bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on Discrete Railway Bulk Transportation Option Based on Game Theory
Authors: Zhang Ji , Yang Ting , Guo Jingwei 
Published: July 2021

Abstract
Railway transportation is an important part of China’s transportation system, and its freight price level has a direct impact on the national economy and social development. In this paper, taking railway freight pricing as the research object, based on pricing theories and theorems, the option theory is introduced into the railway freight pricing problem, a Stackelberg game model of railway freight option is established, and an optimization algorithm is proposed to solve the model. It is helpful for railway transportation enterprises to participate in the market competition of railway freight rate system, which provides the theoretical basis and technical support for the market-oriented reform of railway freight rate.
Optimal design of transportation signal control at the intersection based on Webster signal timing method
Authors: Li Yang , Qin Zhong , Zhu Cheng Ming 
Published: July 2021

Abstract
Urban transportation congestion has become a common phenomenon in the morning and evening peak. As the key node of urban transportation, optimizing the signal timing scheme of intersections is an effective measure to improve its traffic efficiency. In this paper, Webster signal timing method is used to optimize the signal timing scheme of intersection, and then VISSIM software is used to simulate the two schemes, and the queue length, parking times, travel time, delay time and pollution emission of each entrance at the intersection are optimized and analyzed. After optimization, the traffic condition of the intersection is obviously improved.
Ranked choice voting for representative transcripts with TRaCE
Authors: Olson Andrew J , Ware Doreen 
Published: July 2021

Abstract

Summary
Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, Transcript Ranking and Canonical Election (TRaCE) holds an ‘election’ in which a set of RNA-seq samples rank transcripts by annotation edit distance. These sample-specific votes are tallied along with other criteria such as protein length and InterPro domain coverage. The winner is selected as the canonical transcript, but the election proceeds through multiple rounds of voting to order all the transcripts by relevance. Based on the set of expression data provided, TRaCE can identify the most common isoforms from a broad expression atlas or prioritize alternative transcripts expressed in specific contexts.

Availability and implementation
Transcript ranking code can be found on GitHub at {{https://github.com/warelab/TRaCE}}.

Supplementary information
Supplementary data are available at Bioinformatics online.
Transformation and differential abundance analysis of microbiome data incorporating phylogeny
Authors: Zhou Chao , Zhao Hongyu , Wang Tao 
Published: July 2021

Abstract

Motivation
Microbiome data have proven extremely useful for understanding microbial communities and their impacts in health and disease. Although microbiome analysis methods and standards are evolving rapidly, obtaining meaningful and interpretable results from microbiome studies still requires careful statistical treatment. In particular, many existing and emerging methods for differential abundance (DA) analysis fail to account for the fact that microbiome data are high-dimensional and sparse, compositional, negatively and positively correlated and phylogenetically structured. To better describe microbiome data and improve the power of DA testing, there is still a great need for the continued development of appropriate statistical methodology.

Results
In this article, we propose a model-based approach for microbiome data transformation, and a phylogenetically informed procedure for DA testing based on the transformed data. First, we extend the Dirichlet-tree multinomial (DTM) to zero-inflated DTM for multivariate modeling of microbial counts, addressing data sparsity and correlation and phylogeny among bacterial taxa. Then, within this framework and using a Bayesian formulation, we introduce posterior mean transformation to convert raw counts into non-zero relative abundances that sum to one, accounting for the compositionality nature of microbiome data. Second, using the transformed data, we propose adaptive analysis of composition of microbiomes (adaANCOM) for DA testing by constructing log-ratios adaptively on the tree for each taxon, greatly reducing the computational complexity of ANCOM in high dimensions. Finally, we present extensive simulation studies, an analysis of HMP data across 18 body sites and 2 visits, and an application to a gut microbiome and malnutrition study, to investigate the performance of posterior mean transformation and adaANCOM. Comparisons with ANCOM and other DA testing procedures show that adaANCOM controls the false discovery rate well, allows for easy interpretation of the results, and is computationally efficient for high-dimensional problems.

Availability and implementation
The developed R package is available at https://github.com/ZRChao/adaANCOM. For replicability purposes, scripts for our simulations and data analysis are available at https://github.com/ZRChao/Papers_supplementary.

Supplementary information
Supplementary data are available at Bioinformatics online.
Genome-wide gene–smoking interaction study identified novel susceptibility loci for non-small cell lung cancer in Chinese populations
Authors: Wang Yuzhuo , Ji Mengmeng , Zhu Meng , Fan Jingyi , Xie Junxing , Huang Yanqian , Wei Xiaoxia , Jiang Xiangxiang , Xu Jing , Chen Liang , Yin Rong , Wang Cheng , Zhang Ruyang , Zhao Yang , Dai Juncheng , Jin Guangfu , Hu Zhibin , Christiani David C , Ma Hongxia , Xu Lin , Shen Hongbing 
Published: July 2021

Abstract
Gene–smoking interactions play important roles in the development of non-small cell lung cancer (NSCLC). To identify single-nucleotide polymorphisms (SNPs) that modify the association of smoking behavior with NSCLC risk, we conducted a genome-wide gene–smoking interaction study in Chinese populations. The genome-wide interaction analysis between SNPs and smoking status (ever- versus never-smokers) was carried out using genome-wide association studies of NSCLC, which included 13 327 cases and 13 328 controls. Stratified analysis by histological subtypes was also conducted. We used a genome-wide significance threshold of 5 × 10−8 for identifying significant gene–smoking interactions and 1 × 10–6 for identifying suggestive results. Functional annotation was performed to identify potential functional SNPs and target genes. We identified three novel loci with significant or suggestive gene–smoking interaction. For NSCLC, the interaction between rs2746087 (20q11.23) and smoking status reached genome-wide significance threshold [odds ratio (OR) = 0.63, 95% confidence interval (CI): 0.54–0.74, P = 3.31 × 10–8], and the interaction between rs11912498 (22q12.1) and smoking status reached suggestive significance threshold (OR = 0.72, 95% CI: 0.63–0.82, P = 8.10 × 10–7). Stratified analysis by histological subtypes identified suggestive interactions between rs459724 (5q11.2) and smoking status (OR = 0.61, 95% CI: 0.51–0.73, P = 7.55 × 10–8) in the risk of lung squamous cell carcinoma. Functional annotation indicated that both classic and novel biological processes, including nicotine addiction and airway clearance, may modulate the susceptibility to NSCLC. These novel loci provide new insights into the biological mechanisms underlying NSCLC risk. Independent replication in large-scale studies is needed and experimental studies are warranted to functionally validate these associations.
Distinct Contributions of Genes and Environment to Visual Size Illusion and the Underlying Neural Mechanism
Authors: Chen Lihong , Xu Qian , Shen Li , Yuan Tian , Wang Ying , Zhou Wen , Jiang Yi 
Published: July 2021

Abstract
As exemplified by the Ebbinghaus illusion, the perceived size of an object can be significantly biased by its surrounding context. The phenomenon is experienced by humans as well as other species, hence likely evolutionarily adaptive. Here, we examined the heritability of the Ebbinghaus illusion using a combination of the classic twin method and multichannel functional near-infrared spectroscopy. Results show that genes account for over 50% of the variance in the strength of the experienced illusion. Interestingly, activations evoked by the Ebbinghaus stimuli in the early visual cortex are explained by genetic factors whereas those in the posterior temporal cortex are explained by environmental factors. In parallel, the feedforward functional connectivity between the occipital cortex and the temporal cortex is modulated by genetic effects whereas the feedback functional connectivity is entirely shaped by environment, despite both being significantly correlated with the strength of the experienced illusion. These findings demonstrate that genetic and environmental factors work in tandem to shape the context-dependent visual size illusion, and shed new light on the links among genes, environment, brain, and subjective experience.
Enriching Deaf Children’s American Sign Language Phonological Awareness: A Quasi-Experimental Study
Authors: Holcomb Leala , Golos Debbie , Moses Annie , Broadrick Anna 
Published: July 2021

AbstractWith the knowledge that deaf children benefit from early exposure to signed language, questions are raised about the role of specific types of language input that are beneficial in early childhood classrooms. This quasi-experimental study explores the effects of ASL rhyme, rhythm, and handshape awareness activities on 4- to 6-year-old deaf children’s ASL phonological awareness. Deaf children received three-week structured activities and four-week teacher-choice activities that targeted handshape awareness. Results yielded evidence that interventions as brief as 12 minutes daily for up to 2 months can produce positive effects on deaf children’s phonological awareness. Furthermore, although the intervention focused only on handshape awareness, children’s positive gains on the ASL Phonological Awareness Test suggests one targeted phonological awareness skill (e.g., handshape) may generalize to other phonological awareness skills (e.g., location and movement). Further investigation is needed on the relationship between ASL phonological awareness and overall language and literacy skills in both ASL and English.
Myocardial rupture and left ventricular pseudoaneurysm due to late STEMI presentation during the COVID-19 pandemic lockdown: a classical case report
Authors: Banisauskaite Audra , Velavan Periaswamy , Hasleton Jonathan , Mediratta Neeraj , Arzanauskaite Monika , Binukrishnan Sukumaran 
Published: July 2021

Abstract

Background
Left ventricular (LV) pseudoaneurysm is a serious and rare complication of myocardial infarction (MI). It occurs when an injured myocardial wall ruptures and is contained by overlying adherent pericardium or scar tissue, most commonly it develops in patients with late presentation of MI and delayed revascularization.

Case summary
A 64-year-old man presented to the emergency department with intermittent central chest pain radiating to back and neck and increasing on deep inspiration, which was considered to be of musculoskeletal origin for a week, but worsened despite medications. Electrocardiography showed features of ST-elevation MI; a circumflex artery occlusion was found on coronary angiogram and angioplasty was performed. Cardiovascular magnetic resonance (CMR) revealed features of healed lateral wall rupture with adherent parietal pericardium and the patient was managed conservatively. Two months later the patient returned with severe chest pain; echocardiogram and cardiac computed tomography showed significant interval progression of the pseudoaneurysm. Aneurysmectomy was performed, after which the patient recovered and had none of the previous symptoms since. Follow-up CMR study revealed improvement of LV systolic function.

Discussion
A rare case of post-infarction LV pseudoaneurysm was reported. Multimodality imaging helped to detect and to differentiate this complication from the true aneurysm and to follow it up and plan the treatment. Conservative treatment was not effective in this case as the pseudoaneurysm progressed; aneurysmectomy helped to improve LV systolic function.
Pulmonary arteriovenous malformation with unexplained cyanosis as the first presentation of hereditary haemorrhagic telangiectasia, case report, and literature review
Authors: Alakhfash Ali , Alqwaiee Abdullah , Almesned Abdulrahman , Al-Hassnan Zuhair N 
Published: July 2021

Abstract

Background
Pulmonary arteriovenous malformations (PAVMs) are rare pulmonary vascular anomalies. They can result in right-to-left shunt and, if significant, low systemic saturation, cyanosis, polycythaemia, and paradoxical systemic embolization.

Case summary
Eighteen months old female child was referred to our centre due to unexplained central and peripheral cyanosis. Based on the agitated saline contrast echocardiography study, computed tomography scan confirmed the presence of abnormal vasculature at the left lower lobe. Percutaneous closure of the PAVM was performed using Amplatzer Duct Occluder type 1 device. The genetic study revealed a pathogenic mutation in the endoglin gene, which is a known cause of hereditary haemorrhagic telangiectasia (HHT) inhered in an autosomal dominance pattern.

Discussion
PAVM could be the first manifestation of HHT. Closing the malformation percutaneously is feasible, which can eliminate the right to left shunt and improves the saturation. Genetic study is warranted in these cases, as well as long-term follow-up.
Novel concepts and early results of repairing common arterial trunk
Authors: Yacoub Magdi H , Hosny Hatem , Afifi Ahmed , Nagy Mohamed , Mahgoub Ahmed , Simry Walid , AbouZeina Mohammad Gibreel , Doss Ramy , El Sawy Amr , Shehata Nairouz , Elafifi Abdelrahman , Abdullah Hedaia , Romeih Soha 
Published: July 2021

Abstract

OBJECTIVES
Common Arterial Trunk (CAT) continues to have a very poor prognosis globally. To address that, we have developed a novel technique targeting key concepts for the correction of all components of the anomaly, using autologous arterial tissue. This aims to enhance results, availability worldwide, and importantly to avoid the need for repeated reoperations.

METHODS
From January 2019 to 4 January 2021, all patients with isolated CAT had repair of the defect using autologous arterial trunk tissue with direct right ventricle (RV) to pulmonary artery (PA) connection. Clinical outcomes, follow-up which included multi-slice computed tomography 3D segmentation and 4D cardiovascular magnetic resonance flow, are presented.

RESULTS
Twenty patients were included in the study (median age 4.5 months). There were 2 hospital deaths due to systemic infection and pulmonary hypertensive crisis, respectively. Following discharge all patients remained asymptomatic with no signs of heart failure and improved pattern of growth (median follow-up: 8 months). Early postoperative 3D segmentation showed a conical shaped neo-right ventricular outflow chamber connecting the body of the RV to the main PA through a valveless ostium, and normal crossing of PA and neo-aorta. 4D cardiovascular magnetic resonance pattern of flow showed normal rapid laminar flow through the atrioventricular valves followed by a vortex towards the outflow tracts. There was laminar flow through the neo-aorta and neo-PA with velocity not exceeding 2.5 m/s. The PA regurgitant fraction was 25 ± 5% and was limited to early diastole.

CONCLUSIONS
The initial results of utilizing the key concepts, using autologous arterial tissue for the repair of CAT, are encouraging, both clinically and by multimodality imaging.
Cerebral microemboli during extracorporeal life support: a single-centre cohort study
Authors: Kietaibl Clemens , Horvat Menih Ines , Engel Adrian , Ullrich Roman , Klein Klaus U , Erdoes Gabor 
Published: July 2021

Abstract OBJECTIVESThe aim of this study was to investigate the load and composition of cerebral microemboli in adult patients undergoing venoarterial extracorporeal life support (ECLS).METHODSAdult ECLS patients were investigated for the presence of cerebral microemboli and compared to critically ill, pressure-controlled ventilated controls and healthy volunteers. Cerebral microemboli were detected in both middle cerebral arteries for 30 min using transcranial Doppler ultrasound. Neurological outcome (ischaemic stroke, global brain ischaemia, intracerebral haemorrhage, seizure, metabolic encephalopathy, sensorimotor sequelae and neuropsychiatric disorders) was additionally evaluated.RESULTSTwenty ECLS patients (cannulations: 15 femoro-femoral, 4 femoro-subclavian, 1 femoro-aortic), 20 critically ill controls and 20 healthy volunteers were analysed. ECLS patients had statistically significantly more cerebral microemboli than critically ill controls {123 (43–547) [median (interquartile range)] vs 35 (16–74), difference: 88 [95% confidence interval (CI) 19–320], P = 0.023} and healthy volunteers [11 (5–12), difference: 112 (95% CI 45–351), P &lt; 0.0001]. In ECLS patients, 96.5% (7346/7613) of cerebral microemboli were of gaseous composition, while solid cerebral microemboli [1 (0–5)] were detected in 12 out of 20 patients. ECLS patients had more neurological complications than critically ill controls (12/20 vs 3/20, P = 0.003). In ECLS patients, a high microembolic rate (&gt;100/30 min) tended to be associated with neurological complications including ischaemic stroke, neuropsychiatric disorders, sensorimotor sequelae and non-convulsive status epilepticus (odds ratio 4.5, 95% CI 0.46–66.62; P = 0.559).CONCLUSIONSOur results indicate that adult ECLS patients are continuously exposed to many gaseous and, frequently, to few solid cerebral microemboli. Prolonged cerebral microemboli formation may contribute to neurological morbidity related to ECLS treatment.Clinical trial registrationClinicalTrials.gov, NCT02020759, https://clinicaltrials.gov/ct2/show/NCT02020759?term=erdoes&rank=1.
Forms in Motion: The Poetic Prose of Robert Macfarlane and Kathleen Jamie
Authors: John Stefanie 
Published: July 2021

Abstract
This essay examines the use of poetic prose in recent non-fiction by Robert Macfarlane and Kathleen Jamie. Drawing on selected chapters from Macfarlane’s The Old Ways (2012), Jamie’s Sightlines (2012), and a prose poem from Jamie’s The Bonniest Companie (2015), it demonstrates the hybridity of contemporary nature writing by paying attention to the works’ transgressions of the bounds of verse and prose. After introducing the nineteenth-century debate on differences between lyric and prosaic language and outlining Romantic efforts to poeticize prose descriptions of nature and environment, the article discusses Macfarlane’s and Jamie’s role in this conversation. I argue that formal transgressions – evident in metrical and rhyming effects, typographical experiments, imagery, and allusion – are especially strong in passages that describe movement: in accounts of walking or in observations of the shifting motions of light and weather. Prose forms that approximate and integrate lyricism here enhance a sense of transience as well as exhibit the continuity of human and non-human worlds. Self-consciously tracing the footsteps of other poets who have traversed genre boundaries, Macfarlane’s and Jamie’s work establishes nature writing as a form that is persistently on the move.
CRISPR-mediated knock-in of transgenes into the malaria vector Anopheles funestus
Authors: Quinn Charlotte , Anthousi Amalia , Wondji Charles , Nolan Tony 
Published: July 2021

Abstract
The ability to introduce mutations, or transgenes, of choice to precise genomic locations has revolutionized our ability to understand how genes and organisms work. In many mosquito species that are vectors of various human diseases, the advent of CRISPR genome editing tools has shed light on basic aspects of their biology that are relevant to their efficiency as disease vectors. This allows a better understanding of how current control tools work and opens up the possibility of novel genetic control approaches, such as gene drives, that deliberately introduce genetic traits into populations. Yet for the Anopheles funestus mosquito, a significant vector of malaria in sub-Saharan Africa and indeed the dominant vector species in many countries, transgenesis has yet to be achieved. We describe herein an optimized transformation system based on the germline delivery of CRISPR components that allows efficient cleavage of a previously validated genomic site and preferential repair of these cut sites via homology-directed repair (HDR), which allows the introduction of exogenous template sequence, rather than end-joining repair. The rates of transformation achieved are sufficiently high that it should be able to introduce alleles of choice to a target locus, and recover these, without the need to include additional dominant marker genes. Moreover, the high rates of HDR observed suggest that gene drives, which employ an HDR-type mechanism to ensure their proliferation in the genome, may be well suited to work in A. funestus.
Role of gut microbiota in functional constipation
Authors: Zhang Shengsheng , Wang Ruixin , Li Danyan , Zhao Luqing , Zhu Lixin 
Published: July 2021

AbstractFunctional constipation (FC) is common, yet the etiology is not clear. Accumulating evidence suggests an association between FC and abnormal gut microbiota. The relationship between the gut microbiota and the gut transit is likely bidirectional. This review summarizes the current evidence regarding the impact of gut microbiota on the pathogenesis of FC. By modulating the colonic motility, secretion, and absorption, gut microbiota may contribute to the development of FC through microbial metabolic activities involving bile acids, short-chain fatty acids, 5-hydroxytryptamine, and methane. In support of the key roles of the gut microbiota in FC, treatment with probiotics, prebiotics, synbiotics, and traditional Chinese medicine often result in compositional and functional changes in the gut microbiota. Further studies on the pathogenesis of FC and the therapeutic mechanism of microecological agents will provide a knowledge base for better management of FC.