Miracle-dz/UniFAR-FTUs huggingface dataset:
New Tn916-related elements causing erm(B)-mediated erythromycin resistance in tetracycline-susceptible pneumococci.

OBJECTIVES To analyse the as yet unexplored genetic elements encoding erm(B)-mediated erythromycin resistance in tetracycline-susceptible pneumococci. METHODS Sixteen Streptococcus pneumoniae clinical isolates sharing erm(B)-mediated erythromycin resistance and susceptibility to tetracycline were used. Gene detection was performed by PCR using both established and specially designed primers. S. pneumoniae R6, Streptococcus pyogenes 12RF and Enterococcus faecalis JH2-2 were used as recipients in mating experiments. RESULTS Of the 16 test strains, 14 bore an unexpressed tet(M) gene which in 13 strains had a genetic linkage with erm(B). Three isolates yielded a 3.2 kb and 10 an 11.9 kb erm(B)/tet(M) amplicon. The former three showed genetic organizations similar to that of the composite element Tn3872, where the erm(B)-carrying Tn917 transposon is inserted into a Tn916-like element. Of the latter 10 isolates, 9 showed genetic organizations substantially overlapping with that of Tn6002, a newly sequenced erm(B)-containing Tn916-related transposon. The tenth isolate carried a novel composite element (designated Tn6003) resulting from the insertion into a Tn6002-like transposon of a fragment [designated macrolide-aminoglycoside-streptothricin (MAS) element] containing a second erm(B) (lacking the stop codon) and a variant of the aadE-sat4-aphA-3 cluster. The two tet(M)-negative isolates had different Tn3872-related elements, one containing a complete and one a deleted MAS fragment. Conjugative transfer was obtained from donors carrying Tn6002-related elements, not from donors carrying Tn3872-related elements. CONCLUSIONS In tetracycline-susceptible pneumococci with erm(B)-mediated erythromycin resistance, the erm(B) gene is carried on a variety of Tn916-related genetic elements either lacking tet(M) or, more often, carrying an unexpressed tet(M) gene.
Embedding Geometry in Generative Models for Pose Estimation of Object Categories

Regression-based models built on local gradient-based feature descriptors have showed to be successful for continuous pose estimation of object categories. Nonetheless, a crucial weakness of these methods is that no geometric information is taken into account. Therefore, geometrically inconsistent poses may be preferred, and this forces to employ a coarse-grained pose estimator as a pre-processing step to avoid potentially large estimation errors. In this paper, we propose a method that combines generative feature models and graph matching techniques in a unified probabilistic formulation of the continuous pose estimation problem. Our approach retains the lightness and generality of generative feature modeling, while favoring geometrically consistent results. Experiments show that pose pre-processing steps are not needed if geometry is embedded in the matching stage. We evaluated our approach on two different car datasets and we experimentally show that our algorithm outperforms state-of-the-art methods by 25%.
Interference Analysis and Subchannel Allocation Schemes in Tri-Sectored OFDMA Systems

This paper analyzes the interference aspects of tri-sectored OFDMA systems and evaluates the performance of some subchannel allocation schemes to mitigate inter-sector interference. To maximize spectral efficiency, it is preferred to adopt frequency reuse of 1. But, carrier to interference and noise ratio (CINR) values at the boundary of sectors are extremely deteriorated. Two subchannel allocation methods are compared and evaluated in this environment. One is to maximize disparity, which is to maximize the number of subchannels in good CINR values, and the other is to minimize disparity, which is to maximize the number of subchannels in moderate CINR values. These schemes are compared under proportionally fair scheduling algorithm. Simulation results regarding to throughput show that the schemes outperform random allocation schemes in 802.16 based systems.
City Happenings into Wikipedia Category: Classifying Urban Events by Combining Analyses of Location-based Social Networks and Wikipedia

Recently, many researchers have been focusing on the detection and classification of urban events by information analysis on social networks. Previous works mainly use text analysis of users' posts on social networks for detecting urban events. However, this approach has a limitation that the users' posts must mention the event for the analysis to be conducted. We propose a new method for classifying urban events by extracting user interest from the location-based social network information without text analysis. The proposed method includes analyzing common friends of users in the vicinity of the event venue and extracting common the friends' attributes by referring to related Wikipedia information. We designed and implemented the proposed method, and conducted an experiment for evaluating our method. Our experimental result shows that our method can classify events well in cases where participants have similar interests.
Dynamic Replacement of Histone H3 Variants Reprograms Epigenetic Marks in Early Mouse Embryos

Upon fertilization, reprogramming of gene expression is required for embryo development. This step is marked by DNA demethylation and changes in histone variant composition. However, little is known about the molecular mechanisms causing these changes and their impact on histone modifications. We examined the global deposition of the DNA replication-dependent histone H3.1 and H3.2 variants and the DNA replication-independent H3.3 variant after fertilization in mice. We showed that H3.3, a euchromatic marker of gene activity, transiently disappears from the maternal genome, suggesting erasure of the oocyte-specific modifications carried by H3.3. After fertilization, H3.2 is incorporated into the transcriptionally silent heterochromatin, whereas H3.1 and H3.3 occupy unusual heterochromatic and euchromatin locations, respectively. After the two-cell stage, H3.1 and H3.3 variants resume their usual respective locations on heterochromatin and euchromatin. Preventing the incorporation of H3.1 and H3.2 by knockdown of the histone chaperone CAF-1 induces a reciprocal increase in H3.3 deposition and impairs heterochromatin formation. We propose that the deposition of different H3 variants influences the functional organization of chromatin. Taken together, these findings suggest that dynamic changes in the deposition of H3 variants are critical for chromatin reorganization during epigenetic reprogramming.
Identification and Expression Analysis of PIN-Like (PILS) Gene Family of Rice Treated with Auxin and Cytokinin

The phytohormone auxin is one of the most important signaling molecules that undergo accumulation or depletion in a temporal or spatial manner due to wide arrays of changes in developmental or stress programs. Proper distribution, maintenance and homeostasis of auxin molecules across the plant systems are one of the most important phenomena required for proper growth and development of plant. The distribution and homeostasis of auxin is maintained by auxin transport systems across the plant. The auxin transportation is carried out by auxin transporter family proteins, popularly known as auxin efflux carriers (PINs). In this study, a sub-family of auxin efflux carrier (OsPILS) genes was identified from Oryza sativa and relative expression profile was studied by treating them with auxin and cytokinin. Oryza sativa encodes seven putative sub-cellularly localized transmembrane OsPILS genes distributed in five chromosomes. Differential expression of OsPILS genes was found to be modulated by auxin and cytokinin treatment. In auxin treated plants, all OsPILS genes were up-regulated in leaves and down regulated in roots during the third week time period of developmental stages. In the cytokinin treated plants, the maximum of OsPILS genes were up-regulated during the third week time period in root and leaf tissue. Regulation of gene expression of OsPILS genes by auxin and cytokinin during the third week time period revealed its important role in plant growth and development.
Cloning and Expression of an Oligopeptidase, PepO, with Novel Specificity from Lactobacillus rhamnosus HN001 (DR20)

ABSTRACT Oligopeptidases of starter and nonstarter lactic acid bacteria contribute to the proteolytic events important in maturation and flavor development processes in cheese. This paper describes the molecular cloning, expression, and specificity of the oligopeptidase PepO from the probiotic nonstarter strain Lactobacillus rhamnosus HN001 (DR20). The pepO gene encodes a protein of 70.9 kDa, whose primary sequence includes the HEXXH motif present in certain classes of metallo-oligopeptidases. The pepO gene was cloned in L. rhamnosus HN001 and overexpressed in pTRKH2 from its own promoter, which was mapped by primer extension. It was further cloned in both pNZ8020 and pNZ8037 and overexpressed in Lactococcus lactis subsp. cremoris NZ9000 from the nisA promoter. The purified PepO enzyme demonstrated unique cleavage specificity for αs1-casein fragment 1–23, hydrolyzing the bonds Pro-5-Ile-6, Lys-7-His-8, His-8-Gln-9, and Gln-9-Gly-10. The impact of this enzyme in cheese can now be assessed.
Overlapped Speech Detection in Meeting Using Cross-Channel Spectral Subtraction and Spectrum Similarity

We propose an overlapped speech detection method for speech recognition and speaker diarization of meetings, where each speaker wears a lapel microphone. Two novel features are utilized as inputs for a GMM-based detector. One is speech power after cross-channel spectral subtraction which reduces the power from the other speakers. The other is an amplitude spectral cosine correlation coefﬁcient which effectively extracts the correlation of spectral components in a rather quiet condition. We evaluated our method using a meeting speech corpus of four speakers. The accuracy of our proposed method, 74.1%, was signiﬁcantly better than that of the conventional method, 67.0%, which uses raw speech power and power spectral Pearson’s correlation coefﬁcient.
Can police enhance public confidence by improving quality of service? Results from two surveys in England and Wales

Public opinions of the police have been a fixture at the top of the policy agenda in England and Wales in recent years, with successive governments stating they wish to see improvements in ‘trust and confidence’. But significant doubts remain as to how this might be done, and even if it is possible for police to enhance public confidence in any straightforward way. Indeed, it often seems that it is much easier for police to damage public opinion than to improve it. This paper reports findings from two surveys on contact between the public and the police conducted in England and Wales. First, panel data are used to examine the issue of ‘asymmetry’ in the relationship between satisfaction with police contacts and wider public confidence in the police. Negative pre-existing opinions of the police are found to be predictive of negatively received contact, while positive views do not predict well-received contact. Yet, single contacts, both negative and positive, are predictive of subsequent confidence in the police. Second, British Crime Survey data are used to investigate what ‘drives’ satisfaction among crime victims. Personal treatment appears to be valued over criminal justice outcomes, providing support for process-based policing models. It appears that fears about an absolute asymmetry in the effect of contact on confidence may be overstated, and that improving the way officers handle encounters might lead to enhanced trust and confidence.
Contemporary HRD research: a triarchy of theoretical perspectives and their prescriptions for HRD

Addresses some of the key debates within the HRD literature and considers the extent to which HRD can be described as a field of study. The paper addresses the issues raised in the contributions that make up this special issue and identifies a broad range of methodologies and use of research methods. It argues that all of the contributions fit into at least one theoretical perspective: capabilities, psychological contacts and the learning organization/organizational learning. The paper concludes with a consideration of the prescriptions which the perspectives advocate for HRD in organizations.
Automatically Tracking Metadata and Provenance of Machine Learning Experiments

We present a lightweight system to extract, store and manage metadata and provenance information of common artifacts in machine learning (ML) experiments: datasets, models, predictions, evaluations and training runs. Our system accelerates users in their ML workﬂow, and provides a basis for comparability and repeatability of ML experiments. We achieve this by tracking the lineage of produced artifacts and automatically extracting metadata such as hyperparameters of models, schemas of datasets or layouts of deep neural networks. Our system provides a general declarative representation of said ML artifacts, is integrated with popular frameworks such as MXNet, SparkML and scikit-learn, and meets the demands of various production use cases at Amazon.
Guideline-Recommended Medications: Variation Across Medicare Advantage Plans and Associated Mortality

OBJECTIVES: To evaluate variation in the prescription of guideline-recommended medications across Medicare Advantage (MA) plans and to determine whether such variation is associated with increased mortality. METHODS: Observational study of 111,667 patients aged 65 years or older receiving care in 203 MA plans. We linked data from the Medicare Health Outcomes (HOS) Survey cohort 9 (April 2006–May 2008) with the Medicare Part D prescription benefit files (January 1, 2006–December 31, 2007) to examine variation in treatment across MA plans and its association with differences in observed (O)/expected (E) mortality ratio for 5 high-volume chronic conditions: diabetes, coronary artery disease (CAD), congestive heart failure (CHF), chronic obstructive pulmonary disease (COPD)/asthma, and depression. RESULTS: Analysis of variance confirmed that the 203 MA plans differed significantly in their use of guideline-recommended treatment (P≤0.02). Those MA plans with higher use of angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers (r=-0.40; P less than 0.0001) and beta-blockers (r=-0.27; P less than 0.0001) in patients with CHF were significantly associated with lower O/E mortality ratios. Those MA plans with higher use of multiple guideline-recommended medications were significantly associated with lower O/E mortality ratios in CHF (r=-0.45; P less than 0.0001) and diabetes (r=-0.14; P less than 0.042). There were no significant associations between the variation in performance indicators and mortality ratios in patients with CAD and COPD/asthma. Those MA plans with higher use of antidepressant medications had significantly higher O/E mortality ratios (r=0.28, P less than 0.0001). CONCLUSIONS: There was wide variation across MA plans in the prescription of guideline-recommended medications that had a measurable relationship to the mortality of elderly patients with CHF and diabetes. These findings can serve to both motivate and target quality improvement programs.
Exposure to Ionizing Radiation during Dental X-Rays Is Not Associated with Risk of Developing Meningioma: A Meta-Analysis Based on Seven Case-Control Studies

Background Many observational studies have found that exposure to dental X-rays is associated with the risk of development of meningioma. However, these findings are inconsistent. We conducted a meta-analysis to assess the relationship between exposure to dental X-rays and the risk of development of meningioma. Methods The PubMed and EMBASE databases were searched to identify eligible studies. Summary odds ratio (OR) estimates and 95% confidence intervals (95% CIs) were used to compute the risk of meningioma development according to heterogeneity. Subgroup and sensitivity analyses were performed to further explore the potential heterogeneity. Finally, publication bias was assessed. Results Seven case-control studies involving 6,174 patients and 19,459 controls were included in the meta-analysis. Neither exposure to dental X-rays nor performance of full-mouth panorex X-rays was associated with an increased risk of development of meningioma (overall: OR, 0.97; 95% CI, 0.70–1.32; dental X-rays: OR, 1.05; 95% CI, 0.89–1.25; panorex X-rays: OR, 1.01; 95% CI, 0.76–1.34). However, exposure to bitewing X-rays was associated with a slightly increased risk of development of meningioma (OR, 1.73; 95% CI, 1.28–2.34). Similar results were obtained in the subgroup and sensitivity analyses. Little evidence of publication bias was observed. Conclusion Based on the currently limited data, there is no association between exposure to dental X-rays and the risk of development of meningioma. However, these results should be cautiously interpreted because of the heterogeneity among studies. Additional large, high-quality clinical trials are needed to evaluate the association between exposure to dental X-rays and the risk of development of meningioma.
Project STARS (Studies on Trajectories of Adolescent Relationships and Sexuality): A longitudinal, multi-domain study on sexual development of Dutch adolescents

This study gives an overview of Project STARS (Studies on Trajectories of Adolescent Relationships and Sexuality), a four-wave longitudinal study of 1297 Dutch adolescents. First, the sample, measures and four sub-projects are described. Second, hierarchical regression analyses were conducted to examine how key variables from the individual domain (impulsivity), parent domain (parent–adolescent relationship quality), peer domain (involvement with peers) and media domain (time spent on social networking sites), and their interactions predict changes in the experience with sexual behaviour of adolescents across time. Results showed that higher levels of impulsivity, lower quality of relation with parents, more frequent involvement with peers and more time spent on social networking sites at baseline predicted increases in sexual experience of adolescents over a subsequent 1.5-year time period. No interaction effects among the domains were found. The findings highlight the significance of a multi-domain approach to the study of adolescent sexual development.
Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin

The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson–Crick/Hoogsteen base pair. In the presence of a hairpin stem, the UA non-canonical base pair becomes part of the UA-handle motif. To probe the hierarchical organization and energy landscape of the T-loop, we performed replica exchange molecular dynamics (REMD) simulations of the T-loop in isolation and as part of a hairpin. Our simulations reveal that the isolated T-loop adopts coil conformers stabilized by base stacking. The T-loop hairpin shows a highly rugged energy landscape featuring multiple local minima with a transition state for folding consisting of partially zipped states. The U-turn displays a high conformational flexibility both when the T-loop is in isolation and as part of a hairpin. On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle. This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction. Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context.
Performance improved GA based statistical computing technique for retinal image segmentation

Retinal vessel segmentation is important for the detection of numerous eye diseases and plays an important role in automatic retinal screening systems. K-nearest neighbor classifier is used to perform a soft segmentation of retinal vessels and is a supervised method. This method produces segmentation by classifying each image pixel as vessel or nonvessel, based on the output of filters and the pixel values with in the neighborhood. Genetic algorithms are powerful tools for K-nearest neighbors classifier optimization. Genetic Algorithm is used to optimize the feature vector by removing both irrelevant and redundant features and finds optimal ones. In this work, GA is used to estimate the K value. The performance of the unoptimised K-nearest neighbor classifier and the genetic optimized K-NN are analysed in terms of segmentation efficiency and convergence time period. Experimental results show superior results for the genetic algorithm based K-NN in terms of the performance measures.
Using Social Learning Methodologies in Higher Education

It is commonly accepted that contemporary cohorts of students witness and experience the benefits of information technologies in their learning processes. The so-called ``digital natives'' acquire, as a consequence of their early exposure to these technologies, different patterns of work, distinct attention conducts, new learning preferences and, generally, better skills for learning and working within rich online social contexts. So, it seems reasonable that the traditional education systems evolve and shape their practice to leverage those new patterns. Despite the fact that online social networks (OSNs) are widely recognized as a powerful tool for adding a new social dimension to the learning management systems (LMSs), OSNs do not fully integrate the specific features of the learning process yet and LMSs do not exploit the advantages of an active social environment for reinforcing the learning experience. We report in this paper the design, development and use of a software platform which enlarges and adapts the basic features of an OSN in order to be useful for very general learning environments. The software allows the creation, assessment and reporting of a range of collaborative activities based on social interactions among the students, and offers a reward mechanism by means of ranking and reputation. We argue that this approach is helpful in increasing the students' motivation, besides improving the learning experience and performance. The software has been tested in an undergraduate course about computer networks. Different tests confirm that the impact on learning success is statistically significant and positive.
Automating Objective Data Quality Assessment (Experiences in Software Tool Design)

The paper discusses the design goals, current architecture and overall experiences gained in the process of building a software tool aiding human analysts in estimating approximate information quality (information accuracy) of an unknown relational data source. We discuss the algorithms and techniques that we found effective. In particular, we discuss the automated reasoning techniques used to identify common data types for which known data quality rules exist and data mining algorithms discovering unknown probable data quality rules. Tool’s human interface issues are briefly overviewed. In this regard we discuss methods used for information quality rule scripting and graphical result presentation.
Incremental vision-based topological SLAM

In robotics, appearance-based topological map building consists in infering the topology of the environment explored by a robot from its sensor measurements. In this paper, we propose a vision-based framework that considers this data association problem from a loop-closure detection perspective in order to correctly assign each measurement to its location. Our approach relies on the visual bag of words paradigm to represent the images and on a discrete Bayes filter to compute the probability of loop-closure. We demonstrate the efficiency of our solution by incremental and real-time consistent map building in an indoor environment and under strong perceptual aliasing conditions using a single monocular wide-angle camera.