bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound measurement of brain tissue movement in humans: A systematic review
Authors: Ince Jonathan , Alharbi Meshal , Minhas Jatinder S , Chung Emma ML 
Published: December 2019

Introduction It has long been suggested that ultrasound could be used to measure brain tissue pulsations in humans, but potential clinical applications are relatively unexplored. The aim of this systematic review was to explore and synthesise available literature on ultrasound measurement of brain tissue motion in humans. Methods Our systematic review was designed to include predefined study selection criteria, quality evaluation, and a data extraction pro-forma, registered prospectively on PROSPERO (CRD42018114117). The systematic review was conducted by two independent reviewers. Results Ten studies were eligible for the evidence synthesis and qualitative evaluation. All eligible studies confirmed that brain tissue motion over the cardiac cycle could be measured using ultrasound; however, data acquisition, analysis, and outcomes varied. The majority of studies used tissue pulsatility imaging, with the right temporal window as the acquisition point. Currently available literature is largely exploratory, with measurements of brain tissue displacement over a narrow range of health conditions and ages. Explored health conditions include orthostatic hypotension and depression. Conclusion Further studies are needed to assess variability in brain tissue motion estimates across larger cohorts of healthy subjects and in patients with various medical conditions. This would be important for informing sample size estimates to ensure future studies are appropriately powered. Future research would also benefit from a consistent framework for data analysis and reporting, to facilitate comparative research and meta-analysis. Following standardisation and further healthy participant studies, future work should focus on assessing the clinical utility of brain tissue pulsation measurements in cerebrovascular disease states.
Long-Term Results of Hip Arthroplasty Using Extensive Porous-Coated Stem—A Minimum Follow-Up of 15 Years
Authors: Park Myung Hoon , Youn Yung Hun , Kang Joon Soon , Moon Kyoung Ho 
Published: December 2019

Introduction: We report the clinical and radiographic results of hip arthroplasty using extensive porous-coated stems over 15 years in Korea. Methods: This retrospective study included 210 patients (268 hips) who underwent total hip arthroplasties (232 hips) and bipolar hemiarthroplasties (36 hips) between June 1996 and December 2002 for avascular necrosis of the femoral head, hip fracture, or osteoarthritis, after excluding those who died or were lost to follow-up. One senior author (K.H.M.) evaluated Harris Hip Score (HHS); limping gait; and leg length discrepancy, and 3 independent reviewers assessed the radiographic findings, including the level of stress shielding, Dorr classification, subsidence and loosening of femoral stem, heterotopic ossification (Brooker classification), osteolysis of acetabulum, wear rate of the polyethylene liner, component loosening, and revision rate. Results: The mean follow-up duration was 16.9 years and average age at operation was 50.9 years. The HHS improved at the last follow-up. Stress shielding was grade 1 in 185 hips, grade 2 in 35 hips, grade 3 in 37 hips, and grade 4 in 11 hips. Femoral stem subsidence was <3 mm in 4 hips and >3 mm in 6 hips. Femoral stems with stable bony ingrowth were observed in 258 hips, fibrous stable femoral stems in 4 hips, and unstable femoral stems in 6 hips. Heterotopic ossification was class 1 in12 and class 2 in 4 hips. Revision surgery was performed for periprosthetic osteolysis of cup (45 hips), recurrent dislocation (1), unstable femoral stem (1), and infection (1). The Kaplan-Meier survivorship at the 15-year follow-up was 86.2%. The survivorship of femoral stem at 15 years was 99.3%, and if including impending revision due to unstable femoral stem was 97.1%. Disscussion: This study has all the limitations inherent with a retrospective design. However, a large number of patients in this cohort operated on by a single surgeon and a long-term follow-up are some of the potential advantages of the current study. Conclusions: At the 15-year follow-up, extensive porous-coated stem showed relatively good survivorship even in geriatric patients (Dorr type C).
Early Progressive Maxillary Changes with Nasoalveolar Molding: Randomized Controlled Clinical Trial
Authors: Saad M.S. , Fata M. , Farouk A. , Habib A.M.A. , Gad M. , Tayel M.B. , Marei M.K. 
Published: December 2019

Objectives: Quantitative assessment of 3-dimensional progressive changes of the maxillary geometry in unilateral cleft lip palate (UCLP) with and without nasoalveolar molding (NAM). Methods: The study was designed as a prospective 2-arm randomized controlled clinical trial conducted in parallel. Forty infants with nonsyndromic UCLP were randomly assigned into a NAM-treated group (n = 20) and non–NAM treated group (n = 20). A total of 120 laser-scanned maxillary casts were collected and blindly analyzed via a modified algorithm at T0 (initial visit; baseline), T1 (after 3 wk; first interval), and T2 (after 6 wk; second interval). The main outcome measures were the amount and rate of cleft gap changes, the midline position, and the transverse, sagittal, and vertical growth through intervals. Results: More than 50% of the cleft gap (56.42%; P < 0.001) was reduced in the first 3 wk of alveolar molding (AM). The end point of the AM was obtained in 6 wk (86.25%; P < 0.001); then, the kinks of the greater segment were noticed. The AM effect decreased as far as posterior; the anterior arch width reduced slightly (1.23%; P < 0.001), while the middle and posterior arches increased slightly (P > 0.999 and P = 0.288, respectively). The posterior arch width was the least changing and was considered a baseline, while the anterior was the pivot of the segment rotation. Both groups showed different patterns of segment rotation and sagittal growth. The non–NAM treated group showed a slight increase in cleft gap length, arch width, and midline position. Conclusion: Based on this study, it was concluded that the NAM treatment is effective in minimizing cleft severity and realigning maxillary segments without the deterioration of the transverse and vertical arch growth. Near follow-up visits are recommended to monitor the rapid gap reduction within the first 3 wk. Further trials are recommended to compare the outcomes regarding the sagittal growth to reference values ( ClinicalTrials.gov NCT03029195). Knowledge Transfer Statement: The results of this study will help clinicians understand nasoalveolar molding biomechanics that may improve the treatment outcomes for patients with unilateral cleft lip and palate. The trial data can be a valuable guide to the qualitative and quantitative predictive virtual molding in computer aided design–simulated nasoalveolar molding therapy. The modified algorithm can be used by researchers to quantify the rate, the sequence, and the direction of the maxillary segments movement in unilateral cleft lip and palate.
MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals
Authors: Feng Xikang , Wang Zishuai , Li Hechen , Li Shuai Cheng 
Published: December 2019

Abstract
Background
Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation.

Results
Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page.

Conclusion
MIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.
A unified STR profiling system across multiple species with whole genome sequencing data
Authors: Liu Yilin , Xu Jiao , Chen Miaoxia , Wang Changfa , Li Shuaicheng 
Published: December 2019

Abstract
Background
Short tandem repeats (STRs) serve as genetic markers in forensic scenes due to their high polymorphism in eukaryotic genomes. A variety of STRs profiling systems have been developed for species including human, dog, cat, cattle, etc. Maintaining these systems simultaneously can be costly. These mammals share many high similar regions along their genomes. With the availability of the massive amount of the whole genomics data of these species, it is possible to develop a unified STR profiling system. In this study, our objective is to propose and develop a unified set of STR loci that could be simultaneously applied to multiple species.

Result
To find a unified STR set, we collected the whole genome sequence data of the concerned species and mapped them to the human genome reference. Then we extracted the STR loci across the species. From these loci, we proposed an algorithm which selected a subset of loci by incorporating the optimized combined power of discrimination. Our results show that the unified set of loci have high combined power of discrimination, >1−10−9, for both individual species and the mixed population, as well as the random-match probability, <10−7 for all the involved species, indicating that the identified set of STR loci could be applied to multiple species.

Conclusions
We identified a set of STR loci which shared by multiple species. It implies that a unified STR profiling system is possible for these species under the forensic scenes. The system can be applied to the individual identification or paternal test of each of the ten common species which are Sus scrofa (pig), Bos taurus (cattle), Capra hircus (goat), Equus caballus (horse), Canis lupus familiaris (dog), Felis catus (cat), Ovis aries (sheep), Oryctolagus cuniculus (rabbit), and Bos grunniens (yak), and Homo sapiens (human). Our loci selection algorithm employed a greedy approach. The algorithm can generate the loci under different forensic parameters and for a specific combination of species.
A protocol to evaluate RNA sequencing normalization methods
Authors: Abrams Zachary B. , Johnson Travis S. , Huang Kun , Payne Philip R. O. , Coombes Kevin 
Published: December 2019

Abstract
Background
RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization.

Results
In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested.

Conclusion
Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization.
G6PD genetic variations in neonatal Hyperbilirubinemia in Indonesian Deutromalay population
Authors: Wisnumurti Dewi A. , Sribudiani Yunia , Porsch Robert M. , Maskoen Ani M. , Rahayuningsih Sri E. , Asni Eni K. , Sleutels Frank , van Ijcken Wilfred F. J. , Sukadi Abdurachman , Achmad Tri H. 
Published: December 2019

AbstractBackgroundNeonatal jaundice is a common finding in newborns in Asia, including Indonesia. In some cases, the serum total bilirubin levels exceeds the 95th percentile for hours of life (neonatal hyperbilirubinemia). Severe neonatal hyperbilirubinemia (NH) could lead to kernicterus and neonatal death.Glucose-6-Phosphage Dehydrogenase(G6PD)genetic variations and deficiency have been reported in several studies to be associated with NH. This study aimed to analyze theG6PDgenetic variations and its activity in neonates with and without hyperbilirubinemia in the Deutromalay Indonesian population.MethodsDeoxyribose Nucleic Acid (DNA) was isolated from peripheral blood of 116 and 115 healthy term neonates with and without hyperbilirubinemia. All infants underwent the following laboratory examinations: routine hematologic evaluation, Coombs test, G6PD activity measurement using the Randox kit method, and serum total bilirubin level. All exons of theG6PDgene were targeted for deep sequencing using MiSeq (Illumina). An association study ofG6PDpolymorphisms with NH was performed using PLINK.ResultsThe prevalence of G6PD deficiency in neonates with and without hyperbilirubinemia in Indonesian Deutromalay population were 1.72% (95% Confidence Interval (CI): 0.6–4.1%) and 1.74% (95% CI: 0.7–4.1%), respectively. The most commonG6PDpolymorphisms, i.e. rs1050757/c.* + 357A > G, rs2230037/c.1311C > T, and rs2071429/c.1365-13 T/IVS11, were identified. However, none of those polymorphisms and their haplotype were associated with NH (p > 0.05, Odds Ratio (OR) ~1.00). The prevalence ofG6PDmutations in neonates with and without hyperbilirubinemia were 6.8% (95% CI: 2.3–11.5%) and 6.9% (95% CI: 2.3–11.6%), respectively. The most frequently identifiedG6PDmutation was the Viangchan variant (p.V291 M), which was followed by the Canton (p.R459L) and Vanua Lava (p.L128P) variants. Two novel mutations were identified both in case (p.V369A, p.I167F) and control (p.L474=, p.I36T) groups.ConclusionThe prevalence of G6PD deficiency is low in neonates with or without hyperbilirubinemia in Deutromalay Indonesian population. The majority ofG6PDmutations identified among Indonesian Deutromalay population in this study are Viangchan, Canton and Vanua Lava variants.
Traumatic posterior Atlanto-axial dislocation: case report of an atypical C1-C2 dislocation with an anterior arch fracture of C1
Authors: Ghailane Soufiane , Alsofyani Mohammad A. , Pointillart Vincent , Bouloussa Houssam , Gille Olivier 
Published: December 2019

Abstract
Background
An atypical case of a traumatic posterior C1-C2 dislocation with an anterior arch fracture of C1 is reported. A novel conservative treatment for this rare lesion is described.

Case presentation
An eighty-nine-year-old male fell off a ladder at home and presented with an acute traumatic cervical spine trauma, which we believe involved a distraction mechanism. The patient was neurologically intact; he denied any weakness, numbness or paresthesia. A preoperative CT-scan demonstrated a posterior dislocation with an anterior arch of C1 fracture. Conservative management was elected. Reduction was achieved by closed manual reduction under general anesthesia. A postoperative CT demonstrated a complete reduction of the atlanto-axial dislocation.

Conclusion
Based on this case report and relevant literature, we present an unusual lesion of the upper cervical spine treated nonoperatively with closed manual reduction under general anesthesia. To date, there is no available consensus for the management of these lesions.
Antibody blockade of Dectin-2 suppresses house dust mite-induced Th2 cytokine production in dendritic cell- and monocyte-depleted peripheral blood mononuclear cell co-cultures from asthma patients
Authors: Chen Ming-Han , Huang Ming-Ting , Yu Wen-Kuang , Lee Shinn-Shing , Wang Jia-Horng , Cheng Ting-Jen R. , Bowman Michael R. , Hsieh Shie-Liang 
Published: December 2019

AbstractBackgroundDectin-2, which is a C-type lectin, interacts with the house dust mite (HDM)Dermatophagoides pteronyssinusallergen. This study aimed to investigate whether Dectin-2 blockade by antagonistic monoclonal antibodies (MoAbs) attenuates HDM-induced allergic responses.MethodsTwo anti-Dectin-2 MoAbs were generated and validated for specific binding to Dectin-2 Fc fusion protein (Dectin-2.Fc) and inhibition of Dectin-2.Fc/HDM interaction. Patients with asthma exhibiting high titers of anti-D. pteronyssinusIgE were enrolled. Peripheral blood mononuclear cells with depleted CD14+monocytes were obtained from these patients and co-cultured with autologous monocyte-derived conventional dendritic cells in the presence ofD. pteronyssinusor its group 2 allergens (Der p 2). Interleukin (IL)-5 and IL-13 levels in the culture supernatants were determined using ELISA in the presence or absence of anti-Dectin-2 MoAbs.ResultsTwo MoAbs, 6A4G7 and 17A1D10, showed specific binding to recombinant Dectin-2.Fc and inhibited HDM binding to Dectin-2.Fc. Both anti-Dectin-2 MoAbs inhibited IL-5 and IL-13 production in co-cultures with Der p 2 stimulation in a dose-dependent manner. 6A4G7 and 17A1D10 (3 μg/mL) significantly inhibited Der p 2-induced (3 μg/mL) IL-5 production by 69.7 and 86.4% and IL-13 production by 84.0 and 81.4%, respectively. Moreover, this inhibitory effect of the two MoAbs remained significant in the presence ofD. pteronyssinus.ConclusionsAnti-Dectin-2 MoAbs significantly inhibited HDM-induced allergic responses in vitro and therefore have the potential to become therapeutic agents in mite-induced allergic diseases.
Electronic cigarette vapour increases virulence and inflammatory potential of respiratory pathogens
Authors: Gilpin Deirdre F. , McGown Katie-Ann , Gallagher Kevin , Bengoechea Jose , Dumigan Amy , Einarsson Gisli , Elborn J. Stuart , Tunney Michael M. 
Published: December 2019

AbstractIntroductionBacteria have been extensively implicated in the development of smoking related diseases, such as COPD, by either direct infection or bacteria-mediated inflammation. In response to the health risks associated with tobacco exposure, the use of electronic cigarettes (e-cigs) has increased. This study compared the effect of e-cig vapour (ECV) and cigarette smoke (CSE) on the virulence and inflammatory potential of key lung pathogens (Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureusandPseudomonas aeruginosa).MethodsBiofilm formation, virulence in theGalleria mellonellainfection model, antibiotic susceptibility and IL-8/TNF-α production in A549 cells, were compared between bacteria exposed to ECV, CSE and non-exposed bacteria.ResultsStatistically significant increases in biofilm and cytokine secretion were observed following bacterial exposure to either ECV or CSE, compared to non-exposed bacteria; the effect of exposure to ECV on bacterial phenotype and virulence was comparable, and in some cases greater, than that observed following CSE exposure. Treatment of A549 cells with cell signaling pathway inhibitors prior to infection, did not suggest that alternative signaling pathways were being activated following exposure of bacteria to either ECV or CSE.ConclusionsThese findings therefore suggest that ECV and CSE can induce changes in phenotype and virulence of key lung pathogens, which may increase bacterial persistence and inflammatory potential.
Risk factor assessment for clinical malaria among forest-goers in a pre-elimination setting in Phu Yen Province, Vietnam
Authors: Canavati Sara E. , Kelly Gerard C. , Quintero Cesia E. , Vo Thuan Huu , Tran Long Khanh , Ohrt Colin , Ngo Thang Duc , Tran Duong Thanh , Martin Nicholas J. 
Published: December 2019

Abstract
Background
The transition from malaria control to elimination requires understanding and targeting interventions among high-risk populations. In Vietnam, forest-goers are often difficult to test, treat and follow-up for malaria because they are highly mobile. If undiagnosed, forest-goers can maintain parasite reservoirs and contribute to ongoing malaria transmission.

Methods
A case–control study was conducted to identify malaria risk factors associated with forest-goers in three communes in Phu Yen Province, Vietnam. Cases (n = 81) were residents from the study area diagnosed with malaria and known to frequent forest areas. Controls (n = 94) were randomly selected forest-going residents from within the study area with no identified malaria infection. Participants were interviewed face-to-face using a standard questionnaire to identify malaria risk factors. Logistic regression was used to calculate odds ratios (ORs) and 95% CI for risk factors after adjusting for socio-demographic characteristics.

Results
Among the cases, malaria infection varied by species: 66.7% were positive for Plasmodium falciparum, 29.6% for Plasmodium vivax, and 3.7% were diagnosed as mixed infection. Cases were less likely than controls to use treated nets (aOR = 0.31; 95% CI 0.12–0.80), work after dark (aOR = 2.93; 95% CI 1.35, 6.34), bath in a stream after dark (aOR = 2.44; 95% CI 1.02–5.88), and collect water after dark (aOR = 1.99; 95% CI 1.02–3.90).

Conclusions
As Vietnam moves toward malaria elimination, these findings can inform behaviour change communication and malaria prevention strategies, incorporating the risk of after-dark and water-related activities, in this priority and difficult-to-access population group.