LLukas22/scidocs huggingface dataset:
Single Nucleotide Variants of Candidate Genes in Aggrecan Metabolic Pathway Are Associated with Lumbar Disc Degeneration and Modic Changes

INTRODUCTION
Lumbar disc degeneration (LDD) is genetically determined and severity of LDD is associated with Modic changes. Aggrecan is a major proteoglycan in the intervertebral disc and end plate. Progressive reduction of aggrecan is a main feature of LDD and Modic changes.


OBJECTIVES
The study investigated the associations of single nucleotide variants (SNVs) of candidate genes in the aggrecan metabolic pathway with the severity of LDD and Modic changes. In-silico functional analysis of significant SNVs was also assessed.


METHODS
A descriptive cross sectional study was carried out on 106 patients with chronic mechanical low back pain. T1, T2 sagittal lumbar MRI scans were used to assess the severity of LDD and Modic changes. 62 SNVs in ten candidate genes (ACAN, IL1A, IL1B, IL6, MMP3, ADAMTS4, ADAMTS5, TIMP1, TIMP2 and TIMP3) were genotyped on Sequenom MassARRAY iPLEX platform. Multiple linear regression analysis was carried out using PLINK 1.9 in accordance with additive genetic model. In-silico functional analysis was carried out using Provean, SIFT, PolyPhen and Mutation Taster.


RESULTS
Mean age was 52.42±9.42 years. 74 (69.8%) were females. The rs2856836, rs1304037, rs17561 and rs1800587 variants of the IL1A gene were associated with the severity of LDD and Modic changes. The rs41270041 variant of the ADAMTS4 gene and the rs226794 variant of the ADAMTS5 gene were associated with severity of LDD while the rs34884997 variant of the ADAMTS4 gene, the rs55933916 variant of the ADAMTS5 gene and the rs9862 variant of the TIMP3 gene were associated with severity of Modic changes. The rs17561 variant of the IL1A gene was predicted as pathogenic by the PolyPhen prediction tool.


CONCLUSIONS
SNVs of candidate genes in ACAN metabolic pathway are associated with severity of LDD and Modic changes in patients with chronic mechanical low back pain. Predictions of in-silico functional analysis of significant SNVs are inconsistent.
A practical framework to achieve perceptually seamless multi-projector displays

ADITI MAJUMDER: A Practical Framework to Achieve Perceptually Seamless Multi-Projector Displays (Under the direction of Prof. Greg Welch and Prof. Rick Stevens) Arguably the most vexing problem remaining for planar multi-projector displays is that of color seamlessness between and within projectors. While researchers have explored approaches that strive for strict color uniformity, this goal typically results in severely compressed dynamic range and generally poor image quality. In this dissertation, I introduce the emineoptic function that models the color variations in multi-projector displays. I also introduce a general goal of color seamlessness that seeks to balance perceptual uniformity and display quality. These two provide a comprehensive generalized framework to study and solve for color variation in multi-projector displays. For current displays, usually built with same model projectors, the variation in chrominance (hue) is significantly less than in luminance (brightness). Further, humans are at least an order of magnitude more sensitive to variations in luminance than in chrominance. So, using this framework of the emineoptic function I develop a new approach to solve the restricted problem of luminance variation across multi projector displays. My approach reconstructs the emineoptic function efficiently and modifies it based on a perception-driven goal for luminance seamlessness. Finally I use the graphics hardware to reproject the modified function at interactive rates by manipulating only the projector inputs. This method has been successfully demonstrated on three different displays made of 5 × 3 array of fifteen projectors, 3 × 2 array of six projectors and 2 × 2 array of four projectors at the Argonne National Laboratory. My approach is efficient, accurate, automatic and scalable – requiring only a digital camera and a photometer. To the best of my knowledge, this is the first approach and system that addresses the luminance problem in such a comprehensive fashion and generates truly seamless displays with high dynamic range.
External Beam Radiotherapy for Head and Neck Cancers Is Associated with Increased Variability in Retinal Vascular Oxygenation

BACKGROUND
Radiation retinopathy is a possible post-treatment complication of radiation therapy. The pathophysiologic mechanism is hypothesized to be microvascular in origin, but evidence is limited. In an effort to study retinal oxygenation in these patients, we herein evaluate the repeatability and variability of retinal oximetry measurements in subjects who had previously received radiation and make comparisons to a cohort of unirradiated subjects.


METHODS
Using retinal oximetry, a non-invasive imaging modality, we performed in vivo measurements of arteriole (SaO2) and venule SO2 (SvO2) in subjects (n = 9, 18 retinas) who had received incidental radiation to their retinas (≥ 45 Gy to one retina) and in healthy subjects (n = 20, 40 retinas). A total of 1367 SO2 observations on 593 vessels in 29 persons were analyzed to assess three sources of variance in vessel SO2: 1) variance in repeated measurements of the same vessel ("repeatability"), 2) variance in different vessels within the same subject ("within-subject variability"), and 3) variance between subjects ("between-subject variability").


RESULTS
Retinal oximetry measurements were highly repeatable in both irradiated patients and unirradiated subjects. The within-subject variability of SvO2 and SaO2 measurements constituted the highest component of variance in both groups and was significantly higher in venules vs. arterioles (relative effect size 1.8, p<0.001) and in irradiated subjects vs. unirradiated subjects (relative effect size 1.6, p<0.001).


CONCLUSIONS
Retinal oximetry is a highly repeatable technology and can be reliably used to study vascular oxygenation in irradiated subjects. Different vessels within the same subject exhibit a high degree of variability, suggesting that pooled analyses of multiple vessels are most likely to be informative of regional retinal oxygenation. Finally, irradiated subjects exhibited significantly higher within-subject variability in SO2 measurements, suggesting that radiation may cause regional alterations in retinal oxygen delivery and/or metabolism.
Treatment of Complete and Partial Obstruction of the Nasolacrimal System with Polyurethane Stents: Initial Experience

Purpose: To present our experience in the treatment of nasolacrimal occlusion by means of polyurethane stents. Methods: Forty polyurethane stents were placed under fluoroscopic guidance in 35 consecutive patients with epiphora due to total or partial obstruction of the nasolacrimal system. The set designed by Song was used in all patients. The procedure was performed by introducing a guidewire through the superior punctum into the canaliculus and advancing it across the obstruction into the inferior meatus of the nasal cavity. After pulling out the guidewire, the stent was advanced in retrograde fashion and released into the sac and the nasolacrimal duct. Results: The technical success rate was 100%. The average time for the procedure was 25 min (range 10–60 min). Immediate complications were: mild pain (n= 5), severe pain (n= 1), minimal epistaxis (n= 7), and moderate epistaxis (n= 1). No major complications occurred. The last clinical control revealed complete resolution of epiphora in 35 eyes and partial resolution in four; one patient did not improve. Conclusion: This technique for treatment of obstruction of the nasolacrimal system is simple and safe, and may obviate the use of more invasive procedures.
Remission in early rheumatoid arthritis treated with conventional DMARDs. Results of a two-year follow-up study of El Ayachi Moroccan cohort.

OBJECTIVE
This study aimed to evaluate remission in patients with early RA treated by conventional DMARDs and to identify its possible predictor factors.


METHODS
Patients with early RA (<12 months) were enrolled in a 2-year follow-up study. Standard evaluation completed at baseline and at 24 months included clinical, laboratory, functional and structural assessment. Clinical remission after 2 years of follow-up was defined when DAS28 was less than 2.6. Possible predictor factors for remission were analyzed.


RESULTS
Fifty-one patients (88.2% women, mean age of 46.9 [24-72] years, mean disease duration of 24 [6-48] weeks) were enrolled in this study. The delay in referral for specialist care was 140 [7-420] days. Rheumatoid factor, anti-CCP, HLA-DRB1*01 and DRB1*04 alleles were present respectively in 62.5, 56.6, 11.8, and 45.1% of patients. At 24 months, 77.2% received a median dose of 5 (0-8) mg/day of prednisone and 65.2% was taking methotrexate (MTX). 13.6% of patients had stopped their DMARD because of socioeconomic difficulties. At 24 months, we noted a significant improvement of morning stiffness, pain score, swollen joint count, ESR, CRP, DAS28 and HAQ scores. Remission at 2 years was noted in 34.8% of patients and was significantly associated in univariate but not in multivariate analysis to male sex (P=0.02) and to short delay in referral for specialist (P=0.03).


CONCLUSION
In this cohort of early RA patients treated with conventional DMARDs, especially with methotrexate in monotherapy, remission at 2-year of follow-up was obtained in one third of patients. No predictor factors of remission were found out. These results should be verified by further studies.
Comparison of Exact String Matching Algorithms for Biological Sequences

Exact matching of single patterns in DNA and amino acid sequences is studied. We performed an extensive experimental comparison of algorithms presented in the literature. In addition, we introduce new variations of earlier algorithms. The results of the comparison show that the new algorithms are efficient in practice.
Teaching Disciplinary Literacy to Adolescents: Rethinking Content- Area Literacy

In this article, Timothy and Cynthia Shanahan argue that “disciplinary literacy” — advanced literacy instruction embedded within content-area classes such as math, science, and social studies — should be a focus of middle and secondary school settings. Moving beyond the oft-cited “every teacher a teacher of reading” philosophy that has historically frustrated secondary content-area teachers, the Shanahans present data collected during the first two years of a study on disciplinary literacy that reveal how content experts and secondary content teachers read disciplinary texts, make use of comprehension strategies, and subsequently teach those strategies to adolescent readers. Preliminary findings suggest that experts from math, chemistry, and history read their respective texts quite differently; consequently, both the content-area experts and secondary teachers in this study recommend different comprehension strategies for work with adolescents. This study not only has implications for which comprehension strategies might best fit particular disciplinary reading tasks, but also suggests how students may be best prepared for the reading, writing, and thinking required by advanced disciplinary coursework.
Automatic Number Plate Recognition System

Automatic Number Plate Recognition (ANPR) is a mass surveillance system that captures the image of vehicles and recognizes their license number. The objective is to design an efficient automatic authorized vehicle identification system by using the Indian vehicle number plate. In this paper we discus different methodology for number plate localization, character segmentation & recognition of the number plate. The system is mainly applicable for non standard Indian number plates by recognizing single & double line number plates under different varying illumination condition and works on multilingual, multicolour number plates according to Indian condition. Keywords— ANPR, Localization, Segmentation, Artificial Neural Network, Optical Character Recognition
Polymorphisms of adrenoceptors are not associated with an increased risk of adverse event in heart failure: a MERIT-HF substudy.

BACKGROUND
Enhanced sympathetic activation has a central role in the development of heart failure (HF). We assessed whether the alpha(2C)-adrenoceptor (Del322-325) polymorphism exclusively or in combination with a beta(1)-adrenoceptor (Arg389) polymorphism, each with known independent effects on sympathetic function, were associated with an increased risk of adverse events in HF.


METHODS AND RESULTS
A total of 526 patients enrolled in the Metoprolol CR/XL Randomized Intervention Trial in Congestive Heart Failure study were genotyped for both adrenoceptor polymorphisms. The distribution of alpha(2C) genotypes was similar between the event and nonevent groups. However, a reduced prevalence of the Del322-325 allele was found in individuals with ischemic congestive HF (P=.022). Patients possessing both the alpha(2C) Del322-325 and beta(1) Arg389 alleles had no increased risk of events. Adjusting for confounding variables and the beta(1) Arg389Gly polymorphism, the odds ratio of being ins/del + del/del for the alpha(2C) Del322-325 and having an event was 0.89 with 95% CI 0.49-1.63, P=.715. Similarly, adjusting for confounding variables and the alpha(2C) Del322-325 polymorphism the odds ratio of being Arg/Arg or Arg/Gly for the beta(1) Arg389Gly polymorphism and having an event was 1.13 with 95% CI 0.52-2.17, P=.864.


CONCLUSIONS
The alpha(2C) Del322-325 polymorphism exclusively or in combination with the beta(1)Arg389 allele is not associated with an increased risk of adverse events in HF.
Gambling as a Motivation for the Commission of Financial Crime

Disclaimer: This research paper does not necessarily reflect the policy position of the Commonwealth Government. Adam Graycar Director Gambling has always been a popular form of entertainment in Australia, but the advent of poker and gaming machines, casinos, TABs and lotto-style games has contributed to a substantial growth in the gambling industry. The Productivity Commission (1999) reports that 82 per cent of the Australian adult population engaged in some form of gambling in 1997–98, with gambling taxes and levies paid to state and territory governments nearly doubling over the past 10 years. At present, adult Australians spend $13,839 million a year on gambling, or $901 per adult per year (ABS 2002, p. 7). However, with increasing opportunities and venues for gambling, public concern about “problem gambling” has grown. This paper examines one of the social problems said to be associated with gambling—the commission of financial crime by individuals trying to obtain funds to gamble with. Recent data supporting the relationship between problem gambling and financial crime are presented, and the most effective judicial responses are assessed.
Money for Nothing: Speeding Up Evolutionary Algorithms Through Better Initialization

That the initialization can have a significant impact on the performance of evolutionary algorithms (EAs) is a well known fact in the empirical evolutionary computation literature. Surprisingly, it has nevertheless received only little attention from the theoretical community.
 We bridge this gap by providing a thorough runtime analysis for a simple iterated random sampling initialization. In the latter, instead of starting an EA with a random sample, it is started in the best of k search points that are taken from the search space uniformly at random. Implementing this strategy comes at almost no cost, neither in the actual coding work nor in terms of wall-clock time.
 Taking the best of two random samples already decreases the Θ(n log n) expected runtime of the (1+1)~EA and Randomized Local Search on OneMax by an additive term of order √n. The optimal gain that one can achieve with iterated random sampling is an additive term of order √n log n}. This also determines the best possible mutation-based EA for OneMax, a question left open in [Sudholt, IEEE TEC 2013].
 At the heart of our analysis is a very precise bound for the maximum of k independent Binomially distributed variables with success probability 1/2.
Generating test cases for Q-learning algorithm

In this paper, the work addresses the notion of generating test cases by applying Q-learning algorithm in source code to obtain the optimal solution. The test cases are generated manually using the state diagram and automatically using obtained optimal solution from Q-learning algorithm. Here, the shortest path algorithm is chosen and the optimal solution is obtained for each and every initial states. It mainly focuses on the analysis between the manually generated test cases and automatically generated test cases.
Computer graphics in airport management

Abstract Computer graphics technology has been in use for over a decade. This technology has matured to a point where large applications involving databases can now be undertaken. This article describes the use of graphics technology in management of airport utilities, facilities and land. The systems described took over 60 manyears of development effort. This is considered as one of the largest and most complex undertakings in the application of computer graphics technology. As far as can be determined, no other airport in the world has a system of this size, complexity and sophistication. The events that led to a decision to develop the system are summarized. The system and how it is currently used at the airports within the Kingdom of Saudi Arabia are described.
Introduction to Convolutional Neural Networks

6 The convolution layer 11 6.1 What is convolution? . . . . . . . . . . . . . . . . . . . . . . . . . 11 6.2 Why to convolve? . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 6.3 Convolution as matrix product . . . . . . . . . . . . . . . . . . . 15 6.4 The Kronecker product . . . . . . . . . . . . . . . . . . . . . . . 17 6.5 Backward propagation: update the parameters . . . . . . . . . . 17 6.6 Even higher dimensional indicator matrices . . . . . . . . . . . . 19 6.7 Backward propagation: prepare supervision signal for the previous layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 6.8 Fully connected layer as a convolution layer . . . . . . . . . . . . 22
Impairment of cognitive function in women receiving adjuvant treatment for high-risk breast cancer: high-dose versus standard-dose chemotherapy.

BACKGROUND
Although high-dose chemotherapy is rapidly gaining acceptance as a treatment option for a number of cancers, the long-term toxic effects of such therapy are a concern. Cognitive deficits (e.g., problems with memory and concentration) are not uncommon after chemotherapy, but they have not been documented systematically. In this study, we assessed the prevalence of cognitive deficits in a group of patients with high-risk breast cancer who were randomly assigned to receive either high-dose or standard-dose adjuvant chemotherapy plus tamoxifen, and we investigated whether high-dose chemotherapy impaired cognitive functioning more than standard-dose chemotherapy.


METHODS
Cognitive functioning was evaluated by use of a battery of neuropsychologic tests. In addition, patients were interviewed with regard to cognitive problems, health-related quality of life, anxiety, and depression. Results from patients who received adjuvant systemic therapy were compared with results from patients who had early stage breast cancer not treated with such therapy (control patients).


RESULTS
The study population consisted of 34 patients treated with high-dose chemotherapy plus tamoxifen, 36 patients treated with standard-dose chemotherapy plus tamoxifen, and 34 control patients. For all patients, the average time since the completion of last nonhormonal therapy was 2 years. Cognitive impairment was found in 32% of the patients treated with high-dose chemotherapy, in 17% of the patients treated with standard-dose chemotherapy, and in 9% of the control patients. In comparison with the control patients, patients treated with high-dose chemotherapy appeared to have an 8.2-times higher risk of cognitive impairment (odds ratio; 95% confidence interval [CI] = 1.8-37.7); in comparison with the patients who received standard-dose chemotherapy, this risk of impairment was 3.5-times higher (95% CI = 1.0-12.8).


CONCLUSION
High-dose chemotherapy appears to impair cognitive functioning more than standard-dose chemotherapy. Central nervous system toxicity may be a dose-limiting factor in high-dose chemotherapy regimens.
Recent progress on synchrotron-based in-situ soft X-ray spectroscopy for energy materials.

Soft X-ray spectroscopy (SXS) techniques such as photoelectron spectroscopy, soft X-ray absorption spectroscopy and X-ray emission spectroscopy are efficient and direct tools to probe electronic structures of materials. Traditionally, these surface sensitive soft X-ray techniques that detect electrons or photons require high vacuum to operate. Many recent in situ instrument developments of these techniques have overcome this vacuum barrier. One can now study many materials and model devices under near ambient, semi-realistic, and operando conditions. Further developments of integrating the realistic sample environments with efficient and high resolution detection methods, particularly at the high brightness synchrotron light sources, are making SXS an important tool for the energy research community. In this progress report, we briefly describe the basic concept of several SXS techniques and discuss recent development of SXS instruments. We then present several recent studies, mostly in situ SXS experiments, on energy materials and devices. Using these studies, we would like to highlight that the integration of SXS and in situ environments can provide in-depth insight of material's functionality and help researchers in new energy material developments. The remaining challenges and critical research directions are discussed at the end.
Towards semantic interoperability in healthcare: ontology mapping from SNOMED-CT to HL7 version 3

One of the most successful Healthcare Information Models is version 2 of the Health Level 7 (HL7) standard. However, this standard has various problems, mainly its lack of semantic interoperability. This shortfall was addressed in HL7 Version 3, a newer standard which has been designed to solve this problem. Total semantic interoperability cannot be achieved without defined terminology, and to this end the use of the Systemised Nomenclature of Medicine Clinical Terms (SNOMED-CT) is proposed. The difficulty arrives when deciding how to integrate the information model and the terminology. The line between where one ends and the other begins is often indistinct. This paper describes a proposal for normalising the two using ontology mapping and basing HL7 message models on SNOMED-CT concepts and their relationships, in an effort to further total semantic interoperability and seamless communication between healthcare entities.