bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOZ047.51: Swallowing and pulmonary diagnoses in children with EA and TEF
Authors: Maybee J , Deck J , Jensen E , Ruiz A , Corbett B , Deterding R , Friedlander J , Helland S , Soden J , Wine T , Prager J , DeBoer E 
Published: June 2019

Abstract

Introduction
Children with repaired congenital esophageal atresia/tracheoesophageal fistula (EA/TEF) are at high risk of aerodigestive morbidity. We hypothesized that age and coexisting pulmonary diagnoses are associated with dysphagia in this population.

Methods
Retrospective review of children with EA/TEF seen in the aerodigestive program between 2011 and 2015 was carried out and comorbidities, video fluoroscopic swallow studies (VFSS), chest CT, and bronchoscopy results were reviewed. VFSS was considered abnormal if there was aspiration, deep laryngeal penetration, significant residue, or delayed initiation. Mann–Whitney U test was used to examine VFSS results by age. Fisher's exact test was used to assess the relationship between VFSS result and comorbidities.

Results
Ninety VFSS were performed on 44 children with EA/TEF (median 2 studies per patient, range: 0–7). Fifty three percent (23/39) children had at least one abnormal VFSS. Seventeen children had VFSS change between normal and abnormal over time, with 11 normal on their most recent VFSS. Younger children (Mdn = 1.57 years) were more likely to have an abnormal test result than older children (Mdn = 3.55 years) (p = 0.001). Children with severe tracheomalacia (>90% tracheal collapse visualized on flexible bronchoscopy) had a higher incidence of abnormal VFSS (14/20; 70%) than the other children with EA/TEF (9/24; 38%) (P = 0.04). Children with other pulmonary and airway comorbidities, including gestation age <36 weeks (P = 0.24), vocal fold immobility (P = 0.1), abnormal chest CT (P = 0.1), tended to have an increased incidence of abnormal VFSS but did not reach statistical significance in this cohort.

Discussion
Dysphagia was prevalent in this cohort and related to age and severe tracheomalacia. This reinforces the need for a multidisciplinary evaluation including feeding and swallowing evaluation. In this rare disease, we must collaborate between sites to improve our understanding of aerodigestive diagnoses and disease outcomes.
DOZ047.65: Radiofrequency ablation: a promising treatment in children with early onset Barrett's esophagus
Authors: Rea F , Isoldi S , Accarpio F , Baldi F , Giulia A , Romeo E , Faraci S , Contini A , Tambucci R , Balassone V , Caldaro T , Dall’Oglio L , De Angelis P , Trentino P 
Published: June 2019

Abstract

Aim of the Study
Barrett's esophagus (BE) could be a rare late complication in children with repaired esophageal atresia, partly due to a long-term history of gastro-esophageal reflux disease (GERD). Radiofrequency ablation (RFA) is the best endoscopic technique in adults with BE and dysplasia. Guidelines do not support this approach for non-dysplastic BE. Aim of this study is to present our experience as Tertiary Gastroenterology referral Centers in the treatment of children and young adults with BE using RFA.

Methods
A multicenter retrospective study conducted on children with BE, subjected to RFA at the Digestive Surgery and Endoscopy Unit, Bambino Gesù Children's Hospital and the Department of General Surgery ‘Paride Stefanini’, Sapienza University of Rome, between June 2012 and December 2017.Demographic and clinical data were collected. BE characteristics according to Prague classification, presence and grade of dysplasia, number of RFA treatments, complications, clinic and endoscopic outcomes were described. All patients were treated with HALO RF BARRXtm (HALO 360 Covidien, Sunnyvale, California, USA). Endoscopic evaluation and treatment were performed every 3 months until complete eradication. Endoscopic follow-up was: 6 months after eradication, and then annually.

Results
Five patients were evaluated (M:5). Mean age at diagnosis was 14.4 years (range: 9–17); mean age at first treatment was 23 years (range: 13–36). Two patients presented with repaired esophageal atresia (long gap, type 3 atresia), 3 with peptic strictures. All patients exhibited a long-term history of symptomatic GERD and PPI dependency. Four patients underwent Nissen fundoplication before BE diagnosis. All patients presented with long segment BE (mean baseline length was 8,8 cm, range 7–10 cm). According to the Prague classification, patients were classified as follows: C0M7, C0M17, C8M10, C0M9 and C4M8. One patient presented with LGD. Patients received a mean of 3 HALO treatments (range 1–4 sessions). Eradication was 100% during 2- to 6-year follow-up (mean 4.5 year). No complications occurred.

Conclusions
Pediatric patients with EA present an high risk to develop early BE, therefore endoscopic surveillance is mandatory. RFA represents a safe and effective treatment option in patients with early onset BE. Treatment of BE with this technique could be a useful and minimal invasive strategy for dysplasia and cancer prevention.
DOZ047.70: Prevalence of abnormal triple endoscopy findings for tracheoesophageal fistula patients in a multidisciplinary aerodigestive clinic
Authors: Chowdhuri S , Osterbauer B , Bansal M , Hochstim C , Bhardwaj V 
Published: June 2019

Abstract

Introduction
Tracheoesophageal fistula (TEF) is a rare congenital defect involving malformations of the esophagus and trachea, which can be life-threatening if left untreated. Children who have undergone TEF repair often present with symptoms such as cough, vomiting, and growth failure. Although the variety of these symptoms implies a necessity for a multidisciplinary approach to care of TEF repair patients, many are still followed by a single discipline such as gastroenterology or pulmonology. The purpose of this study is to describe the experience of Children's Hospital Los Angeles Aerodigestive team in evaluating TEF patients using an interdisciplinary approach. In particular, we aim to explore the findings obtained during triple endoscopy in order to confirm the necessity of care by multiple specialties, ideally in the setting of an Aerodigestive Clinic.

Methods
Consent was obtained for all children (birth to 18 years) seen in the Children's Hospital Los Angeles (CHLA) Aerodigestive (AERO) Clinic between June 2016 and August 2018. All patients with a diagnosis of TEF were included in the study and data collected included: age, sex, presenting diagnoses and symptoms, and triple endoscopy findings.

Results
Of the first 109 patients in the AERO Clinic, 18 had TEF. Of these, 7 (39%) were female with a mean age of 3.4 years (SD 3), and 44% were Hispanic. Ten TEF patients underwent triple endoscopy and all had at least one abnormal finding. Six were diagnosed with laryngeal cleft (LC); four type I, one type II, and one was unspecified. Other abnormal findings included: bronchomalacia (7), tracheomalacia (8), esophagitis (4), gastritis (2), and duodenitis (1). Additionally, 7 had an abnormal bronchoalveolar lavage (BAL) finding, with 6 culture positive results.

Conclusion
TEF patients can present with feeding and respiratory difficulties months to years after their surgical repair. The triple endoscopy findings of TEF patients presented in this study illustrate that symptoms may arise from the gastrointestinal or respiratory tract. Our experience with TEF patients at CHLA indicates that a multidisciplinary approach to evaluation and management is necessary to serve the complex needs of this population.
DOZ047.92: Oesophageal atresia: a multicenter retrospective study on surgical treatment and 1-year follow-up
Authors: Vercauteren C , Reusens H , De Backer A , Tambucci R , Van Cauwenberge S , Leyman P , Ruppert M , Demarche M , Vervloessem D , Matthyssens L 
Published: June 2019

Abstract

Introduction
No data are available on surgical management and outcomes of oesophageal atresia (OA) in Belgium. In collaboration with the Belgian Association of Paediatric Surgery (BELAPS) a retrospective study was organized to analyze data from children born with OA, with a 1-year follow-up.

Materials and Methods
Out of 17 centers in Belgium, 10 participated in this study. A novel checklist to collect data from OA patients born between the 1st of January 2010 and the 1st of January 2015 was created. Gross type A, B, C and D OA were included.

Results
One hundred children were included. Gross type C OA was seen in 86%. Associated malformations were present in 73%, most frequently cardiac malformations (52%). There was consensus regarding preoperative investigations, anastomotic technique, and transanastomotic tube placement. There was no consensus regarding genetic counseling, placement of a chest tube, and start of enteral feeding. There were six deaths in the first year of life. The majority of patients needed rehospitalization during the first year of life (85.9%) and there was a high occurrence of anastomotic strictures (51.6%).

Conclusions
This is the first study about management and outcome of OA in Belgium. Although the 1-year survival rate is high (93.8%), these data illustrate that OA has an important morbidity. Multidisciplinary follow-up and prospective studies/registries with longer follow-up are needed.
DOZ047.96: Esophageal food impaction presenting as life-threatening airway obstruction in children with esophageal atresia
Authors: Rozycki S , Liou T-N , Brigger M T 
Published: June 2019

Abstract

Objective
An esophageal foreign body rarely presents as an apparent life-threatening event. However, in children with esophageal atresia, strictures and dysmotility can lead to severe food impactions. Given the underlying anatomy of children with esophageal atresia, a unique risk of severe impaction with resultant airway obstruction is possible. This study reports a case of a child in respiratory distress presenting after a choking event where endoscopy revealed near total tracheal compression from esophageal food impaction.

Method
Case discussion and review of literature are undertaken.

Result
A 3-year-old boy with trisomy 21 and history of esophageal atresia who had previously undergone successful repair was transported by helicopter after a choking episode. He was witnessed to have cough followed by apnea, cyanosis, and unresponsiveness, for which he underwent the Heimlich maneuver and required chest compressions for a respiratory arrest. He was immediately taken to the operating room for endoscopy with planned foreign body removal. Rigid bronchoscopy noted near complete obstruction of the airway from posterior tracheal wall compression with no airway foreign body. The airway was secured and a combination of rigid and flexible esophagoscopy subsequently extracted a large bolus of chicken. He was observed in the intensive care unit with no further respiratory event after extubation.

Conclusion
Esophageal dysmotility and strictures are common in children with esophageal atresia who have undergone repair. Mild airway symptoms are common in children with an esophageal foreign body; however, in children with esophageal atresia a high index of suspicion of an esophageal foreign body is requisite in the setting of acute airway obstruction.
Flecainide is a safe and effective treatment for pre-excited atrial fibrillation rapidly conducted to the ventricle in pregnant women: a case series
Authors: Chauveau Samuel , Le Vavasseur Olivier , Morel Elodie , Dulac Arnaud , Chevalier Philippe 
Published: June 2019

AbstractBackgroundPregnancy is associated with an increased incidence of cardiac arrhythmias likely due to hormonal, haemodynamic, and autonomic changes. Yet, there is little data available regarding the efficacy and safety of anti-arrhythmic agents to prevent pre-excited atrial fibrillation (AF) in pregnant women.Case summaryWe report on three pregnant women who developed AF rapidly conducted to the ventricle through an overt accessory pathway as the first manifestation of Wolff–Parkinson–White syndrome.DiscussionAll patients were treated with flecainide with neither arrhythmias recurrence nor adverse events of the treatment. Mechanisms of action and clinical efficacy of flecainide are discussed.
Small intestinal transcriptome analysis revealed changes of genes involved in nutrition metabolism and immune responses in growth retardation piglets1
Authors: Qi Ming , Tan Bie , Wang Jing , Li Jianjun , Liao Simeng , Yan Jiameng , Liu Yanhong , Yin Yulong 
Published: June 2019

Abstract
Postnatal growth retardation (PGR) is common in piglets. Abnormal development in small intestine was casually implicated in impaired growth, but the exact mechanism is still implausible. The present study unveiled transcriptome profile of jejunal mucosa, the major site of nutrient absorption, in PGR and healthy piglets using RNA-sequencing (RNA-seq). The middle segments of jejunum and ileum, and jejunal mucosa were obtained from healthy and PGR piglets at 42 d of age. Total RNA samples extracted from jejunal mucosa of healthy and PGR piglets were submitted for RNA-seq. Lower villus height was observed in both jejunum and ileum from PGR piglets suggesting structural impairment in small intestine (P < 0.05). RNA-seq libraries were constructed and sequenced, and produced average 4.8 × 107 clean reads. Analysis revealed a total of 499 differently expressed genes (DEGs), of which 320 DEGs were downregulated in PGR piglets as compared to healthy piglets. The functional annotation based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted that most DEGs were involved in nutrient metabolism and immune responses. Our results further indicated decreased gene expression associated with glucose, lipid, protein, mineral, and vitamin metabolic process, detoxication ability, oxidoreductase activity, and mucosal barrier function; as well as the increased insulin resistance and inflammatory response in the jejunal mucosa of PGR piglets. These results characterized the transcriptomic profile of the jejunal mucosa in PGR piglets, and could provide valuable information with respect to better understanding the nutrition metabolism and immune responses in the small intestine of piglets.
The effect of bioRxiv preprints on citations and altmetrics
Authors: Fraser Nicholas , Momeni Fakhri , Mayr Philipp , Peters Isabella 
Published: June 2019

1.AbstractA potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals. We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.
Clinical diagnosis of single-gene disorders and chromosomal abnormalities based on BGISEQ-500 platform
Authors: Liu Yanqiu , Mao Liangwei , Wei Xiaoming , Man Jianfen , Zhang Wenqian , Wang Lina , Li Long , Sun Yan , Li Wei , Zhai Teng , Guo Xueqin , Du Lique , Huang Jin , Li Hao , Wan Yang , Huang Hui 
Published: June 2019

AbstractMost of the variation in the human genome is a single nucleotide variation (SNV) based on a single base or small fragment insertions and deletions and genomic copy number variation (CNV). Both types of mutations are involved in many human diseases. Such diseases often have complex clinical symptoms and difficult clinical diagnosis, so an effective detection method is needed to help clinical diagnosis and prevent birth defects. With the development of sequencing technology, the method of chip capture combined with high-throughput sequencing has been extensively used because of its high throughput, high accuracy, high speed and low cost. This study designed a chip that captures the coding region of 3043 genes associated with 4013 monogenic diseases. In addition, 148 chromosomal abnormalities can be identified by setting targets in specific regions. Compared with the whole exon chip, the chip can detect 4013 monogenic diseases and 148 chromosomal abnormalities at a lower cost, including SNV, intra-gene CNV and genomic copy number variation. This study utilized a strategy of combining the BGISEQ500 sequencing platform with the chip to identify 102 disease-associated mutations in 63 patients, 69 of which were new mutations. The evaluation test results also show that this combination complies with the requirements of clinical testing and has good clinical application value.
A revised 1.6 Å structure of the GTPase domain of the Parkinson’s disease-associated protein LRRK2 provides insights into mechanisms
Authors: Wu Chun-Xiang , Liao Jingling , Park Yangshin , Hoang Neo C. , Engel Victoria A. , Wan Li , Oh Misook , Sanishvili Ruslan , Takagi Yuichiro , Johnson Steven M. , Wang Mu , Federici Mark , Nichols R. Jeremy , Beilina Alexandra , Reed Xylena , Cookson Mark R. , Hoang Quyen Q. 
Published: June 2019

Leucine-rich repeat kinase 2 (LRRK2) is a large 286 kDa multi-domain protein whose mutation is a common cause of Parkinson’s disease (PD). One of the common sites of familial PD-associated mutations occurs at residue Arg-1441 in the GTPase domain of LRRK2. Previously, we reported that the PD-associated mutation R1441H impairs the catalytic activity of the GTPase domain thereby traps it in a persistently "on" state. More recently, we reported that the GTPase domain of LRRK2 exists in a dynamic dimer-monomer equilibrium where GTP binding shifts it to the monomeric conformation while GDP binding shifts it back to the dimeric state. We also reported that all of the PD-associated mutations at Arg-1441, including R1441H, R1441C, and R1441G, impair the nucleotide-dependent dimer-monomer conformational dynamics of the GTPase domain. However, the mechanism of this nucleotide-dependent conformational dynamics and how it is impaired by the mutations at residue Arg-1441 remained unclear. Here, we report a 1.6 Å crystal structure of the GTPase domain of LRRK2. Our structure has revealed a dynamic switch region that can be differentially regulated by GTP and GDP binding. This nucleotide-dependent regulation is impaired when residue Arg-1441 is substituted with the PD-associated mutations due to the loss of its exquisite interactions consisting of two hydrogen bonds and a π-stacking interaction at the dimer interface.Significance StatementMutations in LRRK2 are associated with familial Parkinson’s disease, so understanding its mechanism of actions and how they are changed by the disease-associated mutations is important for developing therapeutic strategies. This paper describes an atomic structure of the G-domain of LRRK2 revealing that the conformational dynamics of the switch regions are potentially important for its normal function. It further shows that a disease-associated mutation could lock the G domain in a persistently active-like conformation, thus perturbing its normal function.
PKMYT1 is a computationally predicted target for kidney cancer
Authors: Torre Denis , Fernandez Nicolas F. , Ma’ayan Avi 
Published: June 2019

AbstractProtein Kinase Membrane Associated Tyrosine/Threonine 1 (PKMYT1) is an understudied member of the serine/threonine protein kinase family. PKMYT1 is listed as a dark kinase according to the Illuminating the Druggable Genome (IDG) target development level classification. Using a combination of bioinformatics tools that we developed, we predict that targeting PKMYT1 is potentially beneficial for treating kidney cancer.
Security and Privacy Concerns Regarding Genetic Data in Mobile Health Record Systems: An Empirical Study from Turkey
Authors: Özkan Özlem , Aydin Son Yeşim , Aydinoğlu Arsev Umur 
Published: June 2019

AbstractWith the increasing use of genetic testing and applications of bioinformatics in healthcare, genetic and genomic data needs to be integrated into electronic health systems. We administered a descriptive survey to 174 participants to elicit their views on the privacy and security of mobile health record systems and inclusion of their genetic data in these systems. A survey was implemented online and on site in two genetic diagnostic centres. Nearly half of the participants or their close family members had undergone genetic testing. Doctors constituted the only profession group that people trusted for the privacy of their health and genetic data; however, people chose to limit even their doctor’s access to their genetic/health records. The majority of the respondents preferred to keep full access for themselves. Several participants had negative experience or preconceptions about electronic health records: the medical reports of 9.7% of the respondents had been used or released without their consent, 15.1% stated that they avoided being tested due to violation risks, and 3.5% asked their doctors to enter a less embarrassing health status in their records. The participants wanted to see some regulations and security measurements before using any system for their health/genetic data. In addition, significantly more participants stating that storing genetic data in a mobile system was riskier compared to other health data. Furthermore, the comparative analysis revealed that being young, being a woman and having higher education were associated with having greater privacy concerns.
Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
Authors: Freeman Timothy M. ,   Genomics England Research Consortium, Wang Dennis , Harris Jason 
Published: June 2019

AbstractAccurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloguing population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilise consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations and alternative methods are required to overcome these.We have developed a novel statistical method based on summarising sequenced reads from whole genome clinical samples and cataloguing them in “Incremental Databases” that maintain individual confidentiality. Allele statistics were catalogued for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at ∼1-3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio=23.29-33.69) and the NIST high confidence genomic regions (odds ratio=0.154-0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels.Our results recommend increased caution to address systematic biases in whole genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.