LLukas22/scidocs huggingface dataset:
Tangible mtDNA: A Tangible Tabletop System for Exploring Genetic Mutations on Mitochondrial DNA Cancer Data

Rapid growth in the volume of cancer DNA sequencing data has not been matched by an increase in our ability to understand, explore, and interpret this data. There is a need for new tools that can enhance analyses in order to enable us to interpret the data, discover new or unexpected information, and ultimately form insights. We present Tangible mtDNA, an active tangible and tabletop system that allows multiple users with diverse expertise to collaborate in exploring and understanding mitochondrial DNA sequencing data in breast cancer patients. Five expert biologists evaluated the system and found it to be effective for data exploration and useful in supporting understanding, collaboration and discussion of DNA datasets.
Size optimization of new hybrid stand-alone renewable energy system considering a reliability index

Over last two decades, solar and wind energies have become an alternative to traditional energy sources. These alternative energy sources are non-polluting, free in their availability and are renewable. Another alternative is tidal energy, which is related to falling and rising ocean water levels. Tidal behavior can be predicted easily and this means that if it is enabling to harness tidal energy, it can be produced power for specific periods of time. In this paper, a new hybrid combination of renewable energy sources is considered. The combination of wind, photovoltaic and tidal is taken into account as a primary and battery as an auxiliary source. The aim of design is to minimize the annualized cost of the generation system over its 20 years of operation. Determining the capacity of hybrid wind, photovoltaic, tidal and battery is formulated as an optimization problem. The objective function is the minimization of the cost with the constrain having specific reliability index. To evaluate the system reliability level, the Equivalent Loss Factor (ELF) has been used as an index. Comparison between hybrid wind, solar and battery and new combination of renewable energy is done and it is shown that the combination of wind, solar, tidal and battery is more economical. Particle Swarm Optimization (PSO) is used for optimal sizing the system. Simulation results are carried out by MATLAB software. It is shown that hybrid system is the best configuration that has minimum cost and can satisfy all constrains.
Development of a Liquid-Liquid Extraction Procedure for the Analysis of Amphetamine in Biological Specimens by GC-FID

In the present study liquid-liquid extraction (LLE) of amphetamine from biological samples was systematically optimised. The recovery of amphetamine extraction was studied using a variety of 5 solvents (chloroform, 1-chlorobutan, dichloromethane, diethylether, ethyl acetate) as well as a system of solvents (chloroform: ethyl acetate: ethanol, 3:1:1 v/v). Furthermore the influence of the volume of the extracting solvent and the pH on the recovery of amphetamine was examined. The optimum conditions of LLE procedure were applied for the extraction of amphetamine from biological samples such as urine, blood and also from less commonly used biological specimens such as liver, bile, brain, vitreous humour, pericardial fluid, cerebrospinal fluid, bone marrow and bone. The determination of amphetamine was accomplished by gas chromatography equipped with a flame ionization detector (FID), after derivatization with heptafluorobutyric anhydride (HFBA).
First aid for orthodontic retainers.

UNLABELLED
The need for long-term retention to prevent post-treatment tooth movement is now widely accepted by orthodontists. This may be achieved with removable retainers or permanent bonded retainers. This article aims to provide simple guidance for the dentist on how to maintain and repair both removable and fixed retainers.


CLINICAL RELEVANCE
The general dental practitioner is more likely to review patients over time and needs to be aware of the need for long-term retention and how to maintain and repair the retainers.
Competition and Selection Among Conventions

In many domains, a latent competition among different conventions determines which one will come to dominate. One sees such effects in the success of community jargon, of competing frames in political rhetoric, or of terminology in technical contexts. These effects have become widespread in the on-line domain, where the ease of information transmission makes them particularly forceful, and where the available data offers the potential to study competition among conventions at a fine-grained level. In analyzing the dynamics of conventions over time, however, even with detailed on-line data, one encounters two significant challenges. First, as conventions evolve, the underlying substance of their meaning tends to change as well; and such substantive changes confound investigations of social effects. Second, the selection of a convention takes place through the complex interactions of individuals within a community, and contention between the users of competing conventions plays a key role in the convention’s evolution. Any analysis of the overall dynamics must take place in the presence of these two issues. In this work we study a setting in which we can cleanly track the competition among conventions while explicitly taking these sources of complexity into account. Our analysis is based on the spread of low-level authoring conventions in the e-print arXiv over 24 years and roughly a million posted papers: by tracking the spread of macros and other author-defined conventions, we are able to study conventions that vary even as the underlying meaning remains constant. We find that the interaction among co-authors over time plays a crucial role in the selection of conventions; the distinction between more and less experienced members of the community, and the distinction between conventions with visible versus invisible effects, are both central to the underlying processes. Through our analysis we make predictions at the population level about the ultimate success of different synonymous conventions over time — and at the individual level about the outcome of “fights” between people over convention choices. c ©2017 International World Wide Web Conference Committee (IW3C2), published under Creative Commons CC BY 4.0 License. WWW 2017, April 3–7, 2017, Perth, Australia. ACM 978-1-4503-4913-0/17/04. http://dx.doi.org/10.1145/3038912.3052652
Patient-reported outcomes from EMILIA, a randomized phase 3 study of trastuzumab emtansine (T-DM1) versus capecitabine and lapatinib in human epidermal growth factor receptor 2-positive locally advanced or metastatic breast cancer.

BACKGROUND
This report describes the results of an analysis of patient-reported outcomes from EMILIA (TDM4370g/BO21977), a randomized phase 3 study of the antibody-drug conjugate trastuzumab emtansine (T-DM1) versus capecitabine and lapatinib in human epidermal growth factor receptor 2 (HER2)-positive locally advanced or metastatic breast cancer.


METHODS
A secondary endpoint of the EMILIA study was time to symptom worsening (time from randomization to the first documentation of a ≥ 5-point decrease from baseline) as measured by the Trial Outcome Index Physical/Functional/Breast (TOI-PFB) subset of the Functional Assessment of Cancer Therapy-Breast questionnaire. Predefined exploratory patient-reported outcome endpoints included proportion of patients with a clinically significant improvement in symptoms (per TOI-PFB) and proportion of patients with diarrhea symptoms (per Diarrhea Assessment Scale).


RESULTS
In the T-DM1 arm, 450 of 495 patients had a baseline and ≥ 1 postbaseline TOI-PFB score versus 445 of 496 patients in the capecitabine-plus-lapatinib arm. Time to symptom worsening was delayed in the T-DM1 arm versus the capecitabine-plus-lapatinib arm (7.1 months versus 4.6 months, respectively; hazard ratio = 0.796; P = .0121). In the T-DM1 arm, 55.3% of patients developed clinically significant improvement in symptoms from baseline versus 49.4% in the capecitabine-plus-lapatinib arm (P = .0842). Although similar at baseline, the number of patients reporting diarrhea symptoms increased 1.5- to 2-fold during treatment with capecitabine and lapatinib but remained near baseline levels in the T-DM1 arm.


CONCLUSIONS
Together with the EMILIA primary data, these results support the concept that T-DM1 has greater efficacy and tolerability than capecitabine plus lapatinib, which may translate into improvements in health-related quality of life.
Similar biotherapeutic products in Latin America. Regulation and opportunities for patients with autoimmune diseases

Correspondence: Juan-Manuel Anaya Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24, 63-C-69, third floor, Bogotá, Colombia Tel +57 1 349 9650 Fax +57 1 349 9340 Email juan.anaya@urosario.edu.co Abstract: Biotherapeutic products have revolutionized medicine, changing the way we can treat some chronic diseases, such as autoimmune diseases. The patent expiry and the high costs of reference biotherapeutic products, among other factors, have promoted interest in similar biotherapeutic products (SBPs), also known as biosimilars. The objective of developing an SBP is to manufacture a “highly similar” molecule to a reference biotherapeutic product, by conducting a comparability exercise that can demonstrate similar quality, safety, and efficacy. Regulations like those of the World Health Organization, the European Medicines Agency, and the Food and Drug Administration are international reference standards. Herein, we aim to point out the current status in Latin America on SBPs, focusing on regulatory issues within the context of autoimmune diseases. The regulations of Argentina, Peru, Chile, Guatemala, Panama and Costa Rica follow the World Health Organization guidelines. Other countries, such as Cuba, Mexico, Venezuela, and Brazil have regulations that take into account international standards combined with local features. In Colombia, a draft decree is under revision and the debate is ongoing. Some countries have already approved SBPs. Mexico, Chile, Ecuador, Bolivia, and Peru market SBPs of rituximab, and Colombia markets an SBP of etanercept. The advent of SBPs is definitely beneficial. Safety and efficacy must be ensured following clear and comprehensive regulations.
Knowledge Diffusion for Neural Dialogue Generation

๏ The experimental results show that the proposed model effectively generate more diverse and meaningful responses involving more accurate relevant entities compared with the state-of-the-art baselines. We collect a multi-turn conversation corpus which includes not only facts related inquiries but also knowledge-based chit-chats. The data is publicly available at https:// github.com/liushuman/neural-knowledge-diffusion. We obtain the element information of each movie from https://movie.douban.com/ and build the knowledge base K. The question-answering dialogues and knowledge related chit-chat are crawled from https://zhidao.baidu.com/ and https://www.douban.com/group/. The conversations are grounded on the knowledge using NER, string match, and artificial scoring and filtering rules. The total 32977 conversations consisting of 104567 utterances are divided into training (32177) and testing set (800). Overview
Verifying cloud service-level agreement by a third-party auditor

In this paper, we study the important issue of verifying service-level agreement (SLA) with an untrusted cloud and present an SLA verification framework that utilizes a third-party auditor (TPA). A cloud provides users with elastic computing and storage resources in a pay-as-you-go way. An SLA between the cloud and a user is a contract that specifies the computing resources and performances that the cloud should provide to the user. A cloud service provider (CSP) has incentives to cheat on the SLA, for example, providing a user with less central processing unit and memory resources than specified in the SLA, which allows the CSP to support more users and make more profits. A malicious CSP can easily disrupt the existing SLA monitoring/verification techniques by interfering with the monitoring/measurement process. A TPA resolves the trust dilemma between a CSP and its users. Under the TPA framework and the untrusted-cloud threat model, we design two effective testing algorithms that can detect an SLA violation of the virtual machine memory size. Using real experiments, we demonstrate that our algorithms can detect cloud cheating on a virtual machine’s memory size (i.e., SLA violations). Furthermore, we show that our testing algorithms can defend various attacks from a malicious CSP, which tries to hide an SLA violation. Copyright © 2013 John Wiley & Sons, Ltd.
Evaluation Method of Patent Scope Based on Semantic Information of Words and Dependency Structure of Patent Claims

In patent documents, the "claim" is the most important section because the patent scope is interpreted based on the description of claims. However, because claims are expressed as sentences, the scope and boundaries of patents tend to be ambiguous. Prior studies have not been able to visualize the scope of a claim because they did not include the semantic range of words. Therefore, we develop a method to visualize the description of claims and the patent scope using natural language processing. Specifically, in order to visualize patent claims, we introduce the semantic range of words using the hierarchical structure of words provided by WordNet. Then, we apply the proposed method to two patents included in "PageRank" technology. The results show that parent patents are wider than child patents.
Protective effect of pre-infarction angina on microvascular obstruction after primary percutaneous coronary intervention is blunted in humans by cardiovascular risk factors.

BACKGROUND
Pre-infarction angina (PIA) has been shown to reduce the microvascular obstruction (MVO) rate in patients with ST-segment elevation myocardial infarction (STEMI). We sought to evaluate the potential modulator role of cardiovascular risk factors (CRFs) on this protective effect.


METHODS AND RESULTS
Two hundred patients with STEMI were enrolled. PIA was defined as typical chest pain within the 48 h preceding STEMI onset. Angiographic MVO was defined as TIMI flow grade <2 or TIMI flow 3 with myocardial blush grade <2; electrocardiographic (ECG) MVO was defined as ST-segment elevation resolution <70%. Common CRFs were collected. In the absence of hypertension, both angiographic and ECG MVO rates were lower in patients with PIA as compared with those without, whereas, in the presence of hypertension, they were similar in both study groups (P for interaction=0.01 and P=0.014, respectively). Among nonsmokers, angiographic and ECG MVO rates were lower in patients with PIA as compared with those without, whereas within smokers, they were similar in both study groups (P for interaction=0.037 and P=0.037, respectively). In the absence of dyslipidemia, the angiographic and ECG MVO rates were lower in patients with PIA as compared with those without, whereas within dyslipidemic patients, they were similar in both study groups (P for interaction=0.012 and P=0.04, respectively).


CONCLUSIONS
The protective effect of PIA on MVO is blunted by CRFs.
Management of pediatric tachyarrhythmias on mechanical support.

BACKGROUND
Pediatric patients with persistent arrhythmias may require mechanical cardiopulmonary support. We sought to classify the population, spectrum, and success of current treatment strategies.


METHODS AND RESULTS
A multicenter retrospective chart review was undertaken at 11 sites. Inclusion criteria were (1) patients <21 years, (2) initiation of mechanical support for a primary diagnosis of arrhythmias, and (3) actively treated on mechanical support. A total of 39 patients were identified with a median age of 5.5 months and median weight of 6 kg. A total of 69% of patients were cannulated for supraventricular tachycardia with a median rate of 230 beats per minute. A total of 90% of patients were supported with extracorporeal membrane oxygenation for an average of 5 days. The remaining 10% were supported with ventricular assist devices for an average of 38 (20-60) days. A total of 95% of patients were treated with antiarrhythmics, with 43% requiring >1 antiarrhythmic. Amiodarone was the most frequently used medication alone or in combination. A total of 33% patients underwent electrophysiology study/transcatheter ablation. Radiofrequency ablation was successful in 9 patients on full flow extracorporeal membrane oxygenation with 3 radiofrequency-failures/conversion to cryoablation. One patient underwent primary cryoablation. A total of 15% of complications were related to electrophysiology study/ablation. At follow-up, 23 patients were alive, 8 expired, and 8 transplanted.


CONCLUSIONS
Younger patients were more likely to require support in the presented population. Most patients were treated with antiarrhythmics and one third required electrophysiology study/ablation. Radiofrequency ablation is feasible without altering extracorporeal membrane oxygenation flows. There was a low frequency of acute adverse events in patients undergoing electrophysiology study/ablation, while on extracorporeal membrane oxygenation.
Distinguishing Opinion from News

Newspapers have separate sections for opinion articles and news articles. The goal of this project is to classify articles as opinion versus news and also to do analysis of the results to figure out the factors that distinguish the two. Preliminary results show that classification is possible with unigram features in an SVM with F1 of .94. Introduction This project focuses on subjectivity classification for news articles. Much prior work on subjectivity has focused on distinguishing positive and negative sentiment (for instance, in product reviews) or classifying phrases or clauses as subjective (Liu, 2008). Here we attempt to distinguish entire articles as reporting news or expressing opinion. The task is related but has some key differences. For instance, review-type sentiment analysis often relies on pre-made lexicons or focuses on classifying words as positive or negative (Toprak and Gurevych, 2009; Turney and Littman, 2010; Potts). Words associated with positivity and negativity are not necessarily those associated with editorials and opinion pieces in which authors pose sophisticated arguments about current events, policies, etc. One goal of the project was to gain a lexical understanding of words that can distinguish the two categories, and thus be able to generate a lexicon similar those already existing for sentiment analysis of reviews that would work for articles. Prior Work There has been thorough research into document classification."Machine Learning in Automated Text Categorization" (Sebastiani, 2003) provides an overview of work up to 2002. Within the area of subjectivity/sentiment analysis there is also a wide variety of work. Pang and Lee give an overview of the field of subjectivity (Pang and Lee, 2008). Liu defines many different problems within the field including sentiment and subjectivity classification: (1) classifying an opinionated document as expressing a positive or negative opinion, and (2) classifying a sentence or a clause of the sentence as subjective or objective (Liu, 2010) Liu also gives an overview of the field thus far from a teaching perspective. Turney and Littman provide a method for sentiment for particular words based on their context (Turney and Littman, 2003). Yu and Hatzivassiloglou specifically address distinguishing opinion from news using a Naive Bayes classifier and are able to achieve very high results (Yu and Hatzivassiloglou, 2003). However, their method did not generalize to my dataset. Data I use two datasets, both consisting of articles from the New York Times. The primary dataset consists of 140 articles over the course of the 7 years up to and including 2012. For comparison, I also test on a dataset of articles from October and November 2012 in which news events are covered repeatedly. The data was collected by scraping the New York Times website. The first
Computational Aspects of Curves of Genus at Least 2

This survey discusses algorithms and explicit calculations for curves of genus at least 2 and their Jacobians, mainly over number fields and finite fields. Miscellaneous examples and a list of possible future projects are given at the end.
Dante and Renaissance Florence

List of illustrations Acknowledgements List of abbreviations Introduction Part I. Competing Cults: the Legacy of the Trecento and the Impact of Humanism, 1350-1430: 1. Boccaccio and Petrarch 2. Florentine humanism and vernacular culture: perspectives on Dante, 1375-1430 Part II. New Directions and the Rise of the Vernacular, 1430-1481: 3. Dante as a civic and linguistic model, 1430-1441 4. Dante and Florentine vernacular humanism: critical judgments and literary experiments Part III. Cristoforo Landino and his Comento sopra la Comedia (1481): 5. Cristoforo Landino on Dante and Florence: the prologue to the Comento 6. Tradition and innovation in Cristoforo Landino's Comento: platonism, natural science and classicism Conclusion Notes Selected bibliography Index.
Periodic musical sequences and Lyndon words

When one enumerates periodic musical structures, the computation is done up to a cyclic shift. This means that two solutions which are cyclic shifts of one another are considered the same. Lyndon words provide a powerful way to do so. We illustrate this by two examples taken from African traditional music.
A randomized, double-blind study of certoparin vs. unfractionated heparin to prevent venous thromboembolic events in acutely ill, non-surgical patients: CERTIFY Study.

BACKGROUND
In medically ill patients, no contemporary double-blind head-to-head evaluation of low molecular weight heparin vs. unfractionated heparin (UFH) for the prevention of venous thromboembolic events is available.


OBJECTIVES
To compare the efficacy and safety of certoparin with those of UFH.


PATIENTS/METHODS
In this double-blind, randomized, controlled trial, acutely ill, non-surgical patients aged > or = 70 years were randomized to certoparin (3000 U of anti-factor Xa once daily) or to UFH (5000 IU t.i.d.). The primary endpoint was the composite of proximal deep vein thrombosis as assessed by bilateral compression ultrasonography, symptomatic non-fatal pulmonary embolism and venous thromboembolism-related death, and was assessed by a blinded central adjudication committee. Non-inferiority margins were set at 1.8 for the odds ratio (OR) and 3.45% for the absolute difference.


RESULTS
Three thousand two hundred and thirty-nine patients aged 78.8 + or - 6.3 years were treated for 9.1 + or - 3.4 days. The incidence of the primary endpoint was 3.94% in the certoparin group and 4.52% in the UFH group, with a difference in proportions of - 0.59% [95% confidence interval (CI) -2.09 to 0.92; P < 0.0001 for non-inferiority], and an OR of 0.87 (95% CI 0.60-1.26; P = 0.0001 for non-inferiority). Major bleeding occurred in 0.43% of certoparin-treated patients and 0.62% of UFH-treated patients (OR 0.69; 95% CI 0.26-1.83). Any bleeding occurred at 3.20% in certoparin-treated patients vs. 4.58% in UFH-treated patients (OR 0.69; 95% CI 0.48-0.99; P < 0.05), and 5.73% of certoparin-treated patients and 6.63% of UFH-treated patients experienced serious adverse events. All-cause mortality was 1.27% in certoparin-treated patients and 1.36% in UFH-treated patients.


CONCLUSIONS
In acutely ill, non-surgical elderly patients, thromboprophylaxis with certoparin (3000 U of anti-FXa once daily) was non-inferior to 5000 IU of UFH t.i.d., with a favorable safety profile.