostic gene pairs from the networks. A patient-specific gene correlation network was constructed by comparing a reference gene correlation network from normal samples to a network perturbed by a single patient sample. The main difference of our method from previous ones includes (1) it is focused on finding prognostic gene pairs rather than prognostic genes and (2) it can identify prognostic gene pairs from gene expression profiles even when no significant prognostic genes exist.

Results

Evaluation of our method with extensive data sets of three cancer types (breast invasive carcinoma, colon adenocarcinoma, and lung adenocarcinoma) showed that our approach is general and that gene pairs can serve as more reliable prognostic signatures for cancer than genes.

Conclusions

Our study revealed that prognosis of individual cancer patients is associated with the existence of prognostic gene pairs in the patient-specific network and the size of a subnetwork of the prognostic gene pairs in the patient-specific network. Although preliminary, our approach will be useful for finding gene pairs to predict survival time of patients and to tailor treatments to individual characteristics. The program for dynamically constructing patient-specific gene networks and for finding prognostic gene pairs is available at http://bclab.inha.ac.kr/pancancer.
Differential alternative splicing regulation among hepatocellular carcinoma with different risk factors
Authors: Jin Young-Joo , Byun Seyoun , Han Seonggyun , Chamberlin John , Kim Dongwook , Kim Min Jung , Lee Younghee
Published: December 2019

Background

Hepatitis B virus (HBV), hepatitis C virus (HCV), and alcohol consumption are predominant causes of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying how differently these causes are implicated in HCC development are not fully understood. Therefore, we investigated differential alternative splicing (AS) regulation among HCC patients with these risk factors.

Methods

We conducted a genome-wide survey of AS events associated with HCCs among HBV (n = 95), HCV (n = 47), or alcohol (n = 76) using RNA-sequencing data obtained from The Cancer Genome Atlas.

Results

In three group comparisons of HBV vs. HCV, HBV vs. alcohol, and HCV vs. alcohol for RNA seq (ΔPSI> 0.05, FDR < 0.05), 133, 93, and 29 differential AS events (143 genes) were identified, respectively. Of 143 AS genes, eight and one gene were alternatively spliced specific to HBV and HCV, respectively. Through functional analysis over the canonical pathways and gene ontologies, we identified significantly enriched pathways in 143 AS genes including immune system, mRNA splicing-major pathway, and nonsense-mediated decay, which may be important to carcinogenesis in HCC risk factors. Among eight genes with HBV-specific splicing events, HLA-A, HLA-C, and IP6K2 exhibited more differential expression of AS events (ΔPSI> 0.1). Intron retention of HLA-A was observed more frequently in HBV-associated HCC than HCV- or alcohol-associated HCC, and intron retention of HLA-C showed vice versa. Exon 3 (based on ENST00000432678) of IP6K2 was less skipped in HBV-associated in HCC compared to HCV- or alcohol-associated HCC.

Conclusion

AS may play an important role in regulating transcription differences implicated in HBV-, HCV-, and alcohol-related HCC development.
Altered HDL particle in sickle cell disease: decreased cholesterol content is associated with hemolysis, whereas decreased Apolipoprotein A1 is linked to inflammation
Authors: Yalcinkaya Ahmet , Unal Selma , Oztas Yesim
Published: December 2019

Background

Hypocholesterolemia is the most frequently encountered lipid abnormality in sickle cell disease (SCD). We enrolled pediatric patients to determine the relationships between lipid profile and parameters of hemolysis, oxidative stress and chronic inflammation in SCD.

Methods

The study involved 35 pediatric SCD patients and 19 healthy controls. Patients were crisis-free and had not received transfusions for the last 3 months. Total cholesterol, triglyceride, HDL-C, LDL-C, VLDL-C, apolipoprotein A1, apolipoprotein B, LCAT, LDH, bilirubin, haptoglobin, iron, ferritin, hemin, serum amyloid A (SAA), myeloperoxidase (MPO), uric acid, ALT and GGT levels were evaluated in patients’ blood.

Results

Patients had hypocholesterolemia depicted by lower levels of total cholesterol, HDL-C, LDL-C, as well as Apolipoprotein A1 and Apolipoprotein B compared to controls. The chronic hemolysis of SCD was evident in patients by higher LDH and bilirubin and almost undetectable haptoglobin levels. Hemin levels (as a measure of oxidized heme) were significantly increased in patients with SCD. Inflammation markers, SAA and MPO, were significantly increased in the patients as well. There were negative correlations between HDL-C and LDH, and Apo A1 and SAA. Hemin was positively correlated to MPO.

Conclusion

Hemolysis was associated with decreased HDL –C, and Inflammation was linked to decreased apolipoprotein A1 levels in our SCD patients. Therefore, we suggest that the HDL particle is altered during the course of the disease. The altered HDL in SCD may become dysfunctional and result with a slowing down of the reverse cholesterol transport.
Cross-sectional imaging of acute gynaecologic disorders: CT and MRI findings with differential diagnosis—part II: uterine emergencies and pelvic inflammatory disease
Authors: Foti Pietro Valerio , Tonolini Massimo , Costanzo Valeria , Mammino Luca , Palmucci Stefano , Cianci Antonio , Ettorre Giovanni Carlo , Basile Antonio
Published: December 2019

Due to the growing use of cross-sectional imaging in emergency departments, acute gynaecologic disorders are increasingly diagnosed on urgent multidetector computed tomography (CT) studies, often requested under alternative presumptive diagnoses in reproductive-age women. If clinical conditions and state-of-the-art scanner availability permit, magnetic resonance imaging (MRI) is superior to CT due to its more in-depth characterisationof abnormal or inconclusive gynaecological findings, owing to excellent soft-tissue contrast, intrinsic multiplanar capabilities and lack of ionising radiation.

This pictorial review aims to provide radiologists with a thorough familiarity with gynaecologic emergencies by illustrating their CT and MRI appearances, in order to provide a timely and correct imaging diagnosis. Specifically, this second instalment reviews with examples and emphasis on differential diagnosis the main non-pregnancy-related uterine emergencies (including endometrial polyps, degenerated leiomyomas and uterine inversion) and the spectrum of pelvic inflammatory disease.
Gender, affect, and math: a cross-national meta-analysis of Trends in International Mathematics and Science Study 2015 outcomes
Authors: Ghasemi Ehsan , Burley Hansel
Published: December 2019

Understanding why women are consistently underrepresented in STEM fields has been a constant puzzle, with a consistent feature of the puzzle being performance in math. This study uses data from TIMSS exams to investigate cross-national gender differences in math-related affect, more precisely liking mathematics, confidence in mathematics, and valuing mathematics. We compared fourth and eighth graders to track any differences in these gender-related affective characteristics. Our findings suggest that despite the variability and some changes to the magnitude and direction of gender differences in math affect, boys and girls are similar. We also found that cross-national sociocultural, political, and educational equality of adults does not necessarily predict positive affect for both genders. In fact, the researchers found that some countries with a smaller adult gender gaps have students with higher gender differences in mathematics-relevant affect.
The importance of simulation education for the management of traumatic cardiac injuries: a case series
Authors: Nagata Takashi , Akahoshi Tomohiko , Sugino Michiko , Ishii Wataru , Iizuka Ryoji , Shinjo Takafumi , Izawa Yoshimitsu , Hata Michiaki , Lefor Alan Kawarai
Published: December 2019

Background

The management of cardiac trauma requires rapid intervention in the emergency room, facilitated by a surgeon with prior experience to have good outcomes. Many surgeons have little experience in the requisite procedures. We report here 4 patients who suffered cardiac trauma, and all 4 patients survived with good neurologic outcomes.

Case presentations

Patient 1 suffered blunt cardiac trauma from a motor vehicle accident and presented in shock. Cardiac tamponade was diagnosed and a cardiac rupture repaired with staples through a median sternotomy after rapid transport to the operating room. Patient 2 suffered blunt cardiac trauma and presented in shock with cardiac tamponade. Operating room median sternotomy allowed extraction of pericardial clot with recovery of physiologic stability. Patient 3 presented with self-inflicted stab wounds to the chest and was unstable. She was brought to the operating room and thoracotomy allowed identification of a left ventricle wound which was repaired with a suture. Patient 4 presented in cardiac arrest with multiple self-inflicted stab wounds to the chest. Emergency room thoracotomy allowed repair of a right ventricle laceration with recovery of vital signs.

Conclusions

The management of all 4 patients was according to the principles taught in the ATOM course. Three of the 4 surgeons had no prior experience with management of cardiac trauma and credited the good outcomes to taking the ATOM course. These are uncommon injuries and formal training in their management is beneficial to patients.
Plastic habits – an overview for the collection ‘Plastics and Sustainable Earth’
Authors: Paterson Harriet
Published: December 2019

Over the last 60 years we have modified our behavior to make use of new synthetic material produced from fossil fuels. We have incorporated it into almost every facet of our lives making us more comfortable. The production of plastic material has grown at an alarming rate and huge volumes of non-biodegradable waste now litters the surface of the planet creating a major global problem. To reverse this problem, we need to consider both obvious and novel behavior change and product development. While we are beginning to remove plastic items from the environment, we do have the responsibility to reduce the amount of new plastic material entering the waste stream. In order to achieve this, it is necessary to explore all options relating to the way we design, produce and consume products and determine what acceptable waste is. This article collection is concerned with addressing the problem by exploring a variety of topics as diverse as the history of plastic material use, behavior change, and the development of new, environmentally friendly products and their impact on the environment. The following essay outlines a few ideas that do require further scientific exploration so we can begin the process of weaning society off its current dependence on plastic products.
S100A14 protein as diagnostic and prognostic marker in hepatocellular carcinoma
Authors: Mohamed Basma Fathy , Serag Waleed Mohamed , Abdelal Reda Mahamoud , Elsergany Heba Fadl
Published: December 2019

Background

Protein S100A14 has recently been implicated in the progress of several types of cancers. This study aimed to investigate the clinical significance of S100A14 in the diagnosis of hepatocellular carcinoma (HCC).

Results

S100A14 was significantly elevated in the HCC group. A cut-off value for serum S100A14 between the HCC group and cirrhosis group is > 0.47 with a sensitivity of 100% and specificity of 88.57%. S100A14 level was a significant diagnostic factor for HCC and a good reference for HCC progression.

Conclusion

These results suggest that S100A14 is a good diagnostic marker for HCC.
Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation
Authors: Raab Jesse R. , Tulasi Deepthi Y. , Wager Kortney E. , Morowitz Jeremy M. , Magness Scott T. , Gracz Adam D.
Published: December 2019

Intestinal stem cell (ISC) plasticity is thought to be regulated by broadly permissive chromatin shared between ISCs and their progeny. Here, we have used a Sox9EGFP reporter to examine chromatin across ISC differentiation. We find that open chromatin regions (OCRs) can be defined as broadly permissive or dynamic in a locus-specific manner, with dynamic OCRs found primarily in loci consistent with distal enhancers. By integrating gene expression with chromatin accessibility at transcription factor (TF) motifs in the context of Sox9EGFP populations, we classify broadly permissive and dynamic chromatin relative to TF usage. These analyses identify known and potential regulators of ISC differentiation via association with dynamic changes in chromatin. Consistent with computational predictions, Id3-null mice exhibit increased numbers of cells expressing the ISC-specific biomarker OLFM4. Finally, we examine the relationship between gene expression and 5-hydroxymethylcytosine (5hmC) in Sox9EGFP populations, which reveals 5hmC enrichment in absorptive lineage-specific genes. Our data demonstrate that intestinal chromatin dynamics can be quantitatively defined in a locus-specific manner, identify novel potential regulators of ISC differentiation and provide a chromatin roadmap for further dissecting cis regulation of cell fate in the intestine.
Evidence for a rapid cold hardening response in cultured Drosophila S2 cells
Authors: Nadeau Emily A. W. , Teets Nicholas M.
Published: December 2019

The ability to quickly respond to changes in environmental temperature is critical for organisms living in thermally variable environments. To cope with sudden drops in temperature, insects and other ectotherms are capable of rapid cold hardening (RCH), in which mild chilling significantly enhances cold tolerance within minutes. While the ecological significance of RCH is well-established, the mechanisms underlying RCH are still poorly understood. Previous work has demonstrated that RCH is regulated at the cellular level by post-translational signaling mechanisms, and here we tested the hypothesis that cultured cells are capable of RCH. A 2 h cold shock at -8°C significantly reduced the metabolic viability of Drosophila S2 cells, but pre-treatment with RCH at 4°C for 2 h prevented this decrease in viability. Thus, S2 cells are capable of RCH in a similar manner as whole insects and provide a new system for investigating the cell biology of RCH.
Proton beam therapy: perspectives on the National Health Service England clinical service and research programme
Authors: Burnet Neil G , Mackay Ranald I , Smith Ed , Chadwick Amy L , Whitfield Gillian A , Thomson David J , Lowe Matthew , Kirkby Norman F , Crellin Adrian M , Kirkby Karen J
Published: December 2019

The UK has an important role in the evaluation of proton beam therapy (PBT) and takes its place on the world stage with the opening of the first National Health Service (NHS) PBT centre in Manchester in 2018, and the second in London coming in 2020. Systematic evaluation of the role of PBT is a key objective. By September 2019, 108 patients had started treatment, 60 paediatric, 19 teenagers and young adults and 29 adults. Obtaining robust outcome data is vital, if we are to understand the strengths and weaknesses of current treatment approaches. This is important in demonstrating when PBT will provide an advantage and when it will not, and in quantifying the magnitude of benefit.

The UK also has an important part to play in translational PBT research, and building a research capability has always been the vision. We are perfectly placed to perform translational pre-clinical biological and physical experiments in the dedicated research room in Manchester. The nature of DNA damage from proton irradiation is considerably different from X-rays and this needs to be more fully explored. A better understanding is needed of the relative biological effectiveness (RBE) of protons, especially at the end of the Bragg peak, and of the effects on tumour and normal tissue of PBT combined with conventional chemotherapy, targeted drugs and immunomodulatory agents. These experiments can be enhanced by deterministic mathematical models of the molecular and cellular processes of DNA damage response. The fashion of ultra-high dose rate FLASH irradiation also needs to be explored.
Recent advances in the treatment of chronic heart failure
Authors: Buckley Leo F , Shah Amil M
Published: December 2019

After more than a decade of relatively modest advancements, heart failure therapeutic development has accelerated, with the PARADIGM-HF trial and the SHIFT trial demonstrated significant reductions in cardiovascular death and heart failure hospitalization for sacubitril-valsartan and in heart failure hospitalization alone for ivabradine. Several heart failure therapies have since received or stand on the verge of market approval and promise substantive advances in the treatment of chronic heart failure. Some of these improve clinical outcomes, whereas others improve functional or patient-reported outcomes. In light of these rapid advances in the care of adults living with chronic heart failure, in this review we seek to update the general practitioner on novel heart failure therapies. Specifically, we will review recent data on the implementation of sacubitril-valsartan, treatment of functional mitral regurgitation, sodium-glucose co-transporter-2 (SGLT-2) inhibitor therapy, agents for transthyretin amyloid cardiomyopathy, treatment of iron deficiency in heart failure, and the use of biomarkers or remote hemodynamic monitoring to guide heart failure therapy.
A systematic review and meta-analysis of baseline risk factors for the development of postoperative ileus in patients undergoing gastrointestinal surgery
Authors: Lee MJ , Vaughan-Shaw P , Vimalachandran D ,   on behalf of ACPGBI GI Recovery Group
Published: December 2019

Introduction

Postoperative ileus occurs frequently following abdominal surgery. Identification of groups at high risk of developing ileus before surgery may allow targeted interventions. This review aimed to identify baseline risk factors for ileus.

Methods

A systematic review was conducted with reference to PRISMA and MOOSE guidelines. It was registered on PROSPERO (CRD42017068697). Searches of MEDLINE, EMBASE and CENTRAL were undertaken. Studies reporting baseline risk factors for the development of postoperative ileus based on cohort or trial data and published in English were eligible for inclusion. Dual screening of abstracts and full texts was undertaken. Independent dual extraction was performed. Bias assessment was undertaken using the quality in prognostic studies tool. Meta-analysis using a random effects model was undertaken where two or more studies assessed the same variable.

Findings

Searches identified 2,430 papers, of which 28 were included in qualitative analysis and 12 in quantitative analysis. Definitions and incidence of ileus varied between studies. No consistent significant effect was found for association between prior abdominal surgery, age, body mass index, medical comorbidities or smoking status. Male sex was associated with ileus on meta-analysis (odds ratio 1.12, 95% confidence interval 1.02–1.23), although this may reflect unmeasured factors. The literature shows inconsistent effects of baseline factors on the development of postoperative ileus. A large cohort study using consistent definitions of ileus and factors should be undertaken.
Malignant melanoma of the rectum presenting as cloacogenic polyp: a case report
Authors: Coyne JD , O’Byrne P
Published: December 2019

Mucosal malignant melanomas are uncommon. It is rare for a primary mucosal melanoma to occur in the anorectal region. Anorectal polypoid mucosal prolapse however, is a relatively common condition. We report a case of malignant melanoma presenting as mucosal prolapse and inducing changes similar to inflammatory cloacogenic polyp.