bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radio-sensitivity testing.
Authors: Nur F. , Forster B. P. , Osei S. A. , Amiteye S. , Ciomas J. , Hoeman S. , Jankuloski L. 
Published: September 2018

Abstract

Before physical mutagenesis can be applied for plant breeding purposes, the optimum irradiation dose needs to be determined. This is done using a radio-sensitivity test in which a range of dose treatments are applied to the target material. After irradiation treatments, the materials are grown out and recordings made for growth reduction (RD) and survival (LD). Normally, values of RD30-60 or LD30-60 are selected. Here, the target materials for radio-sensitivity testing are germinated seed.
Services in irradiation treatments.
Authors: Nur F. , Forster B. P. , Osei S. A. , Amiteye S. , Ciomas J. , Hoeman S. , Jankuloski L. 
Published: September 2018

Abstract

Physical mutagens, particularly gamma and X-rays, are well established in plant mutation breeding. Although gamma irradiation has been predominant, it involves the use of radioactive isotopes and requires specialist facilities (gamma cells, gamma houses and gamma fields). X-ray machines are more abundant and easier to use, and so are becoming more popular as they do not involve radioactive isotopes and therefore are not governed by the same stringent regulations as gamma emitters. A brief description and comparison of gamma and X-ray irradiation is given. Physical irradiation services are available at the international, regional and national levels. Other non-physical mutagens are discussed in relation to plant breeding and functional genomics.
FA02.02: TWENTY-FIVE YEARS OF LAPAROSCOPIC TREATMENT FOR ESOPHAGEAL ACHALASIA: OUR EXPERIENCE ON 1000 LAPAROSCOPIC HELLER-DOR OPERATIONS
Authors: Costantini Mario , Salvador Renato , Capovilla Giovanni , Costantini Andrea , Perazzolo Anna , Briscolini Dario , Nicoletti Loredana , Valmasoni Michele , Merigliano Stefano 
Published: September 2018

Abstract

Background
In the past decades, Laparoscopic Heller-Dor (LHD) progressively became the treatment of choice for esophageal achalasia. Aim of this study was to assess our 25-year experience with LHD at a single high-volume institution.

Methods
1000 patients underwent LHD from 1992–2017 by 6 staff surgeons. Patients who had already been treated with surgical or endoscopic myotomy were ruled out. Symptoms were scored using a detailed questionnaire; barium swallow, endoscopy, manometry (conventional or High Resolution) were performed, before and after surgery, while 24-hour pH monitoring was performed 6 months after surgery. Treatment failure was defined as a postoperative symptom score >10th percentile of the preoperative score (i.e. >8).

Results
LHD was performed on 1000 patients (M: F = 536:464); the median age was 46 (IQR 36–54), 183 (18.3%) had a history of endoscopic treatments (pneumatic dilation or botox injections, or both). The surgical procedure was completed laparoscopically in all but 7 patients (0.7%) and there was one perioperative death for heart attack. There were 25 perforations (2.5%): 22 were recognized and repaired during the operation, 3 were detected by postoperative contrast swallow. In 674 patients the manometric pattern was classified as follows: 310 (46%) pattern I, 315 (46.7%) pattern II and 49 (7.3%) pattern III. The outcome was positive in 902 patients (90.2%). In patients who had a previous treatment the failures were 25/183 (13.7%) while in the primary treatment group the failures were 73/817 (8.9%) (P = 0.055). All the 98 patients whose LHD failed underwent one or more pneumatic dilations, which ameliorated their symptoms in all but 11 patients (10 required reoperation). The overall success rate of combined LHD and dilations was 98.4%. At univariate analysis, manometric pattern (P = 0.001), absent sigmoid megaesophagus (P = 0.003) and chest pain score (P = 0.002) were the only factors predictive of the result. At multivariate analysis, these three factors were independently associated with good outcome. Postoperative 24-hour pH was abnormal in 50/590 patients (8.5%). Two patients developed an esophageal cancer during follow-up.

Conclusion
In a university tertiary referral center, LHD relieves achalasia symptoms durably. The preoperative manometric pattern, the absence of a sigmoid esophagus and the chest pain score represent the strongest predictors of outcome.

Disclosure
All authors have declared no conflicts of interest.
FA02.04: LONG—TERM RESULTS OF PERORAL ENDOSCOPIC MYOTOMY (POEM) FOR ACHALASIA
Authors: Rabekova Zuzana , Vackova Zuzana , Lanska Vera , Spicak Julius , Stirand Petr , Hucl Tomas , Kieslichova Eva , Martinek Jan 
Published: September 2018

Abstract

Background
POEM has gained trust by proved safety and short-term efficacy and at present, it is considered as a standard and safe method for treatment of achalasia. The aim of this prospective single-center case series was to assess the long-term efficacy of POEM with emphasis on post-POEM reflux and to summarize adverse events.

Methods
Since 2012 until 10/2017, a total of 223 achalatic patients underwent 233 POEMs. Follow-up visits at 3, 12, 24 and 36M were completed in 194, 144, 80 and 44 patients. Upper GI endoscopy, HRM and 24-hour pH metry were performed 3M after POEM; endoscopy was then repeated between 24–36M. Main outcomes were treatment success (Eckardt score <3), recurrence rate, post-POEM reflux and adverse events.

Results
At 3, 12, 24 and 36 months, treatment success was achieved in 97% (CI 95%; 95–100), 99% (97–100), 94% (88–100) and 93% (86–100) of patients. A total of 15 patients experienced treatment failure (n = 5) or recurrence (n = 10). The recurrences occurred most often in patients with achalasia type I (4 out of 35, 11.4%) followed by type II (5 out of 144; 3.5%) vs. none in type III (0 out of 21.0%); P = 0.022. At 3 months, reflux esophagitis was diagnosed in 68/194 patients. Abnormal acid exposure was detected in 68/194 (39.7%) patients. At 24–36 months reflux esophagitis was present in 15 from 51 patients (29%). The most common adverse event was capnoperitoneum with necessity of a puncture (57.6%), subcutaneous emphysema (36.6%). A total of 3 severe adverse events occured: 2 patients required a prolonged hospitalization due to fluido- and pneumofluidothorax. One patient (67 years) experienced electromechanical dissociation with fatal cardiac arrest during the procedure, the resuscitation was not successful. The autopsy revealed severe coronary disease and pulmonary hypertension (unrecognized prior to POEM), these conditions were considered likely to be the cause of the death.

Conclusion
POEM is effective treatment modality for achalasia with treatment success of 94% at 2 and 3 years. Reflux esophagitis and abnormal acid exposure are diagnosed in almost 40% of patients; reflux is successfully manageable with PPI. Eventhough POEM is considered a safe procedure, severe (fatal) adverse events may occur.

Disclosure
All authors have declared no conflicts of interest.
FA02.08: LONG FOLLOW UP OF BARRETT’S TREATMENT, CLINICAL OR SURGICAL TREATMENT, WHICH ONE BRING BETTER RESULTS TO BARRETT’S EPITHELIUM?
Authors: Szachnowicz Sergio , Duarte Andre , Bianchi Edno , Nasi Ary , Mariano Rocha Julio , Seguro Franscisco , Freitas Natalia , Sallum Rubens , Cecconello Ivan 
Published: September 2018

Abstract

Background
Background: Barrett’ s esophagus is a complication of severe gastroesophageal reflux disease. The major concern aspect is its association to dysplasia and esophageal adenocarcinoma. Endoscopic surveillance of patients treated surgically or clinically allows early detection of cancer. Aim: Compare clinical and surgical treatment of Barrett's esophagus.

Methods
Methods: from January 1980 to December 2017, 565 patients with Barrett's esophagus were followed up at our service. 214 were submitted to Nissen fundoplication and 221 to clinical treatment with PPI. These 434 patients were submitted to a long follow up with routine endoscopic examination each 2 years with multiple biopsies. The statistical analysis was performed through Fisher's exact test and Propensity score regarding epidemiologic and epithelium data.

Results
Comparing the surgical group (Group A) and the clinical group (Group B), we could observe the development of 11 Adenocarcinoma, 3 in the group A e 8 in group B. Any grade of dysplasia was observed in 9 patients of the group B, and six of them developed adenocarcinoma. The clinical group showed a tendency to develop more adenocarcioma and dysplasia than the surgical group (P = 0.38) and statistically significant increase in the development of dysplasia (P = 0032). 16% of patients in Group A showed progression in Columnar epithelium length against 20% in Group B (ns). 23,4% of the patients in group A keep symptoms and use of PPI, and 28.7 in group B (ns).

Conclusion
In our series as in many recent data in international literature, the surgical treatment for GERd in patients with Barrett's esophagus seems to be a good option to keep the columnar epithelium without progression to dysplasia or adenocarcinoma, with good control of the symptoms and the length of the Barrett's esophagus.

Disclosure
All authors have declared no conflicts of interest.
Writing a Clinical Research Question
Authors: Ravindra Vijay M , Kestle John R W 
Published: September 2018

Abstract
The bar for clinical research in surgical subspecialties has been rising over the past 10 yr. It is now essential that neurosurgeons are familiar with the principles of evidence-based medicine to evaluate and conduct sound clinical research. In this review, we highlight the importance of formulating a good research question, which serves as the foundation for meaningful investigation.
Entities of Chronic and Granulomatous Invasive Fungal Rhinosinusitis: Separate or Not?
Authors: Zhou Ling-Hong , Wang Xuan , Wang Rui-Ying , Zhao Hua-Zhen , Jiang Ying-Kui , Cheng Jia-Hui , Huang Li-Ping , Chen Zhong-Qing , Wang De-Hui , Zhu Li-Ping 
Published: September 2018

AbstractBackgroundChronic and granulomatous invasive fungal rhinosinusitis are important causes of blindness and craniocerebral complications. However, the classification of these 2 diseases remains controversial.MethodsWe retrospectively analyzed patients with chronic and granulomatous invasive fungal rhinosinusitus in a Chinese tertiary hospital from 2009 to 2017, with a focus on classification and comparisons.ResultsAmong 55 patients enrolled in our study, 11 (11/55, 20%) had granulomatous invasive fungal rhinosinusitis (GIFRS) and 44 (44/55, 80%) had chronic invasive fungal rhinosinusitis (CIFRS). Aspergillus fumigatus and Dematiaceous hyphomycetes were identified in 2 patients with GIFRS. Compared with granulomatous type, CIFRS was more frequently encountered in immunocompromised patients (P = .022), and the time from onset to diagnosis was much shorter (P = .001). Proptosis and orbital apex syndrome showed no significant difference between granulomatous and CIFRS in our study. The treatment options and prognosis of both diseases also showed no significant difference.ConclusionsDespite the consensus on histopathology, the classification of the chronic and granulomatous types may need further evaluation in clinical considerations.
Using a Positive Deviance Approach to Influence the Culture of Patient Safety Related to Infection Prevention
Authors: Sreeramoju Pranavi , Dura Lucia , Fernandez Maria E , Minhajuddin Abu , Simacek Kristina , Fomby Thomas B , Doebbeling Bradley N 
Published: September 2018

Abstract

Background
Health care–associated infections (HAIs) are a socio-technical problem. We evaluated the impact of a social change intervention on health care personnel (HCP), called “positive deviance” (PD), on patient safety culture related to infection prevention among HCP.

Methods
This observational study was done in 6 medical wards at an 800-bed public academic hospital in the United States. Three of these wards were randomly assigned to receive PD intervention on HCP. After a retrospective 6-month baseline period, PD was implemented over 9 months, followed by 9 months of follow-up. Patient safety culture and social networks among HCP were surveyed at 6, 15, and 24 months. Rates of HAI were measured among patients.

Results
The measured patient safety culture was steady over time at 69% aggregate percent positive responses in wards with PD vs decline from 79% to 75% in wards without PD (F statistic 10.55; P = .005). Social network maps suggested that nurses, charge nurses, medical assistants, ward managers, and ward clerks play a key role in preventing infections. Fitted time series of monthly HAI rates showed a decrease from 4.8 to 2.8 per 1000 patient-days (95% confidence interval [CI], 2.1 to 3.5) in wards without PD, and 5.0 to 2.1 per 1000 patient-days (95% CI, –0.4 to 4.5) in wards with PD.

Conclusions
A positive deviance approach appeared to have a significant impact on patient safety culture among HCP who received the intervention. Social network analysis identified HCP who are likely to help disseminate infection prevention information. Systemwide interventions independent of PD resulted in HAI reduction in both intervention and control wards.
A comprehensive analysis of RNA sequences reveals macroscopic somatic clonal expansion across normal tissues
Authors: Yizhak Keren , Aguet Francois , Kim Jaegil , Hess Julian , Kubler Kirsten , Grimsby Jonna , Frazer Ruslana , Zhang Hailei , Haradhvala Nicholas J. , Rosebrock Daniel , Livitz Dimitri , Li Xiao , Landkof Eila-Arich , Shoresh Noam , Stewart Chip , Segre Ayelet , Branton Philip A. , Polak Paz , Ardlie Kristin , Getz Gad 
Published: September 2018

AbstractCancer genome studies have significantly advanced our knowledge of somatic mutations. However, how these mutations accumulate in normal cells and whether they promote pre-cancerous lesions remains poorly understood. Here we perform a comprehensive analysis of normal tissues by utilizing RNA sequencing data from ∼6,700 samples across 29 normal tissues collected as part of the Genotype-Tissue Expression (GTEx) project. We identify somatic mutations using a newly developed pipeline, RNA-MuTect, for calling somatic mutations directly from RNA-seq samples and their matched-normal DNA. When applied to the GTEx dataset, we detect multiple variants across different tissues and find that mutation burden is associated with both the age of the individual and tissue proliferation rate. We also detect hotspot cancer mutations that share tissue specificity with their matched cancer type. This study is the first to analyze a large number of samples across multiple normal tissues, identifying clones with genomic aberrations observed in cancer.
TheC. elegansSMOC-1 protein acts cell non-autonomously to promote bone morphogenetic protein signaling
Authors: DeGroot Melisa S. , Shi Herong , Eastman Alice , McKillop Alexandra N. , Liu Jun 
Published: September 2018

ABSTRACTBone morphogenetic protein (BMP) signaling regulates many different developmental and homeostatic processes in metazoans. The BMP pathway is conserved inCaenorhabditis elegans, and is known to regulate body size and mesoderm development. We have identified theC. elegans smoc-1(Secreted MOdular Calcium binding protein-1) gene as a new player in the BMP pathway.smoc-1(0)null mutants have a small body size, while overexpression ofsmoc-1led to a long body size and increased expression of the RAD-SMAD BMP reporter, suggesting that SMOC-1 acts as a positive modulator of BMP signaling. Using double mutant analysis, we showed that SMOC-1 antagonizes the function of the glypican LON-2 and acts through the BMP ligand DBL-1 to regulate BMP signaling. Moreover, SMOC-1 appears to specifically regulate BMP signaling without significant involvement in a TGFβ-like pathway that regulates dauer development. We found thatsmoc-1is expressed in multiple tissues, including cells of the pharynx, intestine, and posterior hypodermis, and that the expression ofsmoc-1in the intestine is positively regulated by BMP signaling. We further established that SMOC-1 functions cell non-autonomously to regulate body size. Human SMOC1 and SMOC2 can each partially rescue thesmoc-1(0)mutant phenotype, suggesting that SMOC-1’s function in modulating BMP signaling is evolutionarily conserved. Together, our findings highlight a conserved role of SMOC proteins in modulating BMP signaling in metazoans.ARTICLE SUMMARYBMP signaling is critical for development and homeostasis in metazoans, and is under tight regulation. We report the identification and characterization of a Secreted MOdular Calcium binding protein SMOC-1 as a positive modulator of BMP signaling inC. elegans. We established that SMOC-1 antagonizes the function of LON-2/glypican and acts through the DBL-1/BMP ligand to promote BMP signaling. We identifiedsmoc-1-expressing cells, and demonstrated that SMOC-1 acts cell non-autonomously and in a positive feedback loop to regulate BMP signaling. We also provide evidence suggesting that the function of SMOC proteins in the BMP pathway is conserved from worms to humans.
CRISPRpic: Fast and precise analysis for CRISPR-induced mutations via prefixed index counting
Authors: Cho Seung Woo , Lee HoJoon , Chang Howard Y. , Ji Hanlee P. 
Published: September 2018

AbstractAnalysis of CRISPR-induced mutations at targeted loci can be achieved by PCR amplification followed by massively parallel sequencing. We developed a novel algorithm, called CRISPRpic, to analyze sequencing reads from CRISPR experiments via counting exact-matches and pattern-searching. Compared to other methods that are based on sequence alignment, CRISPRpic provides precise mutation calling and ultrafast analysis of sequencing results. The Python script for CRISPRpic is available at https://github.com/compbio/CRISPRpic.
Cell density-dependent ferroptosis in breast cancer is induced by accumulation of polyunsaturated fatty acid-enriched triacylglycerides
Authors: Panzilius Elena , Holstein Felix , Dehairs Jonas , Planque Mélanie , von Toerne Christine , Koenig Ann-Christine , Doll Sebastian , Bannier-Hélaouët Marie , Ganz Hilary M. , Hauck Stefanie M. , Talebi Ali , Swinnen Johannes V. , Fendt Sarah-Maria , Angeli José P. Friedmann , Conrad Marcus , Scheel Christina H. 
Published: September 2018

AbstractFerroptosis is a regulated form of necrotic cell death caused by iron-dependent phospholipid peroxidation. It can be induced by inhibiting glutathione peroxidase 4 (GPX4), the key enzyme for efficiently reducing peroxides within phospholipid bilayers. Recent data suggest that cancer cells undergoing EMT (dedifferentiation) and those resistant to standard therapy expose a high vulnerability toward ferroptosis. Although recent studies have begun to identify and characterize the metabolic and genetic determinants underlying ferroptosis, many mechanisms that dictate ferroptosis sensitivity remain unknown. Here, we show that low cell density sensitizes primary mammary epithelial and breast cancer cells to ferroptosis induced by GPX4 inhibition, whereas high cell density confers resistance. These effects occur irrespective of oncogenic signaling, cellular phenotype and expression of the fatty acid ligase acyl-CoA synthetase long chain family member 4 (ACSL4). By contrast, we show that a massive accumulation of neutral triacylglycerides (TAG) enriched with polyunsaturated fatty acids (PUFA) is induced at low cell density. In addition, de novo lipogenesis and desaturation pathways were found to be reduced at low cell density, indicative of increased fatty acid uptake. Our study suggests that PUFA-mediated toxicity is limited by the enrichment in TAGs that in turn might pose a vulnerability towards ferroptosis. Conclusively, cell density regulates lipid metabolism of breast epithelial and cancer cells, which results in a ferroptosis-sensitive cell state with the potential to be exploited therapeutically during metastatic dissemination.
Plant leaf tooth feature extraction
Authors: Wang Hu , Tian Di , Li Chu , Tian Yan , Zhou Haoyu 
Published: September 2018

AbstractLeaf tooth can indicate several systematically informative features and is extremely useful for circumscribing fossil leaf taxa. Moreover, it can help discriminate species or even higher taxa accurately. Previous studies extract features that are not strictly defined in botany; therefore, a uniform standard to compare the accuracies of various feature extraction methods cannot be used. For efficient and automatic retrieval of plant leaves from a leaf database, in this study, we propose an image-based description and measurement of leaf teeth by referring to the leaf structure classification system in botany. First, image preprocessing is carried out to obtain a binary map of plant leaves. Then, corner detection based on the curvature scale-space (CSS) algorithm is used to extract the inflection point from the edges; next, the leaf tooth apex is extracted by screening the convex points; then, according to the definition of the leaf structure, the characteristics of the leaf teeth are described and measured in terms of number of orders of teeth, tooth spacing, number of teeth, sinus shape, and tooth shape. In this manner, data extracted from the algorithm can not only be used to classify plants, but also provide scientific and standardized data to understand the history of plant evolution. Finally, to verify the effectiveness of the extraction method, we use leaf tooth features and simple linear discriminant analysis to classify leaves; the results show that the proposed method achieves high accuracy as compared to other methods.
Development of mobile application through design-based research
Authors: Jayatilleke Buddhini Gayathri , Ranawaka Gaya R. , Wijesekera Chamali , Kumarasinha Malinda C.B. 
Published: September 2018

Purpose
The purpose of this paper is to illustrate the development and testing of an innovative mobile application using design-based research.

Design/methodology/approach
This paper reports on the process of transformation of existing printed course material into digitized content through design-based research where design, research and practice were concurrently applied through several iterations of the mobile application. For this transformation, one session each from BSc in Nursing, Bachelor of Pharmacy and Bachelor of Medical Laboratory Sciences was selected. In the first phase of the design-based research, the main research question was formulated. In the second phase, a mobile learning application (OUSL MLearn) was designed and developed to address the research question. In the third phase, this application was evaluated by five groups of stakeholders: content experts to validate the content; educational technologists to check the alignment of technical and pedagogical features; novice users to check the overall effectiveness of the application; developer to develop the application, to check the ease of usage; and researchers to identify the impact of this innovation. These stakeholders were closely involved throughout the whole process which lasted over a period of four months. At the end of this development phase, the results were reflected upon and used for further enrichment.

Findings
It was observed that the developed mobile application was accessible, appealing and pedagogically constructive for users. However, optimization, development time, technical and organizational issues, workload of academics and production costs were identified as major challenges.

Research limitations/implications
This study was based on the findings of a small sample of potential users.

Practical implications
The findings have implications for designing culturally adaptive interactive mobile applications.

Originality/value
This study will benefit practitioners to design culturally sensitive mobile learning courses and researchers to conduct design-based research.