LLukas22/scidocs huggingface dataset:
A Tutorial on Uppaal

This is a tutorial paper on the tool Uppaal. Its goal is to be a short introduction on the flavor of timed automata implemented in the tool, to present its interface, and to explain how to use the tool. The contribution of the paper is to provide reference examples and modeling patterns.
Edoxaban versus warfarin for the treatment of symptomatic venous thromboembolism.

BACKGROUND
Whether the oral factor Xa inhibitor edoxaban can be an alternative to warfarin in patients with venous thromboembolism is unclear.


METHODS
In a randomized, double-blind, noninferiority study, we randomly assigned patients with acute venous thromboembolism, who had initially received heparin, to receive edoxaban at a dose of 60 mg once daily, or 30 mg once daily (e.g., in the case of patients with creatinine clearance of 30 to 50 ml per minute or a body weight below 60 kg), or to receive warfarin. Patients received the study drug for 3 to 12 months. The primary efficacy outcome was recurrent symptomatic venous thromboembolism. The principal safety outcome was major or clinically relevant nonmajor bleeding.


RESULTS
A total of 4921 patients presented with deep-vein thrombosis, and 3319 with a pulmonary embolism. Among patients receiving warfarin, the time in the therapeutic range was 63.5%. Edoxaban was noninferior to warfarin with respect to the primary efficacy outcome, which occurred in 130 patients in the edoxaban group (3.2%) and 146 patients in the warfarin group (3.5%) (hazard ratio, 0.89; 95% confidence interval [CI], 0.70 to 1.13; P<0.001 for noninferiority). The safety outcome occurred in 349 patients (8.5%) in the edoxaban group and 423 patients (10.3%) in the warfarin group (hazard ratio, 0.81; 95% CI, 0.71 to 0.94; P=0.004 for superiority). The rates of other adverse events were similar in the two groups. A total of 938 patients with pulmonary embolism had right ventricular dysfunction, as assessed by measurement of N-terminal pro-brain natriuretic peptide levels; the rate of recurrent venous thromboembolism in this subgroup was 3.3% in the edoxaban group and 6.2% in the warfarin group (hazard ratio, 0.52; 95% CI, 0.28 to 0.98).


CONCLUSIONS
Edoxaban administered once daily after initial treatment with heparin was noninferior to high-quality standard therapy and caused significantly less bleeding in a broad spectrum of patients with venous thromboembolism, including those with severe pulmonary embolism. (Funded by Daiichi-Sankyo; Hokusai-VTE ClinicalTrials.gov number, NCT00986154.).
A phase II study on safety and efficacy of high-dose N-acetylcysteine in patients with cystic fibrosis

OBJECTIVE
We conducted a single-centre, randomised, double-blinded, placebo-controlled phase II clinical study to test safety and efficacy of a 12-week therapy with low-dose (700 mg/daily) or high-dose (2800 mg/daily) of NAC.


METHODS
Twenty-one patients (DeltaF508 homo/heterozygous, FEV1>40% pred.) were included in the study. After a 3-weeks placebo run-in phase, 11 patients received low-dose NAC, and 10 patients received high-dose NAC. Outcomes included safety and clinical parameters, inflammatory (total leukocyte numbers, cell differentials, TNF-alpha, IL-8) measures in induced sputum, and concentrations of extracellular glutathione in induced sputum and blood.


RESULTS
High-dose NAC was a well-tolerated and safe medication. High-dose NAC did not alter clinical or inflammatory parameters. However, extracellular glutathione in induced sputum tended to increase on high-dose NAC.


CONCLUSIONS
High-dose NAC is a well-tolerated and safe medication for a prolonged therapy of patients with CF with a potential to increase extracellular glutathione in CF airways.
One Hundred Consecutive Advanced Breast Biopsy Instrumentation Procedures: Complications, Costs, and Outcome

Background: Needle localization and excision have been the preferred techniques for treating nonpalpable mammographic abnormalities. Recently, a less invasive approach, using the Advanced Breast Biopsy Instrumentation (ABBI) system, was introduced. This study was undertaken to determine the feasibility, utility, and cost of this new alternative approach. Methods: Between April 1996 and May 1997, 100 consecutive women underwent excisional breast biopsies using the ABBI system. Demographic information, mammographic findings, pathological findings, hospital/professional fees, complications, and subsequent interventions were documented. Results: Excisional biopsies using the ABBI system were successful for 99 women (average age, 62 years; range, 34–87 years). Of the 99 lesions removed with the ABBI system, 27 were microcalcifications, 60 were suspicious solid nodules, and 12 were nodules with microcalcifications. The ABBI system was used in an outpatient surgical setting, with only one patient requiring sedation (because of anxiety). Cancer was seen in the biopsy specimens for 18 patients, seven of whom (35%) exhibited no residual tumor at the time of definitive treatment. Postoperative hematomas occurred in two patients; one hematoma required surgical drainage. One missed cancer was detected in follow-up mammograms 6 months after biopsy. The total average procedural cost was $3406.44 ± 486.63 Conclusions: Excisional breast biopsy using the ABBI system is an effective diagnostic method. It has a low complication rate, and its cost is comparable to that of classical needle localization.
On the effect of traditional culture on our ancient city planning theory

Through exposition of unique landscape formed by Confucian culture and Taoism culture in ancient city construction,the author discusses the large effect of Chinese traditional culture on ancient city planning and construction,and points out the realistic meaning of inheriting ancient outstanding city planning theory and method on modern China city planning theory and practice.
A high protein diet (3.4 g/kg/d) combined with a heavy resistance training program improves body composition in healthy trained men and women – a follow-up investigation

BACKGROUND
The consumption of a high protein diet (>4 g/kg/d) in trained men and women who did not alter their exercise program has been previously shown to have no significant effect on body composition. Thus, the purpose of this investigation was to determine if a high protein diet in conjunction with a periodized heavy resistance training program would affect indices of body composition, performance and health.


METHODS
Forty-eight healthy resistance-trained men and women completed this study (mean ± SD; Normal Protein group [NP n = 17, four female and 13 male]: 24.8 ± 6.9 yr; 174.0 ± 9.5 cm height; 74.7 ± 9.6 kg body weight; 2.4 ± 1.7 yr of training; High Protein group [HP n = 31, seven female and 24 male]: 22.9 ± 3.1 yr; 172.3 ± 7.7 cm; 74.3 ± 12.4 kg; 4.9 ± 4.1 yr of training). Moreover, all subjects participated in a split-routine, periodized heavy resistance-training program. Training and daily diet logs were kept by each subject. Subjects in the NP and HP groups were instructed to consume their baseline (~2 g/kg/d) and >3 g/kg/d of dietary protein, respectively.


RESULTS
Subjects in the NP and HP groups consumed 2.3 and 3.4 g/kg/day of dietary protein during the treatment period. The NP group consumed significantly (p < 0.05) more protein during the treatment period compared to their baseline intake. The HP group consumed more (p < 0.05) total energy and protein during the treatment period compared to their baseline intake. Furthermore, the HP group consumed significantly more (p < 0.05) total calories and protein compared to the NP group. There were significant time by group (p ≤ 0.05) changes in body weight (change: +1.3 ± 1.3 kg NP, -0.1 ± 2.5 HP), fat mass (change: -0.3 ± 2.2 kg NP, -1.7 ± 2.3 HP), and % body fat (change: -0.7 ± 2.8 NP, -2.4 ± 2.9 HP). The NP group gained significantly more body weight than the HP group; however, the HP group experienced a greater decrease in fat mass and % body fat. There was a significant time effect for FFM; however, there was a non-significant time by group effect for FFM (change: +1.5 ± 1.8 NP, +1.5 ± 2.2 HP). Furthermore, a significant time effect (p ≤ 0.05) was seen in both groups vis a vis improvements in maximal strength (i.e., 1-RM squat and bench) vertical jump and pull-ups; however, there were no significant time by group effects (p ≥ 0.05) for all exercise performance measures. Additionally, there were no changes in any of the blood parameters (i.e., basic metabolic panel).


CONCLUSION
Consuming a high protein diet (3.4 g/kg/d) in conjunction with a heavy resistance-training program may confer benefits with regards to body composition. Furthermore, there is no evidence that consuming a high protein diet has any deleterious effects.
AutoRec: Autoencoders Meet Collaborative Filtering

This paper proposes AutoRec, a novel autoencoder framework for collaborative filtering (CF). Empirically, AutoRec's compact and efficiently trainable model outperforms state-of-the-art CF techniques (biased matrix factorization, RBM-CF and LLORMA) on the Movielens and Netflix datasets.
[Tardive dyskinesia in patients with schizophrenia treated with olanzapine - results from a 20-month, prospective, open study under naturalistic conditions].

OBJECTIVES
The objective of the study was to assess the prevalence and incidence of tardive dyskinesia in patients treated with olanzapine during the follow-up period of 20 months.


METHODS
It was a prospective, observational, non-interventional study under naturalistic conditions, without a control group. The evaluation of the severity and presence of tardive dyskinesia was performed with the Abnormal Involuntary Movement Scale and research criteria by Schooler and Kane.


RESULTS
The study included 573 patients (woman 43,3%) with the diagnosis of schizophrenia (ICD-10), the mean age of 41.8 (± 12) years. The mean dose of olanzapine was 15.9 (± 4.2) mg. The prevalence of tardive dyskinesia was 16.4%. The cumulative incidence assessed in the group of 479 patients was 6.47%. The annual incidence was 3.9%. An increased risk of tardive dyskinesia was observed in smokers - RR of 1.99 (CI 0.88-4.49), those taking higher doses of olanzapine 1.57 (CI 0.91-2.7) and in those who used polytherapy: 3.55 (CI 1.43-8.82). Only in the case of polytherapy a multidimensional analysis confirmed that this factor had a significant influence on the risk of tardive dyskinesia (p=0.006).


CONCLUSIONS
The study demonstrated high (16,4%) prevalence of tardive dyskinesia, and the annual incidence (3,9%) comparable to the results of a meta-analysis by Corell et al. In the case of olanzapine in monotherapy the annual incidence was lower (1.96%) but the use of antipsychotics in polytherapy more than tripled the risk of tardive dyskinesia.
Automated synthesis of efficient binary decoders for retargetable software toolkits

A binary decoder is a common component of software development tools such as instruction set simulators, disassemblers and debuggers. The efficiency of the decoder can have a significant impact on the efficiency of these software tools. Automated synthesis of efficient binary decoders is therefore necessary for retargetable software tool development frameworks targeting the rapidly growing field of application-specific processor design. This paper describes a decoder synthesis algorithm that translates a simple instruction pattern specification into efficient binary decoders in C under given memory constraints. The algorithm constructs a decision tree with carefully chosen decoding primitives and cost models. As demonstrated through two case studies, the synthesized decoders achieve efficiency comparable to hand-coded decoders with ensured correctness. The algorithm has no limitation on the input instruction patterns and it requires only the least amount of knowledge about the instruction encoding. Therefore it can be used with any machine description scheme containing instruction encoding information.
Islamic Art in the 19th century- Tradition, Innovation, Eclecticism

This collection of essays on Islamic art and architecture in the nineteenth century covers a wide geographical area and draws together different regional elements. The essays devote much attention to social, political, economic and intellectual issues, including the role of tradition and responses to European aesthetics, among them the appropriation of orientalism and the rise of revivalist movements.
Patterns of Sperm Storage in Relation to Sperm Competition in Passerine Birds

Using a technique for observing sperm storage tubules (SSTs) in whole-mount preparations of oviduct tissue, we estimated the number and length of SSTs across 20 species of passerine birds in seven subfamilies. The average number of SSTs per female varied ninefold across the species examined and was correlated positively with body mass and relative egg size, suggesting that much of the interspecific variation in the number of SSTs may be a consequence of allometry. However, after controlling for body mass, the number of SSTs per female was also negatively correlated with the average length of SSTs and we suggest this pattern could result from selection for greater sperm length when access to sperm storage sites is limited by females. SST length varied eight-fold across the species examined but unlike the number of SSTs, SST length was not correlated with body mass. Instead, SST length was strongly and positively correlated with sperm length, suggesting a history of coevolution between male gametes and sperm storage sites in females that is independent of body size. Neither mating system nor any of four other morphological variables (testis length, oviduct length, clutch size, sperm storage capacity) was consistently correlated with either the number or size of SSTs. Variation between species in the potential for sperm layering within an SST, however, indicates that the pattern of sperm precedence (i.e., the pattern of paternity relative to mating order) may vary from species to species. We propose that a conflict of interest between the sexes with respect to sperm storage could lead to an arms race between sperm length and SST length and may help explain both the diversity in sperm storage patterns among species and the influence of sperm storage on the evolution of mating behavior in birds.
Discriminative Feature Selection for Uncertain Graph Classification

Mining discriminative features for graph data has attracted much attention in recent years due to its important role in constructing graph classifiers, generating graph indices, etc. Most measurement of interestingness of discriminative subgraph features are defined on certain graphs, where the structure of graph objects are certain, and the binary edges within each graph represent the "presence" of linkages among the nodes. In many real-world applications, however, the linkage structure of the graphs is inherently uncertain. Therefore, existing measurements of interestingness based upon certain graphs are unable to capture the structural uncertainty in these applications effectively. In this paper, we study the problem of discriminative subgraph feature selection from uncertain graphs. This problem is challenging and different from conventional subgraph mining problems because both the structure of the graph objects and the discrimination score of each subgraph feature are uncertain. To address these challenges, we propose a novel discriminative subgraph feature selection method, Dug, which can find discriminative subgraph features in uncertain graphs based upon different statistical measures including expectation, median, mode and φ-probability. We first compute the probability distribution of the discrimination scores for each subgraph feature based on dynamic programming. Then a branch-and-bound algorithm is proposed to search for discriminative subgraphs efficiently. Extensive experiments on various neuroimaging applications (i.e., Alzheimers Disease, ADHD and HIV) have been performed to analyze the gain in performance by taking into account structural uncertainties in identifying discriminative subgraph features for graph classification.
Prevention of exacerbations in patients with COPD and vitamin D deficiency through vitamin D supplementation (PRECOVID): a study protocol

BACKGROUND
Vitamin D is well known for its function in calcium homeostasis and bone mineralisation, but is increasingly studied for its potential immunomodulatory properties. Vitamin D deficiency is a common problem in patients with COPD. Previous studies have not demonstrated a beneficial effect of vitamin D on exacerbation rate in COPD patients. However, subgroup analyses suggested protective effects in vitamin D deficient patients. Our objective is to assess the effect of vitamin D supplementation on exacerbation rate specifically in vitamin D deficient COPD patients.


METHODS/DESIGN
We will perform a randomised, multi-center, double-blind, placebo-controlled intervention study. The study population consists of 240 COPD patients aged 40 years and older with vitamin D deficiency (25-hydroxyvitamin D concentration < 50 nmol/L). Participants will be recruited after an exacerbation and will be randomly allocated in a 1:1 ratio to receive vitamin D3 16800 IU or placebo orally once a week during 1 year. Participants will receive a diary card to register the incidence of exacerbations and changes in medication during the study period. Visits will be performed at baseline, at 6 months and at 12 months after randomisation. Participants will undergo spirometry, measurement of total lung capacity and assessment of maximal respiratory mouth pressure. Several physical performance and hand grip strength tests will be performed, questionnaires on quality of life and physical activity will be filled in, a nasal secretion sample and swab will be obtained and blood samples will be taken. The primary outcome will be exacerbation rate.


DISCUSSION
This study will be the first RCT aimed at the effects of vitamin D supplementation on exacerbation rate in vitamin D deficient COPD patients. Also, in contrast to earlier studies that used infrequent dosing regimens, our trial will study effects of a weekly dose of vitamin D supplementation. Secondly, the immunomodulatory effects of vitamin D on host immune response of COPD patients and underlying mechanisms will be studied. Finally, the effects on physical functioning will be examined.


TRIAL REGISTRATION
This trial is registered in ClinicalTrials.gov, ID number NCT02122627 . Date of Registration April 2014.
The complex origin of modern humans

HOW TO CITE: Holt E. The complex origin of modern humans. S Afr J Sci. 2017;113(9/10), Art. #a0233, 2 pages. http://dx.doi. org/10.17159/sajs.2017/a0233 Human origins and the factors influencing our evolution are fundamental to understanding our past, reflecting on our present, and determining our future. The seminal work of Charles Darwin provided evidence for a natural process of evolution, and an explanation for the immense abundance of species on earth; it also opened the way for study on the origin of humans.
A combined canonical variate analysis and Fisher discriminant analysis (CVA-FDA) approach for fault diagnosis

This paper proposes a combined canonical variate analysis (CVA) and Fisher discriminant analysis (FDA) scheme (denoted as CVA–FDA) for fault diagnosis, which employs CVA for pretreating the data and subsequently utilizes FDA for fault classification. In addition to the improved handling of serial correlations in the data, the utilization of CVA in the first step provides similar or reduced dimensionality of the pretreated datasets compared with the original datasets, as well as decreased degree of overlap. The effectiveness of the proposed approach is demonstrated on the Tennessee Eastman process. The simueywords: ault diagnosis anonical variate analysis isher discriminant analysis ynamic FDA ennessee Eastman process rocess monitoring lation results demonstrate that (i) CVA–FDA provides better and more consistent fault diagnosis than FDA, especially for data rich in dynamic behavior; and (ii) CVA–FDA outperforms dynamic FDA in both discriminatory power and computational time. © 2015 Elsevier Ltd. All rights reserved.
Understanding intermediate layers using linear classifier probes

Intuitively, for a training sample xi with its associated label yi, a deep model is getting closer to the correct answer in the higher layers. It starts with the difficult job of classifying xi, which becomes easier as the higher layers distill xi into a representation that is easier to classify. One might be tempted to say that this means that the higher layers have more information about the ground truth, but this would be incorrect.
Semantic Highlight Retrieval and Term Prediction

Due to the unprecedented growth of unedited videos, finding highlights relevant to a text query in a set of unedited videos has become increasingly important. We refer this task as semantic highlight retrieval and propose a query-dependent video representation for retrieving a variety of highlights. Our method consists of two parts: 1) “viralets”, a mid-level representation bridging between semantic [Fig. 1(a)] and visual [Fig. 1(c)] spaces and 2) a novel Semantic-MODulation (SMOD) procedure to make viralets query-dependent (referred to as SMOD viralets). Given SMOD viralets, we train a single highlight ranker to predict the highlightness of clips with respect to a variety of queries (two examples in Fig. 1), whereas existing approaches can be applied only in a few predefined domains. Other than semantic highlight retrieval, viralets can also be used to associate relevant terms to each video. We utilize this property and propose a simple term prediction method based on nearest neighbor search. To conduct experiments, we collect a viral video dataset1 including users’ comments, highlights, and/or original videos. Among a testing database with 1189 clips (13% highlights and 87% non-highlights), our highlight ranker achieves 41.2% recall at top-10 retrieved clips. It is significantly higher than the state-of-the-art domain-specific highlight ranker and its extension. Similarly, our method also outperforms all baseline methods on the publicly available video highlight dataset. Finally, our simple term prediction method utilizing viralets outperforms the state-of-the-art matrix factorization method (adapted from Kalayeh et al.). 1 Viral videos refer to popular online videos. We focus on user-generated viral videos, which typically contain short highlight marked by users.