bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

AbstractDue 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

AbstractUnderstanding 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

Abstract
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

AbstractOver 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

Abstract
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

ABSTRACT
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.
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.
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.
Text Analysis on Punishment Clauses in Korean Law: Changes in the Number, Level, and Balance of Punishment Clauses Over 30 Years
Authors: Kim Jaeyoon 
Published: December 2019

Abstract
For this study, I completed a comprehensive review of punishment clauses in the Korean Legal Code from 1985 to 2016. Using a web crawler and text analysis, I gathered data on the laws and then identified the content of the penal sentence in each clause. By investigating the data, I was able to quantify and assess changes over time in: (1) the number of punishment clauses; (2) the severity of sentences; and (3) the balance between imprisonment and fines. In order to examine the causes of these changes, I separated the data into different sentence levels and sectors. I found that low-level punishment clauses had grown quickly, and some of the sectors responsible for the change included civil engineering and sex offenses. This comprehensive review of the penal sentences revealed issues of concern related to overcriminalization, overpenalization, and an imbalance of punishment level in the Korean Legal Code.
Drug interactions and creatinine levels are associated with QTc prolongation in intensive care units: a prospective, observational study
Authors: Hosseinpoor Zeinab , Farzanegan Behrooz , Seyyedi Seyyed Reza , Rajabi Mehdi , Baniasadi Shadi 
Published: December 2019

Abstract

Background
Prolongation of the QTc interval may lead to life threatening arrhythmias. QTc prolongation is common in intensive care unit (ICU) patients. The objectives of this study were to identify the role of drug-drug interactions (DDIs) and other predictors (age, sex, cardiovascular diseases, and electrolyte abnormalities) in life threatening QTc prolongation in patients admitted to medical (M), surgical (S) and emergency (E) ICUs.

Methods
This prospective, observational study included patients above the age of 18 years who were admitted to SICU, EICU, and MICU at a tertiary respiratory referral center. Electrocardiogram (ECG) monitoring was performed during the first 5 days of ICU admission. Risk factors and DDIs which were anticipated to be associated with the prolongation of the QTc interval were assessed for all patients.

Results
Two hundred patients were included in the study. QTc prolongation occurred in 10.7% of patients and the majority of patients presenting with QTc prolongation had creatinine levels above 1.3 mg/dL during their 5 days of ICU admission. Incidence of pharmacodynamic (PD) DDIs was significantly higher in patients with QTc prolongation vs. other patients. Creatinine levels above 1.3 mg/dL and PD DDIs were associated with QTc prolongation during 5 days of ICU admission.

Conclusions
High serum creatinine and PD DDIs can increase the risk of QTc prolongation in patients admitted to the ICU. QTc interval measurements should be performed prior to initiation or after starting any drug that is associated with QT prolongation, specifically in patients with the known risk factors.
Effects of NP Shapes on Non-Newtonian Bio-Nanofluid Flow in Suction/Blowing Process with Convective Condition: Sisko Model
Authors: Eid Mohamed R. 
Published: December 2019

Abstract
The present mathematical simulation deals with the study of heat transfer characteristics of the shape of gold nanoparticles (Au-NPs) on blood flow past an exponentially stretching sheet using Sisko nanofluid taking into account the Biot number effect. Influences of non-linear thermal radiation and suction/injection are considered. The one-phase model is used to describe the Sisko nanofluid flow. Similarity variables are performed to convert the non-linear PDEs into ordinary ones. These equations together with initial and boundary conditions are provided in a non-dimensional form and then resolved numerically utilizing the fourth–fifth-order Runge–Kutta–Fehlberg (RKF45) technique. The attitude of diverse flow quantities is investigated and examined via the study of parameters like the Au-NP volume fraction, the non-linear stretching parameter, and the Biot number. It is found that the Biot number improves the heat transfer rate markedly. In the blowing case, the blade-shaped Au-NPs show the highest heat transfer rate; in the suction case, the contrary is observed for spherical Au-NPs.
Quantum theory of surface-enhanced resonant Raman scattering (SERRS) of molecules in strongly coupled plasmon–exciton systems
Authors: Neuman Tomáš , Aizpurua Javier , Esteban Ruben 
Published: December 2019

Abstract
Localised surface plasmons can couple strongly with the electronic transitions of a molecule, inducing new hybridised states of light and matter, the plasmon–exciton polaritons. Furthermore, molecules support vibrational degrees of freedom that interact with the electronic levels, giving rise to inelastic resonant Raman scattering under coherent laser illumination. Here we show the influence of strong plasmon–exciton coupling on resonant Raman processes that populate the vibrational states of the molecule and that lead to the characteristic surface-enhanced Raman scattering spectra. We develop analytical expressions that give insight into these processes for the case of moderate illumination intensity, weak electron–vibration coupling and no dephasing. These expressions help us to elucidate the twofold role of plasmon–exciton polaritons to pump the system efficiently and to enhance the Raman emission. Our results show a close analogy with the optomechanical process described for off-resonant Raman scattering but with a difference in the resonant reservoir. We also use full numerical calculations to study the effects reaching beyond these approximations and discuss the interplay between the fluorescence background and the Raman lines. Our results allow for better understanding and exploitation of the strong coupling regime in vibrational pumping and in the surface-enhanced resonant Raman scattering signal.
Crystal structure of 4-dimethylamino-pyridin-1-ium uracil-1-acetate, C13H16N4O4
Authors: Zhang Xiao , Wang Lin , Liang Sen 
Published: December 2019

Abstract
C13H16N4O4, monoclinic, P21/n (no. 14), a = 4.7965(12) Å, b = 10.053(2) Å, c = 27.570(6) Å, β = 90.292(8)°, V = 1329.3(5) Å3, Z = 4, R
gt(F) = 0.0426, wR
ref(F
2) = 0.1115, T = 292(3) K.
The crystal structure of 3-carboxy-5-methylpyridin-1-ium-2-carboxylate, C8H7NO4
Authors: Zhu Yuanliang , Ma Jingwei , Li Shaofeng , Cai Bin 
Published: December 2019

Abstract
C8H7NO4, orthorhombic, Pccn (no. 56), a = 14.1361(10) Å, b = 15.8923(12) Å, c = 6.6410(6) Å, V = 1491.9(2) Å3, Z = 8, R
gt(F) = 0.0406, wR
ref(F
2) = 0.1155, T = 150(2) K.
Crystal structure of (2,7-dihexyl-9,9-dimethyl-9H-xanthene-4,5-diyl)bis(diphenylphosphane), C51H56OP2
Authors: Nyalungu Nonjabulo , Alapour Saba , Friedrich Holger B. , Bala Muhammad D. 
Published: December 2019

Abstract
C51H56OP2, monoclinic, C2/c (no. 15), a = 20.1788(4) Å, b = 13.0247(4) Å, c = 18.0172(5) Å, β = 119.874(2)°, V = 4106.1(2) Å3, Z = 4, R
gt(F) = 0.0363, wR
ref(F
2) = 0.0981, T = 173(2) K.