LLukas22/scidocs huggingface dataset:
Light-Field Database Creation and Depth Estimation

Light-field imaging research has been gaining a lot of traction in recent times, especially after the availability of consumer-level light-field cameras like the Lytro Illum. However, there is a dearth of light-field databases publicly available for research. The project is mainly divided into two parts creation of an extensive light-field database and evaluating a state-of-the-art depth estimation algorithm. The database has over 250 light-fields made publicly available for research. These light-fields have been captured using the Lytro Illum camera. The depth-maps, output images, and metadata obtained using the Lytro command line tool have also been included. As the second part of our project, we have implemented the depth estimation algorithm proposed by Tao et al. [7] This algorithm estimates depth by combining correspondence and defocus cues. The algorithm uses the complete 4D epipolar image to create a depth-map which proved to be qualitatively much better than the depth-map generated by the Lytro command line tool. 1. Light-field Database Light-field [4] cameras have the ability to capture the intensity as well as direction of the light hitting the sensor. This makes it possible to refocus the image [5] as well as shift one’s viewpoint of the scene after it has been captured. This also facilitates estimation of depth using light-fields. Light-fields have a wide range of potential applications in fields such as computer vision, and virtual reality. The main motivation for creating a light-field database is the fact that there are few publicly available light-field databases to conduct research in this emerging field. Our light-field database consist of over 250 lightfields of natural scenes captured using the Lytro Illum camera. The scenes and objects are captured taking into consideration different kinds of applications researchers in this field may potentially work on and consequently, these lightfields are divided into different categories. The 9 different categories included in the database are (1) Flowers and plants, (2) Bikes, (3) Fruits and vegetables, (4) Cars, (5) Occlusions, (6) Buildings, (7) People, (8) Miscellaneous, (9) Refractive and Reflective surfaces. These external standardized light fields extracted using the Lytro command line tool help in recreating the 14× 14 shifted views, which can then be used for various applications. Along with the light-fields, the depth-maps, processed images and metadata obtained using the command line tool have also been included. The light-field database can be accessed at http://lightfields.stanford.edu/.
Deep Prior

The recent literature on deep learning offers new tools to learn a rich probability distribution over high dimensional data such as images or sounds. In this work we investigate the possibility of learning the prior distribution over neural network parameters using such tools. Our resulting variational Bayes algorithm generalizes well to new tasks, even when very few training examples are provided. Furthermore, this learned prior allows the model to extrapolate correctly far from a given task’s training data on a meta-dataset of periodic signals. 1 Learning a Rich Prior Bayesian Neural Networks [1, 2, 3, 4] are now scalable and can be used to estimate prediction uncertainty and model uncertainty [5]. While many efforts focus on better approximation of the posterior, we believe that the quality of the uncertainty highly depends on the choice of the prior. Hence, we consider learning a prior from previous tasks by learning a probability distribution p(w|α) over the weights w of a network, parameterized by α, and leveraging this learned prior to reduce sample complexity on new tasks. More formally we consider a hierarchical Bayes approach across N tasks, with hyper-prior p(α). Each task has its own parameters wj , withW = {wj}j=1. Using all datasets D = {Sj}j=1, we have the following posterior:1 p(W, α|D) = p(α|D) ∏ j p(wj |α, Sj) ∝ p(D|W)p(W|α)p(α) ∝ ∏
Sedative Hypnotic Medication Use and the Risk of Motor Vehicle Crash.

OBJECTIVES
We sought to estimate the association between sedative hypnotic use and motor vehicle crash risk.


METHODS
We conducted a new user cohort study of 409 171 adults in an integrated health care system. Health plan data were linked to driver license and collision records. Participants were aged 21 years or older, licensed to drive in Washington State, had at least 1 year of continuous enrollment between 2003 and 2008, and were followed until death, disenrollment, or study end. We used proportional hazards regression to estimate the risk of crash associated with 3 sedatives.


RESULTS
We found 5.8% of patients received new sedative prescriptions, with 11 197 person-years of exposure. New users of sedatives were associated with an increased risk of crash relative to nonuse: temazepam hazard ratio (HR) = 1.27 (95% confidence interval [CI] = 0.85, 1.91), trazodone HR = 1.91 (95% CI = 1.62, 2.25), and zolpidem HR = 2.20 (95% CI = 1.64, 2.95). These risk estimates are equivalent to blood alcohol concentration levels between 0.06% and 0.11%.


CONCLUSIONS
New use of sedative hypnotics is associated with increased motor vehicle crash risk. Clinicians initiating sedative hypnotic treatment should consider length of treatment and counseling on driving risk.
Iterative Refinement in Floating Point

Iterative refinement reduces the roundoff errors in the computed solution to a system of linear equations. Only one step requires higher precision arithmetic. If sufficiently high precision is used, the final result is shown to be very accurate.
Laplacian Regularized Gaussian Mixture Model for Data Clustering

Gaussian Mixture Models (GMMs) are among the most statistically mature methods for clustering. Each cluster is represented by a Gaussian distribution. The clustering process thereby turns to estimate the parameters of the Gaussian mixture, usually by the Expectation-Maximization algorithm. In this paper, we consider the case where the probability distribution that generates the data is supported on a submanifold of the ambient space. It is natural to assume that if two points are close in the intrinsic geometry of the probability distribution, then their conditional probability distributions are similar. Specifically, we introduce a regularized probabilistic model based on manifold structure for data clustering, called Laplacian regularized Gaussian Mixture Model (LapGMM). The data manifold is modeled by a nearest neighbor graph, and the graph structure is incorporated in the maximum likelihood objective function. As a result, the obtained conditional probability distribution varies smoothly along the geodesics of the data manifold. Experimental results on real data sets demonstrate the effectiveness of the proposed approach.
Extraction of Salient Sentences from Labelled Documents

We present a hierarchical convolutional document model with an architecture designed to support introspection of the document structure. Using this model, we show how to use visualisation techniques from the computer vision literature to identify and extract topic-relevant sentences. We also introduce a new scalable evaluation technique for automatic sentence extraction systems that avoids the need for time consuming human annotation of validation data.
Sequential vs concurrent epirubicin and docetaxel as adjuvant chemotherapy for high-risk, node-negative, early breast cancer: an interim analysis of a randomised phase III study from the Hellenic Oncology Research Group

Background:Sequential anthracyclines and taxanes are standard adjuvant chemotherapy for patients with high-risk axillary node-positive breast cancer. We compared a sequential to a concurrent regimen in high-risk node-negative early breast cancer.Methods:Patients were eligible if they had tumours >2 cm or T1c with two of the following characteristics: no oestrogen receptor (ER) and progesterone receptor (PR) expression, histological grade III, Ki67 >40% and vascular, lymphovascular or perineural invasion. They were randomised to receive four cycles of epirubicin 90 mg m−2 followed by four cycles of docetaxel 75 mg m−2 (sequential regimen) or six cycles of epirubicin 75 mg m−2 plus docetaxel 75 mg m−2 (concurrent regimen). All chemotherapy cycles were administered every 21 days with G-CSF prophylaxis only for the concurrent arm. The primary endpoint was disease-free survival (DFS).Results:Between 2001 and 2013, 658 women received the sequential (n=329) or the concurrent (n=329) regimen. The median age was 53 years, 43.9% of the patients were premenopausal and of the tumours 44.2% were ⩽2 cm, 52.7% histological grade 3 and 35.3% hormone receptor-negative. After a median follow-up of 70.5 months, there were 29 (8.8%) vs 42 (12.8%) disease relapses (P=0.102) and 11 (3.3%) vs 19 (5.8%) deaths (P=0.135), in the sequential and concurrent arm, respectively. The 5-year DFS rates were 92.6% vs 88.2% for sequential and concurrent arm, respectively (hazard ratio (HR): 1.591; 95% confidence interval (CI): 0.990–2.556; P=0.055). Toxicity included grade 2–4 neutropenia in 54% vs 41% (P=0.001), febrile neutropenia 2.7% vs 6.1% (P=0.06), nausea/vomiting 18.5% vs 12.4% (P=0.03) of patients in the sequential and concurrent arm. There were no toxic deaths.Conclusions:Sequential compared with the concurrent administration of anthracyclines and taxanes is associated with a non-significant but possibly clinically meaningful improvement in DFS. In the era of molecular selection of patients for adjuvant chemotherapy, this study offers valuable information for the optimal administration of anthracyclines and taxanes in patients with node-negative disease.
Radio-frequency-identification for security and media circulation in libraries

Radio frequency identification (RFID) systems have been in use in libraries for five years for book identification, for selfcheckout, for anti-theft control, for inventory control, and for sorting and conveying of library books and AV materials. These applications can lead to significant savings in labour costs, enhance customer service, and lower book theft and can provide a constant record update of media collections. In this paper the components and technical features of a modern RFID library system are described to provide a guideline for the evaluation of different systems. A short report of three installations in Europe (one university library and two public libraries) is also provided. It is noted that an important point is that non-proprietary systems can be used for libraries today since the new generation of RFID-chips with the ISO standard 15693 are available. With this technology libraries are not dependent on one company for their lifeline.
Breast Milk Fatty Acids, Eicosanoids, and Cytokines in Mothers with and without Allergic Disease

Allergic disease (AD), including atopic eczema, asthma, allergic rhinitis, and food allergy, is characterized by an imbalance between cytokines produced by distinct T-helper cell subtypes. Whether this imbalance can be transferred from mother to breast milk remains to be established. The objective was to investigate the concentrations and interactions of nutritional and inflammatory factors in breast milk. Breast milk samples were collected from mothers with AD (n = 43) and without AD (n = 51). The concentrations of transforming growth factor (TGF)-β2, tumor necrosis factor-α, IL-4, IL-10, prostaglandin E2, and cysteinyl leukotrienes were measured by immunoassays and fatty acid composition by gas chromatography. Mothers with AD had a lower concentration of TGF-β2 in breast milk [median (interquartile range), 420 (278–701) ng/L] compared with those without AD [539 (378–1108) ng/L;p = 0.003], whereas other cytokines, prostaglandin E2, and cysteinyl leukotriene concentrations or fatty acid composition were not significantly different between the groups. The breast milk inflammatory factors and fatty acid composition were shown to be related. A positive association was observed between TGF-β2 and the proportion of polyunsaturated fatty acids (p = 0.038) and a negative association between TGF-β2 and the proportion of saturated fatty acids (p = 0.029) in breast milk. The reduced TGF-β2 concentration in the breast milk of mothers with AD may interfere with the development of the mucosal immune system of the breast-fed infant. The observed associations between nutritional and inflammatory factors in breast milk suggest that it may be possible to influence the immunologic properties of breast milk by dietary intervention of the mother.
Foreign Direct Investment in China: Reward or Remedy?

This paper tests the significance of FDI as a way to alleviate credit constraints. Incoming foreign investment provides additional sources of capital. Specifically in the Chinese case, enterprises may look for foreign investors, being constrained in their activity due to distortions in the state-dominated system. First, the Chinese financial system allocates resources to the least efficient firms - state-owned enterprises - while denying the same resources to Chinese private enterprises, forcing them to look for a foreign investor. Second, the inefficient system of state investment planning leads to mismanagement of public enterprises, increasing 'insolvency-induced FDI'. We propose to analyse determinants of FDI in Chinese provinces to test the above hypotheses. We control for traditional determinants of FDI such as market access, labour costs, productivity, infrastructure, reform advances and banking sector size in order to assess the impact of inter-provincial heterogeneity in terms of the access that private enterprises have to credit and the distortive management in state-owned firms. Copyright 2007 The Authors Journal compilation 2007 Blackwell Publishing Ltd .
The use of multiple respiratory inhalers requiring different inhalation techniques has an adverse effect on COPD outcomes

BACKGROUND
Patients with COPD may be prescribed multiple inhalers as part of their treatment regimen, which require different inhalation techniques. Previous literature has shown that the effectiveness of inhaled treatment can be adversely affected by incorrect inhaler technique. Prescribing a range of device types could worsen this problem, leading to poorer outcomes in COPD patients, but the impact is not yet known.


AIMS
To compare clinical outcomes of COPD patients who use devices requiring similar inhalation technique with those who use devices with mixed techniques.


METHODS
A matched cohort design was used, with 2 years of data from the Optimum Patient Care Research Database. Matching variables were established from a baseline year of follow-up data, and two cohorts were formed: a "similar-devices cohort" and a "mixed-devices cohort". COPD-related events were recorded during an outcome year of follow-up. The primary outcome measure was an incidence rate ratio (IRR) comparing the rate of exacerbations between study cohorts. A secondary outcome compared average daily use of short-acting beta agonist (SABA).


RESULTS
The final study sample contained 8,225 patients in each cohort (mean age 67 [SD, 10], 57% males, 37% current smokers). Patients in the similar-devices cohort had a lower rate of exacerbations compared with those in the mixed-devices cohort (adjusted IRR 0.82, 95% confidence interval [CI] 0.80-0.84) and were less likely to be in a higher-dose SABA group (adjusted proportional odds ratio 0.54, 95% CI 0.51-0.57).


CONCLUSION
COPD patients who were prescribed one or more additional inhaler devices requiring similar inhalation techniques to their previous device(s) showed better outcomes than those who were prescribed devices requiring different techniques.
Factors affecting electrode-gel-skin interface impedance in electrical impedance tomography

The magnitude, mismatch and temporal variations of the electrode-gel-skin interface impedance can cause problems in electrical impedance tomography (EIT) measurement. It is shown that at the high frequencies generally encountered in EIT the capacitive properties of the electrode interface, and especially those of the skin, are of primary importance. A wide range of techniques are reviewed that could possibly be used to minimise these problems. These techniques include the use of skin preparation, penetration enhancers, temperature and electrical impulses. Although several of these techniques appear very attractive, they are not without serious potential drawbacks. A combination of some of these techniques may well hold the key to success.
A Bayesian approach to combining animal abundance and demographic data

A Bayesian approach to combining animal abundance and demographic data.— In studies of wild animals, one frequently encounters both count and mark–recapture–recovery data. Here, we consider an integrated Bayesian analysis of ring–recovery and count data using a state–space model. We then impose a Leslie– matrix–based model on the true population counts describing the natural birth–death and age transition processes. We focus upon the analysis of both count and recovery data collected on British lapwings (Vanellus vanellus) combined with records of the number of frost days each winter. We demonstrate how the combined analysis of these data provides a more robust inferential framework and discuss how the Bayesian approach using MCMC allows us to remove the potentially restrictive normality assumptions commonly assumed for analyses of this sort. It is shown how WinBUGS may be used to perform the Bayesian analysis. WinBUGS code is provided and its performance is critically discussed.
Chronic pain acceptance questionnaire: confirmatory factor analysis, reliability, and validity in Italian subjects with chronic low back pain.

STUDY DESIGN
Cross-sectional evaluation of the psychometric properties of a translated questionnaire.


OBJECTIVE
To validate the Italian version of the Chronic Pain Acceptance Questionnaire (CPAQ) to allow its use with Italian-speaking patients with chronic low back pain (LBP).


SUMMARY OF BACKGROUND DATA
Growing attention is being given to cognitive-behavioral measures to improve interventions for LBP. The CPAQ has never been validated in Italian subjects with chronic LBP.


METHODS
The psychometric testing included confirmatory factor analysis, reliability by internal consistency (Cronbach α), test-retest reliability (intraclass correlation coefficient), sensitivity to change by calculating the smallest detectable change, and construct validity by comparing CPAQ with a pain numerical rating scale, the Roland-Morris Disability Questionnaire Scale, the Hospital Anxiety and Depression Scale, the Pain Catastrophizing Scale, and the Tampa Scale of Kinesiophobia (Pearson correlations). Hierarchical multiple regression analyses were computed to further investigate construct validity of the CPAQ subscales.


RESULTS
The questionnaire was administered to 142 subjects with chronic LBP. Factor analysis confirmed a 2-factor (viz., Activities Engagement and Pain Willingness) 20-item solution, achieving a good data-model fit. Internal consistency (α = 0.88) and test-retest reliability (intraclass correlation coefficient = 0.86) were good. The smallest detectable change was 22. Construct validity showed a moderate correlation between the CPAQ and numerical rating scale (r = -0.485), Roland-Morris Disability Questionnaire Scale (r = -0.594), and Tampa Scale of Kinesiophobia (r = -0.595), and a close correlation with Hospital Anxiety and Depression Scale (r = -0.610 for the Anxiety score and r = -0.659 for the Depression score) and Pain Catastrophizing Scale (r = -0.658). The standardized regression coefficients for Activity Engagement were significant in all of the equations, and those for Pain Willingness were significant in the anxiety, depression, and disability equations.


CONCLUSION
The Italian CPAQ had a good factorial structure and psychometric properties that replicated the results of other versions. Its use is recommended for clinical and research purposes.


LEVEL OF EVIDENCE
2.
The micro-rhetorics of Game-o-Matic

Micro-rhetorics are the representational units of meaning that emerge from the rhetorical affordances of videogame mechanics, abstract gameplay patterns, and thematic depiction. This paper explains the concept of micro-rhetorics, how game dynamics can be interpreted, and how designers can make use of game mechanics to express ideas through simple videogames. This theoretical framework is informed by the design of Game-O-Matic, a videogame authoring tool that generates games to represent ideas. It takes a network of basic relationships between actors and assembles simple arcade-style game mechanics into videogames that are able to make arguments and depict ideas.
Analytical performance and diagnostic accuracy of immunometric assays for the measurement of circulating oxidized LDL.

BACKGROUND
Oxidized LDL (ox-LDL) plays an important role in the pathogenesis of coronary heart disease (CHD). Several tests for circulating ox-LDL have been published. We believe it is critical to carefully evaluate these assays because small differences in performance may have profound effects when results are compared; we therefore compared the analytical and clinical performances of 2 assays: one developed in our laboratory and a commercial assay (Mercodia) that uses the same monoclonal antibody (4E6).


METHODS
We determined the variance of ox-LDL in both tests, including its longitudinal stability (n = 225; 3 time points per person) and its diagnostic accuracy, by ROC analysis of 95 consecutive CHD patients and 20 controls.


RESULTS
The between-person variability was 77% for the in-house assay (with the remaining 23% being within-person and analytical variance) and 74% for the commercial assay. For comparison, previously reported values were 66% for high-sensitivity C-reactive protein and 82% for total cholesterol. The areas under the curves for CHD in the 2 assays were identical (0.85). The odds ratios (logistic regression) for CHD among persons with high ox-LDL (>or=15 mg/L) compared with persons with low ox-LDL were not different: 4.3 (95% confidence interval, 1.4-12) for the in-house assay and 3.3 (1.1-10) for the commercial assay.


CONCLUSIONS
The longitudinal stability of ox-LDL, as assessed by multiple measures in people over time, is similar to that of total cholesterol and high-sensitivity C-reactive protein. Both assays tested similarly distinguish between healthy controls and CHD patients.
Applicability of nTMS in locating the motor cortical representation areas in patients with epilepsy

Transcranial magnetic stimulation (TMS) is increasingly used for non-invasive functional mapping in preoperative evaluation for brain surgery, and the reliability of navigated TMS (nTMS) motor representation maps has been studied in the healthy population and in brain tumor patients. The lesions behind intractable epilepsy differ from typical brain tumors, ranging from developmental cortical malformations to injuries early in development, and may influence the functional organization of the cortical areas. Moreover, the interictal cortical epileptic activity and antiepileptic medication may affect the nTMS motor threshold. The reliability of the nTMS motor representation localization in epilepsy patients has not been addressed. We compared the nTMS motor cortical representation maps of hand and arm muscles with the results of invasive electrical cortical stimulation (ECS) in 13 patients with focal epilepsy. The nTMS maps were projected to the cortical surface segmented from preoperative magnetic resonance images (MRI), and the positions of the subdural electrodes were extracted from the postoperative low-dose computed tomography (CT) images registered with preoperative MRI. The 3D distance between the average nTMS site and average ECS electrode location was 11 ± 4 mm for the hand and 16 ± 7 mm for arm muscle representation areas. In all patients the representation areas defined with nTMS and ECS were located on the same gyrus, also in patients with abundant interictal epileptic activity on the motor gyrus. nTMS can reliably locate the hand motor cortical representation area with the accuracy needed for pre-surgical evaluation in patients with epilepsy.