bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-omics supervised autoencoder for pan-cancer clinical outcome endpoints prediction
Authors: Tan Kaiwen , Huang Weixian , Hu Jinlong , Dong Shoubin 
Published: July 2020

Abstract
Background
With the rapid development of sequencing technologies, collecting diverse types of cancer omics data become more cost-effective. Many computational methods attempted to represent and fuse multiple omics into a comprehensive view of cancer. However, different types of omics are related and heterogeneous. Most of the existing methods do not consider the difference between omics, so the biological knowledge of individual omics may not be fully excavated. And for a given task (e.g. predicting overall survival), these methods prefer to use sample similarity or domain knowledge to learn a more reasonable representation of omics, but it’s not enough.

Methods
For the purpose of learning more useful representation for individual omics and fusing them to improve the prediction ability, we proposed an autoencoder-based method named MOSAE (Multi-omics Supervised Autoencoder). In our method, a specific autoencoder were designed for each omics according to their size of dimension to generate omics-specific representations. Then, a supervised autoencoder was constructed based on specific autoencoder by using labels to enforce each specific autoencoder to learn both omics-specific and task-specific representations. Finally, representations of different omics that generate from supervised autoencoders were fused in a traditional but powerful way, and the fused representation was used for subsequent predictive tasks.

Results
We applied our method over TCGA Pan-Cancer dataset to predict four different clinical outcome endpoints (OS, PFI, DFI, and DSS). Compared with traditional and state-of-the-art methods, MOSAE achieved better predictive performance. We also tested the effects of each improvement, which all have a positive effect on predictive performance.

Conclusions
Predicting clinical outcome endpoints are very important for precision medicine and personalized medicine. And multi-omics fusion is an effective way to solve this problem. MOSAE is a powerful multi-omics fusion method, which can generate both omics-specific and task-specific representation for given endpoint predictive tasks and improve the predictive performance.
A machine learning framework for accurately recognizing circular RNAs for clinical decision-supporting
Authors: Wang Yidan , Zhang Xuanping , Wang Tao , Xing Jinchun , Wu Zhun , Li Wei , Wang Jiayin 
Published: July 2020

Abstract
Background
Circular RNAs (circRNAs) are those RNA molecules that lack the poly (A) tails, which present the closed-loop structure. Recent studies emphasized that some circRNAs imply different functions from canonical transcripts, and further associated with complex diseases. Several computational methods have been developed for detecting circRNAs from RNA-seq data. However, the existing methods prefer to high sensitivity strategies, which always introduce many false positives. Thus, in clinical decision-supporting system, a comprehensive filtering approach is needed for accurately recognizing real circRNAs for decision models.

Methods
In this paper, we first reviewed the detection strategies of the existing methods. According to the features from RNA-seq data, we showed that any single feature (data signal) selected by the existing strategies cannot accurately distinguish a circRNA. However, we found that some combinations of those features (data signals) could be used as signatures for recognizing circRNAs. To avoid the high computational complexity of the combinational optimization problem, we present CIRCPlus2, which adopts a machine learning framework to recognize real circRNAs according to multiple data signals captured from RNA-seq data. By comparing multiple machine learning frameworks, CIRCPlus2 adopts a Gradient Boosting Decision Tree (GBDT) framework.

Results
Given a set of candidate circRNAs, reported by any existing detection tool(s), the features of each candidate are extracted from the aligned reads. The GBDT framework can be trained by a training dataset. By applying the selected features on the framework, the predictions on true/false positives are reported. To verify the performance of the proposed approach, we conducted several groups of experiments on both real RNA-seq datasets and a series of simulation datasets with different preset configurations. The results demonstrated that CIRCPlus2 clearly improved the specificities, while it also maintained high levels of sensitivities.

Conclusions
Filtering false positives is quite important in RNA-seq data analysis pipeline. Machine learning framework is suitable for solving this filtering problem. CIRCPlus2 is an efficient approach to identify the false positive circRNAs from the real ones.
A benchmark dataset and case study for Chinese medical question intent classification
Authors: Chen Nan , Su Xiangdong , Liu Tongyang , Hao Qizhi , Wei Ming 
Published: July 2020

Abstract
Background
To provide satisfying answers, medical QA system has to understand the intentions of the users’ questions precisely. For medical intent classification, it requires high-quality datasets to train a deep-learning approach in a supervised way. Currently, there is no public dataset for Chinese medical intent classification, and the datasets of other fields are not applicable to the medical QA system. To solve this problem, we construct a Chinese medical intent dataset (CMID) using the questions from medical QA websites. On this basis, we compare four intent classification models on CMID using a case study.

Methods
The questions in CMID are obtained from several medical QA websites. The intent annotation standard is developed by the medical experts, which includes four types and 36 subtypes of users’ intents. Besides the intent label, CMID also provides two types of additional information, including word segmentation and named entity. We use the crowdsourcing way to annotate the intent information for each Chinese medical question. Word segmentation and named entities are obtained using the Jieba and a well-trained Lattice-LSTM model. We loaded a Chinese medical dictionary consisting of 530,000 for word segmentation to obtain a more accurate result. We also select four popular deep learning-based models and compare their performances of intent classification on CMID.

Results
The final CMID contains 12,000 Chinese medical questions and is organized in JSON format. Each question is labeled the intention, word segmentation, and named entity information. The information about question length, number of entities, and are also detailed analyzed. Among Fast Text, TextCNN, TextRNN, and TextGCN, Fast Text and TextCNN models have achieved the best results in four types and 36 subtypes intent classification, respectively.

Conclusions
In this work, we provide a dataset for Chinese medical intent classification, which can be used in medical QA and related fields. We performed an intent classification task on the CMID. In addition, we also did some analysis on the content of the dataset.
Magnetic compression anastomosis for non-anastomotic stenosis of the proximal jejunum after total gastrectomy with Roux-en-Y reconstruction: a case report
Authors: Kamada Teppei , Ohdaira Hironori , Takeuchi Hideyuki , Takahashi Junji , Marukuchi Rui , Suzuki Norihiko , Narihiro Satoshi , Hoshimoto Sojun , Yoshida Masashi , Yamanouchi Eigoro , Suzuki Yutaka 
Published: July 2020

Abstract
Background
Postoperative non-anastomotic stenosis of the proximal jejunum after total gastrectomy with Roux-en-Y reconstruction is a rare complication. If endoscopic balloon dilation proves ineffective, patients need re-operation under general anesthesia and experience a high rate of postoperative complications. Magnetic compression anastomosis is a nonsurgical procedure that can create an anastomosis similar to that obtained through surgery. We report a case in which magnetic compression anastomosis was successfully performed to avoid re-operation for non-anastomotic stenosis of the proximal jejunum after total gastrectomy with Roux-en-Y reconstruction.

Case presentation
A 70-year-old woman was admitted to our hospital for treatment of non-anastomotic stenosis of the proximal jejunum. Open total gastrectomy and Roux-en-Y reconstruction were performed 2 years previously for advanced gastric cancer at another hospital. She complained of anorexia and obstructed passage of food. No recurrence of gastric cancer was identified. Esophagogastroduodenoscopy showed circumferential membranous stenosis of the jejunum 3 cm distal to the esophago-jejunal anastomosis. Endoscopic balloon dilation was performed three times, but proved ineffective. Magnetic compression anastomosis was planned because the stenosis existed near the esophago-jejunal anastomosis and re-operation was a highly invasive procedure requiring intrathoracic anastomosis. Endoscopic balloon dilation preceded placement of the parent magnet on the anal side of the stenosis. Confirming the improvement of stenosis, the parent magnet was placed on the anal side of the stenosis during esophagogastroduodenoscopy. The parent magnet attached to nylon thread was fixed to the cheek to prevent magnet migration. A week after placing the parent magnet, restenosis was confirmed and the daughter magnet was placed via nylon thread on the oral side of the stenosis. The two magnets were adsorbed in the end-to-end direction across the stenosis. Magnets adsorbed in the end-to-end direction moved to the anal side 11 days after placement. Wide anastomosis was confirmed by esophagogastroduodenoscopy. Endoscopic balloon dilation was regularly performed to prevent restenosis after magnetic compression anastomosis. No complications were observed postoperatively. The patient was able to eat normally and successfully reintegrated into society.

Conclusions
Magnetic compression anastomosis could be a feasible procedure to avoid surgery for non-anastomotic stenosis of the proximal jejunum after gastrectomy with Roux-en-Y reconstruction.
The impact of the COVID-19 crisis on meeting needs for family planning: a global scenario by contraceptive methods used
Authors: Dasgupta Aisha , Kantorová Vladimíra , Ueffing Philipp 
Published: July 2020

The COVID-19 crisis could leave significant numbers of women and couples without access to essential sexual and reproductive health care. This research note analyses differences in contraceptive method mix across Sustainable Development Goal regions and applies assumed method-specific declines in use to produce an illustrative scenario of the potential impact of COVID-19 on contraceptive use and on the proportion of the need for family planning satisfied by modern methods. Globally, it had been estimated that 77 per cent of women of reproductive age (15-49 years) would have their need for family planning satisfied with modern contraceptive methods in 2020. However, taking into account the potential impact of COVID-19 on method-specific use, this could fall to 71 per cent, resulting in around 60 million fewer users of modern contraception worldwide in 2020. Overall declines in contraceptive use will depend on the methods used by women and their partners and on the types of disruptions experienced. The analysis concludes with the recommendation that countries should include family planning and reproductive health services in the package of essential services and develop strategies to ensure that women and couples are able to exercise their reproductive rights during the COVID-19 crisis.
The Books of Sigismund II Augustus in Vilnius University Library: Decorations of Book Covers and New Data about Provenances
Authors: Rankelienė Sondra 
Published: July 2020

In this article, the latest data about the personal book collection items of King of Poland and Grand Duke of Lithuania Sigismund II Augustus in Vilnius University (VU) Library are presented. The authors that have been doing research on these books have not ascertained all of the embossed images that were used for cover decoration and have not identified the locations of where these books were bound and have not disclosed all of the provenances. In order to amend the lack of knowledge about the books of Sigismund II Augustus in VU library, the book covers of the King’s personal library were reviewed de visu and decorative ornaments were described. The ownership signs of the books were registered once again. While describing and comparing these books with the copies in various libraries of the world, the number of physical books (14) and publications in composite volumes (21) kept in VU library was assessed. The name of one book and a publisher’s imprint of two books were specified, eight provenances that were not mentioned by previous authors were registered. While describing book covers, the embossed images were given provisory names. Connections between the supralibros, dates of binding, decorative wheels, single embossed images, and other decorative elements were detected and lead to a reasonable conclusion that eight out of fourteen books from the Sigismund II Augustus collection were bound in Kraków, five were bound by bookbinders in Vilnius, while one was rebound in the 18th century. The identification of tools used by craftsmen that worked in Kraków and Vilnius will allow to ascertain the manufacturing location of similar book covers made in the middle of the 16th century.
La responsabilidad por daños constitucionales en la acción de Tutela
Authors: MONDRAGÓN DUARTE SERGIO LUIS , PÉREZ MEDINA ANDRÉS GUSTAVO 
Published: July 2020

El cometido de este documento es el desarrollo de una teoría de responsabilidad por daños constitucionales, a través de la facultad que tiene el juez constitucional en sede de tutela de realizar condenas en abstracto ante acciones que trasgredan los Derechos Fundamentales, así partiendo del texto del artículo 25 del Decreto 2591 de 1992 se ha hecho un gran desarrollo jurisprudencial por parte de la Corte Constitucional que se sincroniza con el principio de reparación integral.

De esta forma, la estrategia metodológica empleara un componente deductivo, como lo es el estudio de unas nociones genéricas, como también un componente inductivo, ello es el estudio de casos, para a partir de allí, intentar ofrecer algunos cimientos que permitan la construcción de una teoría de daños constitucionales en sede de tutela.
Epidemiology and pattern of paediatric trauma in one of the biggest trauma centres of India
Authors: Kunwar Abhijeet , Manjhi Birju , Saurabh Anand , Shekhar Shubhanshu 
Published: July 2020

<p class="abstract"><strong>Background:</strong> The objective of the study was to assess the epidemiology and pattern of trauma in paediatric patients coming to a tertiary care trauma centre in Purvanchal region of country.</p><p class="abstract"><strong>Methods:</strong> Study was conducted at Trauma Centre, Institute of Medical Sciences, BHU. A retrospective data was collected from the emergency entry record book for the paediatric patients coming to emergency with trauma from January to December 2018. A total of 328 patients were included in study. Patient with accidental hanging and those of sexual assault and drowning were not taken in study.<strong></strong></p><p class="abstract"><strong>Results:</strong> Patients in the age group of above 6 years were most numerous 61%. Boys were more commonly injured then girls of same age group with M: F being 1.4:1. Fall was the most common mode of injury overall 45.12% and for the children below 6 years of age 63%. However, RTA was the most common cause in children of above 6 years age group 40.5%, closely followed by fall. Home was found to be the most common location of injury. Females outnumbered males in case of assault injury (7 of 12). Musculoskeletal injury was most common 42%, head injury 27%, polytrauma 12%, while superficial injuries in form of abrasion, contusion etc were 19%. Of all 42% were taken inpatient, 50% discharged on OPD basis and 8% went LAMA. </p><p class="abstract"><strong>Conclusions:</strong> Most of the times the paediatric traumas occur in foreseeable circumstances, most of them occurring at home or around it suggesting the need for more supervision during playing and identification of specific risk factors for these injuries in our setting. Planning of strategies should be according to the epidemiological trends.</p>
« Parler ce n'est pas voir. » L’écriture polyphonique dans Les clandestins et C’est beau, la guerre de Youssouf Amine Elalamy
Authors: Schulte Nordholt Annelies 
Published: July 2020

Cet article propose une étude comparée de deux romans de Youssouf Elalamy. Dans son œuvre, ces deux romans forment un diptyque, non seulement par leur thématique commune – celle du drame de l’émigration et de l’exil – mais aussi par leur forme polyphonique, mettant en scène une pluralité de voix narratrices. Le choix de cette forme polyphonique, particulièrement apte à exprimer la voix de l’individu, fait que ces deux romans remettent en question les approches médiatiques courantes du drame de l’émigration : celles du reportage journalistique et de la photographie, qui préfèrent l’immédiateté de la vue à la médiation de la parole fictionnelle. This article is a comparative study of two novels by Youssouf Elalamy. These two novels form a diptych: they share both their central theme – the drama of emigration and exile – and their polyphonic literary form, staging a plurality of narrative voices. This polyphonic form is particularly apt to express the individual’s voice. Through it, the two novels question current accounts of the drama of emigration in the mass media, such as newspaper reportage and photography; these media prefer the immediacy of sight to the mediation of literary fiction.
Short-term Outcomes of Robotic- versus Laparoscopic-Assisted Total Gastrectomy for Advanced Gastric Cancer: A Propensity Score Matching Study
Authors: Yang Changdong , Shi Yan , Xie Shaohui , Chen Jun , Zhao Yongliang , Qian Feng , Hao Yingxue , Tang Bo , Yu Pei-Wu 
Published: July 2020

Abstract
Background: Few studies have been designed to evaluate the short-term outcomes between robotic-assisted total gastrectomy (RATG) and laparoscopy-assisted total gastrectomy (LATG) for advanced gastric cancer (AGC). The purpose of this study was to assess the short-term outcomes of RATG compared with LATG for AGC. Methods: We retrospectively evaluated 126 and 257 patients who underwent RATG or LATG, respectively. In addition, we performed propensity score matching (PSM) analysis between RATG and LATG for clinicopathological characteristics to reduce bias and compared short-term surgical outcomes. Results: After PSM, the RATG group had a longer mean operation time (291.14±59.18 vs. 270.34±52.22 min, p=0.003), less intraoperative bleeding (154.37±89.68 vs. 183.77±95.39 ml, p=0.004) and more N2 tier RLNs (9.07±5.34 vs. 7.56±4.50, p=0.016) than the LATG group. Additionally, the total RLNs of the RATG group were almost significantly different compared to that of the LATG group (34.90±13.05 vs. 31.91±12.46, p=0.065).Moreover, no significant differences were found between the two groups in terms of the length of incision, proximal resection margin, distal resection margin, residual disease and postoperative hospital stay. There was no significant difference in the overall complication rate between the RATG and LATG groups after PSM (23.8% vs. 28.6%, p=0.390). Grade II complications accounted for most of the complications in the two cohorts after PSM. The conversion rates were 4.55% and 8.54% in the RATG and LATG groups, respectively, with no significant difference (p=0.145), and the ratio of splenectomy were 1.59% and 0.39% (p=0.253). The mortality rates were 0.8% and 0.4% for the RATG and LATG groups, respectively (p=1.000). Conclusion : This study demonstrates that RATG is comparable to LATG in terms of short-term surgical outcomes.
Estimating the number of usability problems affecting medical devices: modelling the discovery matrix
Authors: Vandewalle Vincent , Caron Alexandre , Delettrez Coralie , Périchon Renaud , Pelayo Sylvia , Duhamel Alain , Dervaux Benoit 
Published: July 2020

Abstract
Background. Usability testing of medical devices are mandatory for market access. The testings’ goal is to identify usability problems that could cause harm to the user or limit the device’s effectiveness. In practice, human factor engineers study participants under actual conditions of use and list the problems encountered. This results in a binary discovery matrix in which each row corresponds to a participant, and each column corresponds to a usability problem. One of the main challenges in usability testing is estimating the total number of problems, in order to assess the completeness of the discovery process. Today’s margin-based methods fit the column sums to a binomial model of problem detection. However, the discovery matrix actually observed is truncated because of undiscovered problems, which corresponds to fitting the marginal sums without the zeros. Margin-based methods fail to overcome the bias related to truncation of the matrix. The objective of the present study was to develop and test a matrix-based method for estimating the total number of usability problems.Methods. The matrix-based model was based on the full discovery matrix (including unobserved columns) and not solely on a summary of the data (e.g. the margins). This model also circumvents a drawback of margin-based methods by simultaneously estimating the model’s parameters and the total number of problems. Furthermore, the matrix-based method takes account of a heterogeneous probability of detection, which reflects a real-life setting. As suggested in the usability literature, we assumed that the probability of detection had a logit-normal distribution.Results. We assessed the matrix-based method’s performance in a range of settings reflecting real-life usability testing and with heterogeneous probabilities of problem detection. In our simulations, the matrix-based method improved the estimation of the number of problems (in terms of bias, consistency, and coverage probability) in a wide range of settings. We also applied our method to five real datasets from usability testing.Conclusions. Estimation models (and particularly matrix-based models) are of value in estimating and monitoring the detection process during usability testing. Matrix-based models have a solid mathematical grounding and, with a view to facilitating the decision-making process for both regulators and device manufacturers, should be incorporated into current standards.