LLukas22/scidocs huggingface dataset:
A prospective multicenter study of systemic reactions in standardized specific immunotherapy for allergic rhinitis in China.

BACKGROUND
Standardized allergen-specific immunotherapy (SIT) has been used in China for years. However, there is no extensive study of the safety of standardized SIT in Chinese patients until now. The aim of the current study is to perform a prospective and multicenter study to evaluate the systemic reactions (SRs) of standardized SIT in Chinese patients.


METHODS
The study was performed in 13 allergy centers in China, using the same vaccine and practice procedure. The length of observation period was 2 years. SRs were recorded and analyzed.


RESULTS
There were 666 patients included (261 children and 405 adults). All patients finished the initial phase and 47 patients withdrew during the maintenance phase. There were 0.47% (94/19,963) SRs in all injections (0.72% in children and 0.31% in adults); 8.26% (55/666) patients experienced SRs (12.26% children and 5.68% adults). The occurrence of SRs was significantly higher in children than that in adults (p < 0.01). A higher ratio of SRs was found among patients accompanied with asthma. There were 74.47% SRs of grade I, 15.96% SRs of grade II, 7.45% SRs of grade III, and 2.13% SRs of grade IV. There were 90.43% of SRs associated with the discomfort of lower respiratory tract.


CONCLUSION
This multicenter study showed that properly conducted standardized SIT was a safe treatment for allergic rhinitis in China. The incidence of SRs was higher in children than that in adults.
An Adaptive Thresholding Method for BTV Estimation Incorporating PET Reconstruction Parameters: A Multicenter Study of the Robustness and the Reliability

OBJECTIVE
The aim of this work was to assess robustness and reliability of an adaptive thresholding algorithm for the biological target volume estimation incorporating reconstruction parameters.


METHOD
In a multicenter study, a phantom with spheres of different diameters (6.5-57.4 mm) was filled with (18)F-FDG at different target-to-background ratios (TBR: 2.5-70) and scanned for different acquisition periods (2-5 min). Image reconstruction algorithms were used varying number of iterations and postreconstruction transaxial smoothing. Optimal thresholds (TS) for volume estimation were determined as percentage of the maximum intensity in the cross section area of the spheres. Multiple regression techniques were used to identify relevant predictors of TS.


RESULTS
The goodness of the model fit was high (R(2): 0.74-0.92). TBR was the most significant predictor of TS. For all scanners, except the Gemini scanners, FWHM was an independent predictor of TS. Significant differences were observed between scanners of different models, but not between different scanners of the same model. The shrinkage on cross validation was small and indicative of excellent reliability of model estimation.


CONCLUSIONS
Incorporation of postreconstruction filtering FWHM in an adaptive thresholding algorithm for the BTV estimation allows obtaining a robust and reliable method to be applied to a variety of different scanners, without scanner-specific individual calibration.
Celator: A Multi-algorithm Cryptographic Co-processor

Nowadays hi-tech secure products offer more services and more security. The corresponding market is now oriented towards more flexibility. As an answer we propose here a multi-algorithm cryptographic co-processor called Celator. A main processor entrusts to the Celator the cryptographic tasks like encrypting or decrypting data blocks using secret key encryption algorithms such as advanced encryption standard (AES) or data encryption standard (DES). Moreover Celator allows hashing data using the secure hash algorithms (SHA). These algorithms are frequently implemented in hi-tech secure products in software or in hardware mode. Celator corresponds to their flexible hardware implementation. Moreover an user can (under specific conditions) implement its own cryptographic algorithm in Celator. Celator can perform an AES encryption with a throughput of 47 Mbps, the DES encryption with a throughput of 26 Mbps, condense a 512 bit SHA message with a throughput of 36 Mbps. Finally we report performance comparisons among Celator, general purpose processors, and some dedicated and dynamically reconfigurable circuits.
Genome analysis IMEx : Imperfect Microsatellite Extractor

Motivation: Microsatellites, also known as simple sequence repeats, are the tandem repeats of nucleotide motifs of the size 1–6bp found in every genome known so far. Their importance in genomes is well known. Microsatellites are associated with various disease genes, have been used as molecular markers in linkage analysis and DNA fingerprinting studies, and also seem to play an important role in the genome evolution. Therefore, it is of importance to study distribution, enrichment and polymorphism of microsatellites in the genomes of interest. For this, the prerequisite is the availability of a computational tool for extraction of microsatellites (perfect as well as imperfect) and their related information from whole genome sequences. Examination of available tools revealed certain lacunae in them and prompted us to develop a new tool. Results: In order to efficiently screen genome sequences for microsatellites (perfect as well as imperfect), we developed a new tool called IMEx (Imperfect Microsatellite Extractor). IMEx uses simple string-matching algorithm with sliding window approach to screen DNA sequences for microsatellites and reports the motif, copy number, genomic location, nearby genes, mutational events and many other features useful for in-depth studies. IMEx is more sensitive, efficient and useful than the available widely used tools. IMEx is available in the form of a stand-alone program as well as in the form of a web-server. Availability: A World Wide Web server and the stand-alone program are available for free access at http://203.197.254.154/IMEX/ or http://www.cdfd.org.in/imex Contact: han@cdfd.org.in
Navigational blocks: tangible navigation of digital information

Navigational Blocks provide a tangible user interface for applications such as information kiosks. Orientation, movement, and relative position of electronically and microprocessor augmented physical blocks support visitor querying, retrieving, understanding, navigation and exploration of an historical information database.
Properties of surface waveguides derived from inversion of fundamental and higher mode dispersive GPR data

Thin surface layers of high-permittivity material (e.g., water-saturated soil) can cause a pronounced dispersion of ground-penetrating radar waves. The dispersion characteristics depend on the permittivity and thickness of the effective surface waveguide and the permittivity of the material below it. As for the analogous seismic case, the values of these parameters can be estimated by applying a scheme that includes calculating the phase-velocity spectra, picking dispersion curves from the spectra, and inverting the dispersion curves using a combined local and global minimization procedure. Here, this scheme is extended by incorporating higher order modes. Explicit expressions for the cutoff frequencies of the fundamental and higher order transverse electric (TE) and transverse magnetic (TM) modes are derived. These expressions demonstrate that the cutoff frequency decreases as the thickness and/or permittivity of the waveguide increase and/or the permittivity of the lower half-space decreases. In addition, the TE cutoff frequencies are shown to be generally lower than the TM cutoff frequencies. Numerical modeling of realistic models demonstrates the presence of the higher order modes with the correct cutoff frequencies. Application of the modified inversion scheme to synthetic and field data demonstrates its efficacy in providing the required physical property information. In particular, better-constrained models are obtained by including higher order modes in the inversion
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping

Motivation
High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms.


Results
We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10.


Availability and implementation
https://github.com/BilkentCompGen/GateKeeper.


Contact
mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr.


Supplementary information
Supplementary data are available at Bioinformatics online.
Automated Player Selection for a Sports Team using Competitive Neural Networks

The use of data analytics to constitute a winning team for the least cost has become the standard modus operandi in club leagues, beginning from Sabermetrics for the game of basketball. Our motivation is to implement this phenomenon in other sports as well, and for the purpose of this work we present a model for football, for which to the best of our knowledge, previous work does not exist. The main objective is to pick the best possible squad from an available pool of players. This will help decide which team of 11 football players is best to play against a particular opponent, perform prediction of future matches and helps team management in preparing the team for the future. We argue in favour of a semi-supervised learning approach in order to quantify and predict player performance from team data with mutual influence among players, and report win accuracies of around 60%. Keywords—Team selection; match outcome prediction; neural networks
Goal detection in football by using support vector machines for classification

In this paper we present a technique for detecting goals during a football match b y using images acquired by a single camera placed externally to the eld. The method does not require the modiication neither of the ball nor of the goalmouth. Due to the attitude of the camera with respect to football ground, the system can be thought of as an electronic linesman which helps the referee in establishing the occurrence of a goal during a football match. The occurrence of the event is established detecting the ball and comparing its position with respect to the location of the goalpost in image. The ball detection technique relies on a supervised learning scheme called Support Vector Machines for classiication. The examples used for training are appropriately ltered version of views of the object to be detected, previously stored in form of image patterns. We h a ve extensively tested the technique on real images in which the ball is both fully visible and partially occluded. The performance of the proposed detection scheme are measured in terms of detection rate, false positive rate and precision in the ball local-ization in image. 1 I n troduction In this paper we focus on the problem of detecting the occurrence of a goal during a football match, by using methods and devices which does not require the modiication neither of the ball nor of the goalmouth. Automatic goal detection in football is an open problem which is getting particular attention from referee associations, sport press and supporters. In fact, there are not rare situations in which a goal occurres 1 , but the referee and his collaboratores linesmen are not able to detecting the goal and, more important, do not award any point to neither teams correctly. Such situations occur for example when, after a shooting, the ball touches the internal side of the crossbar, bounces oo the eld having crossed completely the goal line and goes back, without touching the net. One of the most signiicative evidences of this event, named ghost goal, occurred during the World Cup nal match on 1966 between England and West Germany. In that case, an english player struck a shot towards the German goal and the ball cannoned down from the crossbar, hit the ground and bounced back out into the play. English players claimed a goal, that the ball had passed completely over the line, …
Aggregate production : Fines generation during rock crushing

The energy required to crush rocks is proportional to the amount of new surface area that is created; hence, a very important percentage of the energy consumed to produce construction aggregates is spent in producing non-commercial fines. Data gathered during visits to quarries, an extensive survey and laboratory experiments are used to explore the role of mineralogy and fracture mode in fines production during the crushing of single aggregates and aggregates within granular packs. Results show that particle-level loading conditions determine the failure mode, resulting particle shape and fines generation. Point loading (both single particles and grains in loose packings) produces clean fractures and a small percentage of fines. In choked operations, high inter-particle coordination controls particle-level loading conditions, causesmicro-fractures on new aggregate faces and generates a large amount of fines. The generation of fines increases when shear is imposed during crushing. Aggregates produced in current crushing operations show the effects of multiple loading conditions and fracture modes. Results support the producers' empirical observations that the desired cubicity of aggregates is obtained at the expense of increased fines generation when standard equipment is used. © 2006 Elsevier B.V. All rights reserved.
Support vector machine classification for large data sets via minimum enclosing ball clustering

Support vector machine (SVM) is a powerful technique for data classification. Despite of its good theoretic foundations and high classification accuracy, normal SVM is not suitable for classification of large data sets, because the training complexity of SVM is highly dependent on the size of data set. This paper presents a novel SVM classification approach for large data sets by using minimum enclosing ball clustering. After the training data are partitioned by the proposed clustering method, the centers of the clusters are used for the first time SVM classification. Then we use the clusters whose centers are support vectors or those clusters which have different classes to perform the second time SVM classification. In this stage most data are removed. Several experimental results show that the approach proposed in this paper has good classification accuracy compared with classic SVM while the training is significantly faster than several other SVM classifiers. r 2007 Elsevier B.V. All rights reserved.
The effects of balance and postural stability exercises on spa based rehabilitation programme in patients with ankylosing spondylitis.

BACKGROUND
Ankylosing spondylitis (AS) can cause severe functional disorders that lead to loss of balance.


OBJECTIVE
The aim of this study was to investigate the effects of balance and postural stability exercises on spa based rehabilitation programme in AS subjects.


METHODS
Twenty-one participants were randomized to the study (n= 11) and control groups (n= 10). Patients balance and stability were assessed with the Berg Balance Scale (BBS), Timed Up and Go (TUG) Test, Single Leg Stance Test (SLST) and Functional Reach Test (FRT). AS spesicied measures were used for assessing to other parameters. The treatment plan for both groups consisted of conventional transcutaneous electrical nerve stimulation (TENS), spa and land-based exercises 5 days per week for 3 weeks. The study group performed exercises based on postural stability and balance with routine physiotherapy practice in thermal water and in exercise room.


RESULTS
The TUG, SLST and FUT scores were significantly increased in the study group. In both groups, the BASMI, BASFI, BASDAI and ASQoL scores decreased significantly by the end of the treatment period (p< 0.05).


CONCLUSIONS
In AS rehabilitation, performing balance and stability exercises in addition to spa based routine approaches can increase the duration of maintaining balance and can improve the benefits of physiotherapy.
Longest Common Extensions in Sublinear Space

The longest common extension problem (LCE problem) is to construct a data structure for an input string T of length n that supports LCE(i, j) queries. Such a query returns the length of the longest common prefix of the suffixes starting at positions i and j in T . This classic problem has a well-known solution that uses O(n) space and O(1) query time. In this paper we show that for any trade-off parameter 1 ≤ τ ≤ n, the problem can be solved in O( τ ) space and O(τ) query time. This significantly improves the previously best known time-space trade-offs, and almost matches the best known time-space product lower bound.
Implementing Gentry's Fully-Homomorphic Encryption Scheme

We describe a working implementation of a variant of Gentry’s fully homomorphic encryption scheme (STOC 2009), similar to the variant used in an earlier implementation effort by Smart and Vercauteren (PKC 2010). Smart and Vercauteren implemented the underlying “somewhat homomorphic” scheme, but were not able to implement the bootstrapping functionality that is needed to get the complete scheme to work. We show a number of optimizations that allow us to implement all aspects of the scheme, including the bootstrapping functionality. Our main optimization is a key-generation method for the underlying somewhat homomorphic encryption, that does not require full polynomial inversion. This reduces the asymptotic complexity from Õ(n) to Õ(n) when working with dimension-n lattices (and practically reducing the time from many hours/days to a few seconds/minutes). Other optimizations include a batching technique for encryption, a careful analysis of the degree of the decryption polynomial, and some space/time trade-offs for the fully-homomorphic scheme. We tested our implementation with lattices of several dimensions, corresponding to several security levels. From a “toy” setting in dimension 512, to “small,” “medium,” and “large” settings in dimensions 2048, 8192, and 32768, respectively. The public-key size ranges in size from 70 Megabytes for the “small” setting to 2.3 Gigabytes for the “large” setting. The time to run one bootstrapping operation (on a 1-CPU 64bit machine with large memory) ranges from 30 seconds for the “small” setting to 30 minutes for the “large” setting.
Effects of clarithromycin in patients with active rheumatoid arthritis.

OBJECTIVE
To evaluate the clinical efficacy, safety, and tolerability of clarithromycin in patients with rheumatoid arthritis.


RESEARCH DESIGN AND METHODS
This was a 6-month, monocenter, randomized, double-blind, placebo-controlled study. A total of 81 patients with early rheumatoid arthritis were treated with either once-daily oral clarithromycin (500 mg) or daily oral placebo for 6 months.


MAIN OUTCOME MEASURES
The primary efficacy variable was the percentage of patients who had a 20% improvement according to American College of Rheumatology (ACR) criteria (an ACR 20 response) at 6-months. Secondary outcome measures were 50% improvement and 70% improvement according to ACR criteria (an ACR 50 response and an ACR 70 response, respectively).


RESULTS
A significantly greater percentage of patients treated with 500 mg clarithromycin met the ACR 20 response at 6 months compared with patients who received placebo (59 vs. 33%; p < 0.001). Greater percentages of patients treated with 500 mg clarithromycin also achieved ACR 50 responses (34 vs. 10%; p < 0.001) and ACR 70 responses (20 vs. 3%; p = 0.003) compared with patients who received placebo, respectively. Clarithromycin was well tolerated. There were no dose-limiting toxic effects.


CONCLUSIONS
In patients with early active rheumatoid arthritis, treatment with clarithromycin significantly improved the signs and symptoms of rheumatoid arthritis. Clarithromycin has been shown to be effective against rheumatoid arthritis.
Effect of low doses of scopolamine on RR interval variability, baroreflex sensitivity, and exercise performance in patients with chronic heart failure.

OBJECTIVE
To study the effect of transdermal scopolamine on heart rate variability, baroreflex sensitivity, and exercise performance in patients with heart failure and age matched healthy volunteers.


DESIGN
Double blind, randomised, placebo controlled, crossover study.


PATIENTS
16 patients with chronic, stable heart failure due to ischaemic cardiomyopathy (mean (SEM) age 58 (2) years; mean (SEM) radionuclide left ventricular ejection fraction 28 (2)%; New York Heart Association class II-III) and eight age matched healthy controls.


INTERVENTION
Transdermal scopolamine (500 micrograms delivered over 72 h) or a placebo patch was administered for 48 h.


MAIN OUTCOME MEASURES
Indices of tonic and reflex cardiac vagal activity and exercise performance.


RESULTS
In both groups scopolamine produced a reduction in the 24 h average heart rate and an increase in the time domain measures of heart rate variability. Both the incidence and severity of ventricular arrhythmias remained unchanged. Baroreflex sensitivity, evaluated by the phenylephrine technique, increased significantly (P < 0.001) with scopolamine in patients with heart failure (6.22 (2.81) ms/mm Hg) and in healthy volunteers (5.97 (2.20) ms/mm Hg) as did the amplitude of respiratory sinus arrhythmia, computed by autoregressive spectral analysis of 10 min electrocardiographic recordings (319.9 (123.5) and 657.3 (126.6) ms2 respectively, P < 0.001). While exercise performance did not change, heart rate at submaximal exercise was significantly reduced by scopolamine in each group.


CONCLUSIONS
In patients with mild to moderate heart failure low doses of scopolamine increased tonic and reflex cardiac vagal activity. This was achieved without affecting exercise tolerance or the incidence and severity of ventricular arrhythmias.