bluuebunny/crossref_metadata_2025 huggingface dataset:
DOZ047.102: Previously undescribed association of esophageal atresia, congenital microgastria, and pyloric atresia: a difficult case of ‘pure’ atresia.
Authors: Laughlin D Mc , Sue T , Thambipillai S P
Published: June 2019

This study reports the case of a male infant born at full term with antenatal suspicion for esophageal atresia (EA). At birth inability to pass a feeding tube and a gasless abdomen on plain film X-ray led to the diagnosis of pure EA according to international guidelines. In the first week of life a stomach could not be identified at surgery for open gastrostomy and a feeding jejunostomy was formed. Subsequent investigations including CT scan did not detect the presence of a stomach. Cervical esophagostomy was performed at 8 weeks old as there was no expectation of achieving an esophageal anastomosis and a deviated septum had complicated the placement of nasal tubes for management of the proximal esophageal pouch. At 6 months of age esophageal replacement with a jejunal pull-up graft was undertaken as staged surgery. At mobilization of a large midline liver to expose the hiatus, a microstomach was revealed, in association with a type 2 pyloric atresia (PA) and a distal tracheoesophageal fistula (TEF). Following ligation of the TEF by lateral thoracotomy, the TEF and microstomach were resected and the jejunal pull-up graft was completed. Discharge home was achieved 1 month post-op. Oral intake was established for solids by 1 year of age. The patient is thriving at 4 years of age with additional overnight jejunal feeds. A unifying genetic diagnosis has not been made to date. Congenital microgastria or PA has been described to co-exist with EA but never previously have all these anomalies been reported occurring together. This unique scenario permitted the distal TEF to be clinically silent and present as a pure atresia. In turn congenital microgastria together with a diagnosis of pure EA obscured the presence of PA, which classically presents with vomiting of feeds and massive gastric distension. Investigations, and in particular cross-sectional imaging, were on the whole unhelpful. This case illustrates that correct diagnosis in this complex case ultimately could only be made at the time of definitive surgery.
DOZ047.108: Utilizing dynamic CT imaging to map tissue regeneration in a porcine model of esophageal loss
Authors: Jensen T , Sharma I , Fodor W , Sundaram S , Roffidal T , Finck C
Published: June 2019

Esophageal atresia (EA) is a congenital defect in which the esophagus is not fully connected. Current treatments to bring together long gaps between the esophagus have very high complication rates and the replacement tissue does not possess the correct structure or physiologic properties. Tissue engineering and regenerative medicine have been suggested as a new patient-specific treatment for EA utilizing the patient's own cells and a tubular scaffold. Our group recently published on the successful regeneration of an esophagus using a retrievable scaffold seeded with amniotic derived MSCsFurther evaluation with dynamic computed tomography has suggested that the regenerative process entails ingrowth of native esophageal cells from both proximal and distal ends including robust vascular ingrowth. This confirms our gene expression findings and lends support to our hypothesis that the regenerative process is driven by vascular ingrowth. The role of the cells seeded on esophageal scaffolds and how this affects the regenerative process is the focus of current investigation with animal studies that are ongoing.
DOZ047.122: Inadequate response of atretic esophagus during acidic gastroesophageal reflux
Authors: Scaillon M , Cadranel S
Published: June 2019

Patients with atretic esophagus (OA) are candidates to severe gastroesophageal reflux. In a previous study, we observed that in OA operated children the complete transmission of contractions during the whole day and during acid reflux periods is poor compared to controls (C). Investigate the motor response of OA during periods of meal (M) and periods of acid reflux (GOR) in OA patients.

Methods

Prolonged monitoring of esophageal motor function recorded with three sensors: P1 above and P2, P3 below the suture, combined with pH-metry between P2 and P3. Number/min and amplitude of contractions and transmissions between P1-2-3 or P2-3 are compared during total time, meal and reflux periods and between OA with or without GOR.

Population

13 operated patients (OA) mean age 7.75 years and 10 controls (C).

Results

Contractions/min in OA at P1 M = 1.4 SD 1.2 versus GOR = 0.8 SD 1.1: P < 0.05 at P2 M = 2.0 SD 1.4 versus GOR = 1.4 SD1.4: P < 0.05 at P3 M = 2.2 SD 1.3 versus GOR = 1.5 SD1.4: P < 0.05 Complete transmission (P1-2-3) in OA during M compared with total time (T) is increased (29 vs. 32%: P < 0.5), but not during GOR (29 vs. 28%: NS). No difference in distal transmission (P2-3) between C and OA during M (68.8 vs. 63.2) but difference during GOR (69.8 vs. 43 P < 0.01). Contractions/min are not different during M between 7/13 patients with normal (OAN) and 6/13 with abnormal (OAR) reflux index but differ during GOR: P2 OAN = 2.1 vs. P2 OAR = 0.6, P < 0.01; P3 OAN = 2.2 vs. OAR = 0.6, P < 0.05. Complete transmission (P1-2-3) in OAN is not different during M or GOR but different in OAR (M: 74.2 SD 33.5 vs. GOR 54.7 SD 30.5: P < 0.005); distal transmission (P2-3) is not different between OAN and OAR during M and RGO periods.

Conclusion

Esophageal motility remains impaired in the operated OA. GOR stimulations produce weaker responses than meals. In OAR alterations of response to GOR are more important in terms of decreased number of distal contractions and total transmission suggesting a motility disorder but also an altered sensitivity reducing primary peristaltic response to reflux.
DOZ047.17: Characterization of esophageal motility in children with operated esophageal atresia using high-resolution impedance manometry and pressure flow analysis
Authors: Courbette O , Omari T , Aspirot A , Faure C
Published: June 2019

Background

Esophageal dysmotility is common in patients with esophageal atresia (EA). High-resolution impedance manometry (HRIM) and pressure flow analysis (PFA) allow characterization of biomechanical bolus flow and swallow properties. The aim of this study was to characterize esophageal motility and bolus flow propulsion in children who underwent surgical EA repair.

Patients and Methods

HRIM was used in 14 children with EA (type C, n = 13; type A, n = 1). Study was performed at a median (range) age of 11 years (5–17). The HRIM recordings were analyzed using conventional esophageal pressure topography and PFA (AIMplot software deployed via the open access Swallow Gateway application) and were compared with 13 patient controls (median age 14 years, range 5.75–17; P = NS vs patients) who underwent HRIM considered as normal according to Chicago classification and for whom the manometry results did not lead to treatment changes. Medical charts were reviewed for medical/surgical history and symptoms were assessed by standardized questionnaires.

Results

Esophageal peristaltic motor patterns were abnormal in all EA patients and were subdivided in two groups: Group A with presence of distal contraction in ≥ 50% of the swallows (n = 6) and Group B with presence of distal contractions in < 50% of the swallows (n = 8). IRP4s was similar in EA and controls. Bolus transport was impaired as shown by the higher impedance ratio (IR) in EA than in controls (0.47 vs 0.22, P < 0.001). In Group A, proximal and distal contractile integrals were lower than in controls (P < 0.001) and distal contractile velocity was shorter in EA (P < 0.01). IR was lower in Group A than in Group B (P < 0.01). In this sample, symptoms of dysphagia and presence of gastric metaplasia or esophagitis were not correlated with any of the measures determined.

Conclusions

Bolus transport as measured by impedance ratio is severely altered in EA patients but is not predictive of symptoms. The presence of residual distal contractions is associated with a more efficient bolus propulsion. Whether this is associated with a better outcome warrants further studies.
DOZ047.18: Diagnosing reflux aspiration in esophageal atresia: role of microbiome and pepsin
Authors: Krishnan U , Singh H , Kaakoush N , Leach S
Published: June 2019

Background

Children with esophageal atresia (EA) often suffer from gastroesophageal reflux disease (GERD) and it's complications, including reflux aspiration. Reflux aspiration can be difficult to diagnose in these patients who often have other causes for their respiratory symptoms. Tracheal pepsin has been studied as a marker of reflux aspiration in other conditions but not in EA. The role of the airway microbiome in the diagnosis of reflux aspiration has not been studied previously.

Aims

The aim of this study was to examine the composition of the airway (tracheal aspirate) microbiome of EA patients and correlate the results of the microbial analysis with the presence of gastric pepsin in the airways as a marker of reflux aspiration.

Methods

A cohort of children with EA was prospectively recruited at Sydney Children's Hospital in 2018. The EA group were subdivided into children with GERD, eosinophilic esophagitis (EoE), and those with no disease. Tracheal aspirates were collected. The bacterial component (16S rRNA gene) of the microbiome was amplified. Pepsin was assayed using a monoclonal antibody specific for pepsin A by the ELISA technique.

Results

There were 26 EA patients. The mean age was 6.96 years (0.7–18) and 15 (58%) were female. Eighteen (69%) children were on proton pump inhibitors for GERD and 8 (30%) were on swallowed steroids for EoE. GERD, defined as reflux esophagitis on biopsy and/or abnormal result on pH/impedance testing, was present in 7 (27%) and EoE defined as >15 eosinophils/HPF was seen in 5 (19%) children. Tracheal pepsin was detected in a significant proportion of EA patients and correlation between the pepsin results and the airway microbial analysis was seen in some of the EA patients who were pepsin positive.

Conclusions

This study is the first to examine the role of the microbiome and pepsin in tracheal aspirates as markers of reflux aspiration in children with EA. These results require validation in larger cohorts.
DOZ047.42: The value of rigid tracheobronchoscopy for the diagnosis of tracheomalacia in esophageal atresia patients
Authors: Aanen I P , Pullens B , van Rosmalen J , Wijnen R M H
Published: June 2019

Aim of the Study

The aim of this study is to evaluate routine airway endoscopy prior to the closure of the trachea-esophageal fistula (TOF) and esophageal atresia (EA) repair in a tertiary medical center concerning pre- and postoperative tracheomalacia.

Methods

We evaluated all patients with EA born between 2013 and 2016 who underwent routine rigid tracheobronchoscopy (TBS) before primary repair of the EA at our center. Inclusion criteria included peroperative rigid TBS performed by an otolaryngologist. Exclusion criteria included impossibility to determine pre- and or postoperative TM (because of logistic or medical reasons). Demographic data, comorbidities, surgical intervention, TBS findings, and subsequent surgical management were analyzed.

Main Results

Twenty-four patients with EA were included in this study. Eight of the 24 patients developed postoperative TM. Of these 8 patients with TM, 5 were diagnosed at the preoperative TBS (62.5%). Of the 16 patients without postoperative TM, there were 6 patients (37.5%) with peroperative diagnosed TM. So the sensitivity and specificity of routine airway endoscopy prior to EA-repair are, respectively, 62.5% (CI 30.4%–86.5%) and 62.5% (CI 38.5%–81.6%).

Concerning postoperative TM, there is a significant higher appearance in females versus males (P-value 0.021). There was no significant causality between mean gestational age, birth weight, type of EA, type of surgery (open or thoracoscopic), presence of gastroesophageal reflux disease, and the appearance of postoperative TM.

Conclusions

Preoperative TBS can be useful for the evaluation of tracheoesophageal fistula but has a low sensitivity and specificity to detect postoperative TM.
DOZ047.44: Coblation supraglottoplasty for symptomatic laryngomalacia
Authors: Saravanamuthu T , Tajne N , Tarnoom S , Kamakoti K
Published: June 2019

Background

Laryngomalacia is the commonest cause of congenital laryngeal stridor and supraglottoplasty is the mainstay of surgical treatment for symptomatic laryngomalacia. A variety of techniques used for ablating redundant tissue in the supraglottis. Novel supraglottoplasty surgical technique is needed to achieve better safety and efficacy. The purpose of this study is to evaluate the outcome and effectiveness of supraglottoplasty.

Methods

A total of 71 patients with laryngomalacia were studied retrospectively. Of 20 patients with symptomatic laryngomalacia underwent supraglottoplasty and 48 patients were treated conservatively. Two patients refused surgical management. Of 80% underwent successive apnea technique, rest under ETGA. The number of patients who underwent supraglottoplasty technique 14 was of coblation, 3 were of cold steel, 1 was of coagulation, 1 was of laser, and 1 was of microdebrider. The patients were kept under observation in intensive care unit (ICU) from 1 to 3 days then in step downward for 3 to 5 days. No child was intubated in the postoperative period. The patient's demographic information, symptoms, comorbidities, type of laryngomalacia, synchronous airway lesions, and final outcomes were examined.

Results

The common indications for surgery were feeding problems and failure to thrive along with inspiratory stridor. Most common type of laryngomalacia was type 2 (71%). Good weight gain happened for 18 patients, one patient had to be continued on gastrostomy feeding, one patient did not gain weight. Majority of the patients continued to have some amount of noisy breathing and eventually settled in 3 months postoperatively. No perioperative deaths and no long-term complications occurred, 2 patients were readmitted for increasing stridor and treated with nebulizations and improved.

Conclusions

Supraglottoplasty is an effective and safe treatment for symptomatic laryngomalacia and has the potential to provide better breathing and feeding outcomes. Among all the techniques, in our retrospective study, we found that successive apnea technique and coblator ablation is safe and effective methods in supraglottoplasty because it gives good exposure of supraglottis, no concern of airway fire, less collateral damage. The advantage is easy instrumentation with single wand for ablation, coagulation, and aspiration. Multicenter cooperative studies of comparison between coblator and conventional approaches would lend further evidence-based support for this surgical method.
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

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

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

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

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

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

Background

Pregnancy 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 summary

We 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.

Discussion

All 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

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.
NADPH Oxidase Is Crucial for the Cellular Redox Homeostasis in Fungal Pathogen Botrytis cinerea
Authors: Li Hua , Tian Shiping , Qin Guozheng
Published: June 2019

During interactions, both plants and pathogens produce reactive oxygen species (ROS). Plants generate ROS for defense induction, while pathogens synthesize ROS for growth, sporulation, and virulence. NADPH oxidase (NOX) complex in the plasma membrane represents a main protein complex for ROS production in pathogens. Although NOX plays a crucial role in pathogenicity of pathogens, the underlying molecular mechanisms of NOX, especially the proteins regulated by NOX, remain largely unknown. Here, we applied an iodoacetyl tandem mass tag-based redox proteomic assay to investigate the protein redox dynamics in deletion mutant of bcnoxR, which encodes a regulatory subunit of NOX in the fungal pathogen Botrytis cinerea. In total, 214 unique peptidyl cysteine (Cys) thiols from 168 proteins were identified and quantified in both the wild type and ∆bcnoxR mutant. The Cys thiols in the ∆bcnoxR mutant were generally more oxidized than those in the wild type, suggesting that BcNoxR is essential for maintaining the equilibrium of the redox state in B. cinerea. Site-specific thiol oxidation analysis indicated that 142 peptides containing the oxidized thiols changed abundance significantly in the ∆bcnoxR mutant. Proteins containing these differential peptides are classified into various functional categories. Functional analysis revealed that one of these proteins, 6-phosphate dehydrogenase, played roles in oxidative stress response and pathogenesis of B. cinerea. These results provide insight into the potential target proteins and the ROS signal transduction pathway regulated by NOX.
Rapid Detection of Alternaria Species Involved in Pear Black Spot Using Loop-Mediated Isothermal Amplification
Authors: Yang Xue , Qi Yong-Jie , Al-Attala Mohamed N. , Gao Zheng-Hui , Yi Xing-Kai , Zhang Ai-Fang , Zang Hao-Yu , Gu Chun-Yan , Gao Tong-Chun , Chen Yu
Published: June 2019

Alternaria species are the most important fungal pathogens that attack various crops as well as fruit trees such as pear and cause black spot disease. Here, a loop-mediated isothermal amplification (LAMP) assay is developed for the detection of Alternaria species. A. alternata cytochrome b (cyt-b) gene was used to design two pairs of primers and amplified a 229-bp segment of Aacyt-b gene. The results showed that LAMP assay is faster and simpler than polymerase chain reaction (PCR). LAMP assay is highly sensitive method for the detection of about 1 pg of genomic DNA of A. alternata by using optimized concentration of MgCl2 (4 mM) in final LAMP reaction. In contrast, the limit of detection was 1 ng of target DNA via conventional PCR. Among the genomic DNA of 46 fungal species, only the tubes containing DNA of Alternaria spp. except A. porri, A. solani, and A. infectoria changed color from orange to yellowish green with SYBR Green I including the main pathogens of pear black spot. The yellowish green color was indicative of DNA amplification. Moreover, LAMP assay was used for testing infected tissues among 22 healthy and diseased pear tissues; the orange color changed to yellowish green for infected tissues only. Altogether, we conclude that cyt-b gene can be used for the detection of Alternaria spp. via LAMP assay, which is involved in pear black spot disease.
A Negative Binomial Regression Model of the Observed Population Density of Heterodera glycines after Annual Corn Rotation in Nebraska
Authors: Pérez-Hernández Oscar , Giesler Loren J. , Hilbe Joseph M.
Published: June 2019

In Nebraska, rotation of soybean (Glycine max) fields to corn (Zea mays) is a major practice to manage the soybean cyst nematode (SCN; Heterodera glycines). However, factors associated with SCN population density decline during corn rotation are not clearly defined. This study addresses that question using a modeling approach. Seventy-nine fields were sampled in 2009, 2010, and 2011 to determine SCN population densities (eggs/100 cm3 of soil) before and after rotation. After rigorous field screening and model testing and validation, the regression model [Formula: see text] was developed, where Log Pf is the natural log of SCN eggs at the end of the rotation year, Pi is the population density before rotation, and pH is the soil pH. Model goodness-of-fit was assessed through residual analysis, information criteria, and other remedial measures. Model overdispersion was 1.04. Validation in a 50 and a 75% random sample from the original data set showed little change in model regression coefficients, standard errors, and associated significance, confirming model fit and performance. The model indicates that for one-unit increase in soil pH, SCN Pf is expected to increase by 53.7% at constant Pi, and correspondingly, a 10% change in Pi will result in about 8.3% change in Pf at constant soil pH. The model suggested that SCN population levels before corn rotation and soil pH are major determinants of observed SCN population density reduction after annual corn rotation in Nebraska. This model has potential for use in SCN risk analysis and in predicting SCN population decline after corn rotation in the state.
Relating Peanut Rx Risk Factors to Epidemics of Early and Late Leaf Spot of Peanut
Authors: Fulmer Abraham M. , Mehra Lucky K. , Kemerait Robert C. , Brenneman Timothy B. , Culbreath Albert K. , Stevenson Katherine L. , Cantonwine Emily G.
Published: June 2019

Previous research has demonstrated the efficacy of prescription fungicide programs, based upon Peanut Rx, to reduce combined effects of early leaf spot (ELS), caused by Passalora arachidicola (Cercospora arachidicola), and late leaf spot (LLS), caused by Nothopassalora personata (syn. Cercosporidium personatum), but the potential of Peanut Rx to predict each disease has never been formally evaluated. From 2010 to 2016, non-fungicide-treated peanut plots in Georgia and Florida were sampled to monitor the development of ELS and LLS. This resulted in 168 cases (unique combinations of Peanut Rx risk factors) with associated total leaf spot risk points ranging from 40 to 100. Defoliation ranged from 13.9 to 100%, and increased significantly with increasing total risk points (conditional R2 = 0.56; P < 0.001). Leaf spot onset (time in days after planting [DAP] when either leaf spot reached 1% lesion incidence), ELS onset, and LLS onset ranged from 29 to 140, 29 to 142, and 50 to 143 DAP, respectively, and decreased significantly with increasing risk points. Standardized AUDPC of ELS was significantly affected by risk points (conditional R2 = 0.53, P < 0.001), but not for LLS. After removing redundant Peanut Rx factors, planting date, rotation, historical leaf spot prevalence, cultivar, and field history were used as fixed effects in mixed effect regression models to evaluate their contribution to leaf spot, ELS or LLS prediction. Results from mixed effects regression confirmed that the selected Peanut Rx risk factors contributed to the variability of at least one measurement of development of combined or separate epidemics of ELS and LLS, but not all factors affected ELS and LLS equally. Historical leaf spot prevalence, a new potential preplant risk factor, was a consistent predictor of the dominant disease(s) observed in the field. Results presented here demonstrate that Peanut Rx is a very effective tool for predicting leaf spot onset regardless of which leaf spot is predominant, but also suggest that associated risk does not reflect the same development for each disease. These data will be useful for refining thresholds for differentiating high, moderate, and low risk fields, and reevaluating the timing of fungicide applications in reduced input programs with respect to disease onset.
Assessment of Factors Associated with Molecular Quantification of Stubby Root Nematode Paratrichodorus allius from Field Soil DNA
Authors: Huang Danqiong , Yan Guiping , Gudmestad Neil C. , Whitworth Jonathan
Published: June 2019

Factors relating to SYBR Green-based quantitative real-time PCR (qPCR) quantification of stubby root nematode Paratrichodorus allius using soil DNA were evaluated in this study. Soils used were loamy sand from potato fields in North Dakota and Idaho. Results showed that the largest nematode individuals (body length >720 µm) produced significant lower Cq values than the smallest individuals (<359 µm), indicating more total DNA amount in the largest nematodes. Soil pre-treatments showed that autoclaved field soil had significantly reduced DNA amount and quality. The air- or oven-dried soil yielded a lower amount of DNA with similar purity, compared with natural field soil. PCR inhibitors were detected in soil DNA substrates targeting pBluescript II SK(+)-plasmid DNA. Al(NH4)(SO4)2 treatment during DNA preparation significantly reduced the inhibitors compared with post-treatment of soil DNA with polyvinylpolypyrrolidone column. The effect of PCR inhibitors on qPCR was suppressed by bovine serum albumin. Quantification results did not significantly change when increasing the number of DNA extractions from three to six per soil sample when soil grinding and grid sampling strategies were used. Two standard curves, generated from serial dilutions of plasmid DNA containing P. allius ITS1 rDNA and soil DNA containing known nematode numbers, produced similar correlations between Cq values and amount of targets. The targets in soil DNA quantified by qPCR using either standard curve correlated well with microscopic observations using both artificially and naturally infested field soils. This is the first study for assessing various factors that may affect qPCR quantification of stubby root nematodes. Results will be useful during the setup or optimization of qPCR-based quantification of plant-parasitic nematodes from soil DNA.
The effect of bioRxiv preprints on citations and altmetrics
Authors: Fraser Nicholas , Momeni Fakhri , Mayr Philipp , Peters Isabella
Published: June 2019

1.

A 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

Most 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 Statement

Mutations 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

Protein 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.
Genetic screens in isogenic mammalian cell lines without single cell cloning
Authors: DeWeirdt Peter C , Sanson Kendall R , Hanna Ruth E , Hegde Mudra , Sangree Annabel K , Strand Christine , Persky Nicole S , Doench John G
Published: June 2019

Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs for mammalian cells, however, is labor-intensive, time-consuming, and impossible in some cell types. Here we present an approach to create isogenic pairs of cells and screen them with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. We queried the anti-apoptotic genes BCL2L1 and MCL1, and the DNA damage repair gene PARP1, via 25 genome-wide screens across 4 cell lines. For all three genes, we identify a rich set of both expected and novel buffering and synthetic lethal interactions. Further, we compare the interactions observed in genetic space to those found when targeting these genes with small molecules and identify hits that may inform the clinical uses for these inhibitors. We anticipate that this methodology will be broadly useful to comprehensively study genes of interest across many cell types.
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

With 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.