Miracle-dz/UniFAR-FTUs huggingface dataset:
Post-Tooth Extraction Bacteraemia: A Randomized Clinical Trial on the Efficacy of Chlorhexidine Prophylaxis

Objectives To investigate the development of post-extraction bacteraemia (PEB) after the prophylactic use of chlorhexidine (CHX). Patients and Methods A total of 201 patients who underwent a tooth extraction were randomly distributed into four groups: 52 received no prophylaxis (CONTROL), 50 did a mouthwash with 0.2% CHX before the tooth extraction (CHX-MW), 51 did a mouthwash with 0.2% CHX and a subgingival irrigation with 1% CHX (CHX-MW/SUB_IR) and 48 did a mouthwash with 0.2% CHX and a continuous supragingival irrigation with 1% CHX (CHX-MW/SUPRA_IR). Peripheral venous blood samples were collected at baseline, 30 seconds after performing the mouthwash and the subgingival or supragingival irrigation, and at 30 seconds and 15 minutes after completion of the tooth extraction. Blood samples were analysed applying conventional microbiological cultures under aerobic and anaerobic conditions performing bacterial identification of the isolates. Results The prevalences of PEB in the CONTROL, CHX-MW, CHX-MW/SUB_IR and CHX-MWSUPRA_IR groups were 52%, 50%, 55% and 50%, respectively, at 30 seconds and 23%, 4%, 10% and 27%, respectively, at 15 minutes. The prevalence of PEB at 15 minutes was significantly higher in the CONTROL group than in the CHX-MW group (23% versus 4%; p = 0.005). At the same time, no differences were found between CONTROL group and CHX-MW/SUB_IR or CHX-MW/SUPRA_IR groups. Streptococci (mostly viridans group streptococci) were the most frequently identified bacteria (69–79%). Conclusions Performing a 0.2% CHX mouthwash significantly reduces the duration of PEB. Subgingival irrigation with 1% CHX didn’t increase the efficacy of the mouthwash while supragingival irrigation even decreased this efficacy, probably due to the influence of these maneuvers on the onset of bacteraemia. Clinical Relevance These results confirm the suitability of performing a mouthwash with 0.2% CHX before tooth extractions in order to reduce the duration of PEB. This practice should perhaps be extended to all dental manipulations. Trial Registration Clinicaltrials.gov NCT02150031
Boosted local binaries for object detection

We propose a novel binary feature for object detection encoding local neighbor patterns of different sizes and locations. Each region pair of the proposed feature is selected by RealAdaBoost algorithm with a penalty term on the structure diversity. As a result, useful features that are good at describing specific objects will be chosen to build the classifier. Moreover, the encoding scheme is applied in both the gradient domain and the intensity domain, which is complementary to standard binary features (e.g. LBP and LAB). The proposed method was tested using the CMU-MIT frontal face dataset, INRIA pedestrian dataset, and UIUC car dataset respectively. Experimental results show that the proposed method outperforms traditional binary features LBP and LAB, which contributes to a significant improvement on detection accuracy and converges 2 times faster. It also achieves comparable performance with some state-of-the-art algorithms.
The estimation of spatial positions by using an omnidirectional camera system

With an omnidirectional camera system, it is possible to take 360°views of the surrounding area at each camera position. These systems are used particularly in robotic applications, in autonomous navigation and supervision technology for ego­motion estimation. In addition to the visual capture of the environment itself, we can compute the parameters of orientation and position from image sequences, i.e. we get three parameters of position and three of orientation (yaw rate, pitch and roll angle) at each time of acquisition. The aim of the presented project is to investigate the quality of the spatial trajectory of a mobile survey vehicle from the recorded image sequences. In this paper, we explain the required photogrammetric background and show the advantages of omnidirectional camera systems for this task. We present the first results on our test set and discuss alternative applications for omnidirectional cameras.
Image reconstruction based on back propagation learning in Compressed Sensing theory

Over the past few years, a new framework known as compressive sampling has been developed for simultaneous sampling and compression. It can significantly reduce the number of measurements required for a given signal in traditional compression methods. One way to increase the compression ratio during the sampling is that we can apply different compression ratio to different part of the image. Thus we can increase the compression ratio to the background of an image in order to increase the total compression ratio. However, we know nothing of the original image before we start sampling. So we can use sampling data to judge which part of the image belongs to the background then we apply second-time sampling to these parts of the image. Before sampling an image, we should use a lot of images to be the training data to compute the weights of the classification. Then in the second-sampling, we use these weights to decide which part belongs to the background. In the first-sampling, I apply the algorithm of block based Compressed Sensing and use the sampling data as feature vectors. In the construction step, I use OMP method and DCT matrix to reconstruct the image.
Extracting Relations among Embedded Software Design Patterns

Pattern is a reusable description of knowledge. Efficient software development can be achieved by sharing and reusing knowledge using patterns and their relations. Because the manual analysis of relations among patterns is costly, we proposed an automatic relation analysis technique for software patterns. Knowledge management in embedded software design has fallen behind. However, in these days, some patterns in embedded software design have become available on the World Wide Web (WWW) and other resources.The purpose of this paper is to obtain some useful relations among embedded software design patterns and GoF's design patterns. Our technique will be useful for the automated relation analysis among patterns. As a result of experiments, some relations among different pattern catalogs (e.g., GoF's design pattern catalog and real-time system design pattern catalog) are extracted. These relations are thought to be useful in software development.
Linear Multiuser Detection for Asynchronous CDMA Systems: Chip Pulse Design and Time Delay Distribution

The large system performance analysis of linear multiuser detectors (e.g. MMSE, MSWF, multistage detectors) for asynchronous CDMA systems is provided. While the performance of synchronous systems with square-root waveforms is independent of the chip bandwidth, the performance of asynchronous systems depends on the pulse shape and the bandwidth. It increases as the bandwidth increases beyond half on the chip rate and, in such a case, asynchronous systems outperform the synchronous ones.
c-Myc Is a Critical Target for C/EBPα in Granulopoiesis

ABSTRACT CCAAT/enhancer binding protein α (C/EBPα) is an integral factor in the granulocytic developmental pathway, as myeloblasts from C/EBPα-null mice exhibit an early block in differentiation. Since mice deficient for known C/EBPα target genes do not exhibit the same block in granulocyte maturation, we sought to identify additional C/EBPα target genes essential for myeloid cell development. To identify such genes, we used both representational difference analysis and oligonucleotide array analysis with RNA derived from a C/EBPα-inducible myeloid cell line. From each of these independent screens, we identified c-Myc as a C/EBPα negatively regulated gene. We mapped an E2F binding site in the c-Myc promoter as thecis-acting element critical for C/EBPα negative regulation. The identification of c-Myc as a C/EBPα target gene is intriguing, as it has been previously shown that down-regulation of c-Myc can induce myeloid differentiation. Here we show that stable expression of c-Myc from an exogenous promoter not responsive to C/EBPα-mediated down-regulation forces myeloblasts to remain in an undifferentiated state. Therefore, C/EBPα negative regulation of c-Myc is critical for allowing early myeloid precursors to enter a differentiation pathway. This is the first report to demonstrate that C/EBPα directly affects the level of c-Myc expression and, thus, the decision of myeloid blasts to enter into the granulocytic differentiation pathway.
On error estimators in finite element analysis

In this work, first a review and an analysis of various recovery-based error estimators for elliptic problems are given. We consider the Zhu Zienkiewicz estimator, the Hinton Campbell estimator, the estimator used in ADINA and a simple nodal averaging scheme, all of which are recovery-based algorithms. In the second part of this work, we discuss higher-order-accuracy points and demonstrate how their locations can be calculated exactly in a number of cases. In particular we show how these points do not always coincide with the points used by Barlow, nor with lower order Gauss points, as used by Zhu and Zienkiewicz. The use of the exact locations of the higherorder-accuracy points instead of the Barlow points or lower order Gauss points could result in improvements in the performance of recovery-based algorithms. From a more theoretical standpoint, our findings regarding the higher-order-accuracy points also allow us to show what analogies exist between implicit algorithms and recovery-based algorithms and to gain a better understanding of these two classes of error estimators. Most importantly, based on our findings, we develop a new error estimator for onedimensional problems. The new error estimator makes use of shape functions which are perpendicular to the finite element space in a local sense in general, and in a global sense in some cases. This means that all calculations required by this new error estimator are carried out at the element level rather than at the patch level. This is a significant improvement over patch-based error estimators. The performance of the new error estimator is then evaluated in some example solutions. Thesis Supervisor: Klaus-Jiirgen Bathe Title: Professor
Observation of dually decoded regions of the human genome using ribosome profiling data

The recently developed ribosome profiling technique (Ribo-Seq) allows mapping of the locations of translating ribosomes on mRNAs with subcodon precision. When ribosome protected fragments (RPFs) are aligned to mRNA, a characteristic triplet periodicity pattern is revealed. We utilized the triplet periodicity of RPFs to develop a computational method for detecting transitions between reading frames that occur during programmed ribosomal frameshifting or in dual coding regions where the same nucleotide sequence codes for multiple proteins in different reading frames. Application of this method to ribosome profiling data obtained for human cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame (from different transcripts as well as from the same mRNA) and revealed the translation of hitherto unpredicted coding open reading frames.
Determining the Vulnerabilities of the Power Transmission System

Determining the vulnerabilities in power transmission systems requires two distinct steps because most large blackouts have two distinct parts, the triggers/initiating event followed by the cascading failure. Finding the important triggers for large blackouts is the first and standard step. Next, the cascading part of the extreme event (which can be long or short) is critically dependent on the "state" of the system, how heavily the lines are loaded, how much generation margin exists, and where the generation exists relative to the load. However, during large cascading events there are some lines whose probability of overloading is higher that the others. Statistical studies of blackouts using the OPA code allow the identification of such lines or groups of line for a given network model, thereby providing a technique for identifying at risk (or critical) clusters. This paper addresses both parts of the vulnerability question.
Reinterpreting the Transformation Posterior in Probabilistic Image Registration

Probabilistic image registration methods estimate the posterior distribution of transformation. The conventional way of interpreting the transformation posterior is to use the mode as the most likely transformation and assign its corresponding intensity to the registered voxel. Meanwhile, summary statistics of the posterior are employed to evaluate the registration uncertainty, that is the trustworthiness of the registered image. Despite the wide acceptance, this convention has never been justified. In this paper, based on illustrative examples, we question the correctness and usefulness of conventional methods. In order to faithfully translate the transformation posterior, we propose to encode the variability of values into a novel data type called ensemble fields. Ensemble fields can serve as a complement to the registered image and a foundation for developing advanced methods to characterize the uncertainty in registration-based tasks. We demonstrate the potential of ensemble fields by pilot examples
Secure localization in wireless sensor networks

Wireless sensor networks have very promising future to many applications. Ensuring that sensor nodes locations are verified and are protected from malicious attacks will enable sensor networks deployment in mission critical applications. Due to the deployment nature, sensor nodes are highly vulnerable to localization attacks where an adversary can capture the nodes, changes its location or replaces it with a malicious node. In this paper we study this problem and present a secure localization scheme where nodes can securely locate themselves and send a message about their location to the neighboring nodes, eventually that message reaches the cluster leader and then to a secure base station. To find the location of nodes, we take advantage of triangulation method and protect the message transmission with a secure triple key management scheme.
Bartonella Species and Trombiculid Mites of Rats from the Mekong Delta of Vietnam

Abstract A survey of Bartonella spp. from 275 rats purchased in food markets (n=150) and trapped in different ecosystems (rice field, forest, and animal farms) (n=125) was carried out during October, 2012–March, 2013, in the Mekong Delta of Vietnam. The overall Bartonella spp. prevalence detected by culture and PCR in blood was 14.9% (10.7–19.1%), the highest corresponding to Rattus tanezumi (49.2%), followed by Rattus norvegicus (20.7%). Trapped rats were also investigated for the presence and type of chiggers (larvae of trombiculid mites), and Bartonella spp. were investigated on chigger pools collected from each rat by RT-PCR. A total of five Bartonella spp. were identified in rats, three of which (B. elizabethae, B. rattimassiliensis, and B. tribocorum) are known zoonotic pathogens. Among trapped rats, factors independently associated with increased prevalence of Bartonella spp. included: (1) Rat species (R. tanezumi); (2) the number of Trombiculini–Blankaartia and Schoengastiini–Ascoschoengastia mites found on rats; and (3) the habitat of the rat (i.e., forest/fields vs. animal farms). The prevalence of Bartonella infection among chiggers from Bartonella spp. –positive R. tanezumi rats was 5/25 (25%), compared with 1/27 (3.7%) among Bartonella spp. –negative R. tanezumi rats (relative risk [RR]=5.4, 95% confidence interval [CI] 0.68–43.09). The finding of Bartonella spp. –positive chiggers on Bartonella spp. –negative rats is strongly suggestive of a transovarial transmission cycle. Rats are ubiquitous in areas of human activity and farms in the Mekong Delta; in addition, trapping and trading of rats for food is common. To correctly assess the human risks due to rat trapping, marketing, and carcass dressing, further studies are needed to establish the routes of transmission and cycle of infection. The widespread presence of these zoonotic pathogens in rats and the abundance of human—rat interactions suggest that surveillance efforts should be enhanced to detect any human cases of Bartonella infection that may arise.
Recognizing the impact of ambient air pollution on skin health

Ambient air pollution is a known public health hazard that negatively impacts non‐cutaneous organs; however, our knowledge regarding the effects on skin remains limited. Current scientific evidence suggests there are four mechanisms by which ambient air pollutants cause adverse effects on skin health: (i) generation of free radicals, (ii) induction of inflammatory cascade and subsequent impairment of skin barrier, (iii) activation of the aryl hydrocarbon receptor (AhR) and (iv) alterations to skin microflora. In this review, we provide a comprehensive overview on ambient air pollutants and their relevant sources, and highlight current evidence of the effects on skin.
A reinforcement learning approach for the circle agent of geometry friends

Geometry Friends (GF) is a physics-based platform game, used in one of the AI competitions of the IEEE CIG Conference in 2013 and 2014. The game engages two characters, a circle and a rectangle, in a cooperative challenge involving collecting a set of objects in a 2D platform world. In this work, we propose a novel learning approach to the control of the circle character that circumvents the excessive specialization to the public levels in the competition observed in the other existing solutions for GF. Our approach proposes a method that partitions solving a level of GF into three sub-tasks: solving one platform (SP1), deciding the next platform to solve (SP2) and moving from one platform to another (SP3). We use reinforcement learning to solve SP1 and SP3 and a depth-first search to solve SP2. The quality of the agent implemented was measured against the performance of the winner of the Circle Track of the 2014 GF Game AI Competition, CIBot. Our results show that our agent is able to successfully overcome the over-specialization to the public levels, showing comparatively better performance on the private levels.
Asthma and allergies: is the farming environment (still) protective in Poland? The GABRIEL Advanced Studies

Evidence exists that a farming environment in childhood may provide protection against atopic respiratory disease. In the GABRIEL project based in Poland and Alpine regions of Germany, Austria and Switzerland, we aimed to assess whether a farming environment in childhood is protective against allergic diseases in Poland and whether specific exposures explain any protective effect.
Quantitative Evaluation of Model-Driven Performance Analysis and Simulation of Component-Based Architectures

During the last decade, researchers have proposed a number of model transformations enabling performance predictions. These transformations map performance-annotated software architecture models into stochastic models solved by analytical means or by simulation. However, so far, a detailed quantitative evaluation of the accuracy and efficiency of different transformations is missing, making it hard to select an adequate transformation for a given context. This paper provides an in-depth comparison and quantitative evaluation of representative model transformations to, e.g., queueing petri nets and layered queueing networks. The semantic gaps between typical source model abstractions and the different analysis techniques are revealed. The accuracy and efficiency of each transformation are evaluated by considering four case studies representing systems of different size and complexity. The presented results and insights gained from the evaluation help software architects and performance engineers to select the appropriate transformation for a given context, thus significantly improving the usability of model transformations for performance prediction.
MMR: a tool for read multi-mapper resolution

Motivation: Mapping high throughput sequencing data to a reference genome is an essential step for most analysis pipelines aiming at the computational analysis of genome and transcriptome sequencing data. Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase, but also has significant impact on the results of downstream analyses. We present the multimapper resolution (MMR) tool that infers optimal mapping locations from the coverage density of other mapped reads. Results: Filtering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. We illustrate that the accuracy (Spear-man correlation) of transcript quantification increases by 17% when using reads of length 51. In addition, MMR decreases the alignment file sizes by more than 50% and this leads to a reduced running time of the quantification tool. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs. Supplementary Material: Source code and documentation are available for download at github.com/ratschlab/mmr. Supplementary text and figures, comprehensive testing results and further information can be found at bioweb.me/mmr. Contact akahles@cbio.mskcc. org and raetsch@cbio.mskcc. org
Fundamental limits of electronic dispersion compensation in optical communications with direct photodetection

The information theoretical limits of electronic dispersion compensation (EDC) for on-off keying non-return-to-zero optical transmission systems with direct photodetection are investigated. The results obtained show that the optical signal-to-noise ratio penalty entailed by EDC can be limited to about 2 dB at most values of chromatic dispersion of interest in current applications.