Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Spoligotyping Defined Genotypic Lineages among Drug-Resistant Mycobacterium tuberculosis Complex Clinical Isolates in Ankara, Turkey

Background Investigation of genetic heterogeneity and spoligotype-defined lineages of drug-resistant Mycobacterium tuberculosis clinical isolates collected during a three-year period in two university hospitals and National Tuberculosis Reference and Research Laboratory in Ankara, Turkey. Methods and Findings A total of 95 drug-resistant M. tuberculosis isolates collected from three different centers were included in this study. Susceptibility testing of the isolates to four major antituberculous drugs was performed using proportion method on Löwenstein–Jensen medium and BACTEC 460-TB system. All clinical isolates were typed by using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) methods. Seventy-three of the 95 (76.8%) drug resistant M. tuberculosis isolates were isoniazid-resistant, 45 (47.4%) were rifampicin-resistant, 32 (33.7%) were streptomycin-resistant and 31 (32.6%) were ethambutol-resistant. The proportion of multidrug-resistant isolates (MDR) was 42.1%. By using spoligotyping, 35 distinct patterns were observed; 75 clinical isolates were grouped in 15 clusters (clustering rate of 79%) and 20 isolates displayed unique patterns. Five of these 20 unique patterns corresponded to orphan patterns in the SITVIT2 database, while 4 shared types containing 8 isolates were newly created. The most prevalent M. tuberculosis lineages were: Haarlem (23/95, 24.2%), ill-defined T superfamily (22/95, 23.2%), the Turkey family (19/95, 20%; previously designated as LAM7-TUR), Beijing (6/95, 6.3%), and Latin-America & Mediterranean (LAM, 5/95 or 5.3%), followed by Manu (3/95, 3.2%) and S (1/95, 1%) lineages. Four of the six Beijing family isolates (66.7%) were MDR. A combination of IS6110-RFLP and spoligotyping reduced the clustering rate from 79% to 11.5% among the drug resistant isolates. Conclusions The results obtained showed that ill-defined T, Haarlem, the Turkey family (previously designated as LAM7-TUR family with high phylogeographical specifity for Turkey), Beijing and LAM were predominant lineages observed in almost 80% of the drug-Resistant M. tuberculosis complex clinical isolates in Ankara, Turkey.
Spectro-temporal post-smoothing in NMF based single-channel source separation

In this paper, we propose a new, simple, fast, and effective method to enforce temporal smoothness on nonnegative matrix factorization (NMF) solutions by post-smoothing the NMF decomposition results. In NMF based single-channel source separation, NMF is used to decompose the magnitude spectra of the mixed signal as a weighted linear combination of the trained basis vectors. The decomposition results are used to build spectral masks. To get temporal smoothness of the estimated sources, we deal with the spectral masks as 2-D images, and we pass the masks through a smoothing filter. The smoothing direction of the filter is the time direction of the spectral masks. The smoothed masks are used to find estimates for the source signals. Experimental results show that, using the smoothed masks give better separation results than enforcing temporal smoothness prior using regularized NMF.
Performance Analysis of a Multicast System in WDM Single-hop Broadcast-and-Select Optical Network

In this paper we use an approximate analytical solution to show the influence of tuning delay on the system performance under different network conditions and characteristics such as number of wavelength channels and offered load. We also examine the effect of average packet delay and tuning time on receiver throughput. Finally, we demonstrate the channel blocking probability versus network offered load characteristics
Scalable distributed event detection for Twitter

Social media streams, such as Twitter, have shown themselves to be useful sources of real-time information about what is happening in the world. Automatic detection and tracking of events identified in these streams have a variety of real-world applications, e.g. identifying and automatically reporting road accidents for emergency services. However, to be useful, events need to be identified within the stream with a very low latency. This is challenging due to the high volume of posts within these social streams. In this paper, we propose a novel event detection approach that can both effectively detect events within social streams like Twitter and can scale to thousands of posts every second. Through experimentation on a large Twitter dataset, we show that our approach can process the equivalent to the full Twitter Firehose stream, while maintaining event detection accuracy and outperforming an alternative distributed event detection system.
In Older Men, Lower Plasma 25-Hydroxyvitamin D Is Associated with Reduced Incidence of Prostate, but Not Colorectal or Lung Cancer

Context and objective Prostate, colorectal and lung cancers are common in men. In this study, we aimed to determine whether vitamin D status is associated with the incidence of these cancers in older men. Design Prospective cohort study. Setting and participants 4208 older men aged 70–88 years in Perth, Western Australia Main outcome measures Plasma 25-hydroxyvitamin D [25(OH)D] concentration was measured by immunoassay. New diagnoses of prostate, colorectal and lung cancers were determined via electronic record linkage. Results During a mean follow-up of 6.7±1.8 years, there were 315, 117 and 101 new diagnoses of prostate, colorectal and lung cancer. In multivariate competing risks proportional hazards models, every 10 nmol/l decrease in 25(OH)D concentration was associated with a 4% reduction in prostate cancer incidence (sub-hazard ratio [SHR] 0.96, 95% confidence interval [CI] 0.92–1.00). Every halving of 25(OH)D concentration was associated with a 21% reduction in incident prostate cancer in multivariate analysis (SHR 0.79, 95% CI 0.63–0.99). Following exclusion of prostate cancer cases diagnosed within 3 years of blood sampling, low 25(OH)D <50 nmol/l was associated with lower incident prostate cancer, and higher 25(OH)D >75 nmol/l was associated with higher incidence, when compared to the reference range 50–75 nmol/l, respectively (p = 0.027). Significant associations were also observed when 25(OH)D was modeled as a quantitative variable. No associations were observed between plasma 25(OH)D concentration with incidence of colorectal or lung cancer. Conclusion Lower levels of vitamin D may reduce prostate cancer risk in older men. By contrast, levels of vitamin D did not predict incidence of colorectal or lung cancers. Further studies are needed to determine whether a causal relationship exists between vitamin D and prostate cancer in ageing men.
Partial Profiles of Quasi-Complete Graphs

We enumerate graph homomorphisms to quasi-complete graphs, i.e., graphs obtained from complete graphs by removing one edge. The source graphs are complete graphs, quasi-complete graphs, cycles, paths, wheels and broken wheels. These enumerations give rise to sequences of integers with two indices; one of the indices is the number of vertices of the source graph, and the other index is the number of vertices of the target graph.
Improved flatness of a supercontinuum at 1.55 µm in tapered microstructured optical fibres

Supercontinuum (SC) generation occurs when high-power ultrashort optical pulses propagate through a nonlinear optical medium and it has been investigated since 1970s [1]. Microstructured optical fibres (MOFs) have enabled major advances in obtaining SC spectral broadening over the past decade, leading to the development of new inexpensive and efficient sources. Low cost SC will find new applications in diverse areas such as telecommunications, optical frequency metrology, spectroscopy etc. [1].
DNA replication origins in archaea

DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator–initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.
Adaptive Synchronization of Lorenz System and Third-order CNN with Uncertain Parameters

This work presents chaos synchronization between the uncertain chaotic Lorenz system and the certain chaotic third-order Cellular Neural Networks (CNN) via adaptive control. Based on Lyapunov stability theory, an adaptive controller and parameters estimation update laws for unknown parameters are given such that the two different chaotic systems are to be synchronized globally and asymptotically. Theoretical analysis and numerical simulations are shown to verify the results.
The ICS-FORTH RDFSuite: Managing Voluminous RDF Description Bases

Metadata are widely used in order to fully exploit information resources available on corporate intranets or the Internet. The Resource Description Framework (RDF) aims at facilitating the creation and exchange of metadata as any other Web data. The growing number of available information resources and the proliferation of description services in various user communities, lead nowadays to large volumes of RDF metadata. Managing such RDF resource descriptions and schemas with existing low-level APIs and file-based implementations does not ensure fast deployment and easy maintenance of real-scale RDF applications. In this paper, we advocate the use of database technology to support declarative access, as well as, logical and physical independence for voluminous RDF description bases. We present RDFSuite, a suite of tools for RDF validation, storage and querying. Specifically, we introduce a formal data model for RDF description bases created using multiple schemas. Next, we present the design of a persistent RDF Store (RSSDB) for loading resource descriptions in an ORDBMS by exploring the available RDF schema knowledge. Our approach preserves the flexibility of RDF in refining schemas and/or enriching descriptions at any time, whilst it outperforms, both in storage volumes and query execution time, other approaches using a monolithic table to represent resource descriptions and schemas under the form of triples. Last, we briefly present RQL, a declarative language for querying both RDF descriptions and schemas, and sketch query evaluation on top of RSSDB.
A Hybrid Grid-Particle Method for Moving Bodies in 3D Stokes Flow with Variable Viscosity

This article presents a new approach for the resolution of large three-dimensional Stokes equations with variable viscosity fluids, coupled with transport equations. After building the model, we will write these equations in the context of highly viscous flows and penalization, in order to consider complex geometries moving in a fluid. From a mathematical point of view, the solutions show nonlinear dynamics. Beside the use of standard tools such as finite differences and staggered grids, we have built a new methodology based on large three-dimensional simulations, including operators splitting for an efficient use of fast solvers, multi-index fixed point methods, Lagrangian methods with fast and accurate grid-particle transfers, and the multiresolution description of variables. Among the main original aspects of this method, both accurate incompressibility and variable viscosity are treated in the same fixed point. Hence the computation costs for variable and constant viscosity flows are similar. Several .
Therapy using labelled somatostatin analogues: comparison of the absorbed doses with 111In-DTPA-D-Phe1-octreotide and yttrium-labelled DOTA-D-Phe1-Tyr3-octreotide

ObjectiveWe estimated the absorbed doses for 111In-DTPA-D-Phe1-octreotide and 90Y-DOTA-D-Phe1-Tyr3-octreotide in the same patients in order to compare the potential effectiveness (tumour dose) and safety (kidney and red marrow dose) of these drugs for peptide-targeted radiotherapy of somatostatin receptor positive tumours. MethodsSix patients with neuroendocrine tumours underwent quantitative 111In-DTPA-D-Phe1-octreotide SPECT and 86Y-DOTA-D-Phe1-Tyr3-octreotide PET scan at intervals of 1 week. All studies were performed with a co-infusion of amino acids for renal protection. PET and SPECT were reconstructed using iterative algorithms, incorporating attenuation and scatter corrections. Tissue uptakes (IA%) were measured and used to calculate residence times. Absorbed doses to tissues were estimated and the maximal allowed activity, defined as either the activity delivering 23 Gy to the kidneys (MAAK) or 2 Gy to the red marrow (MAARM), was calculated and the resulting tumour absorbed doses were computed. ResultsFor the MAAK the mean absorbed dose to the red marrow was lower for 90Y-DOTA-D-Phe1-Tyr3-octreotide than for 111In-DTPA-D-Phe1-octreotide (1.8±0.9 Gy vs. 6.4±1.6 Gy; P<0.001). The median absorbed dose to tumours for the MAAK was two-fold higher for 90Y-DOTA-D-Phe1-Tyr3-octreotide as compared to 111In-DTPA-D-Phe1-octreotide (30.1 vs. 12.6 Gy; P<0.05). The median absorbed dose to tumours estimated for the MAARM was 10-fold higher for 90Y-DOTA-D-Phe1-Tyr3-octreotide than for 111In-DTPA-D-Phe1-octreotide (35.1 Gy vs. 3.9 Gy; P<0.05). ConclusionsThis direct intra-patient comparison confirms that the use of 90Y-DOTA-D-Phe1-Tyr3-octreotide is more appropriate for therapy of somatostatin receptor bearing tumours. When using 111In-DTPA-D-Phe1-octreotide, the red marrow represents the major critical organ; this can result in significant toxicity if high activities have to be administered to obtain efficient tumour irradiation.
ASETS: A Self-Managing Transaction Scheduler ∗

User satisfaction determines the success of webdatabase applications. User satisfaction can be expressed in terms of expected response time or expected delay. Given the bursty and unpredictable behavior of web user populations, we model user requests as transactions with softdeadlines. For such a model of user requests with softdeadlines, the hit ratio is not the most expressive metric. Instead, the average tardiness is a better measure in such cases. In this paper; we propose and evaluate an adaptive self-managing algorithm called ASETS, which optimizes for the average tardiness. ASETS prioritize resources as needed in order to keep users satisfied under varying workloads. Our performance evaluation shows ASETS to outperform both EDF and SRPT which are known to be optimal for the under and over utilization system conditions respectively.
[Patients with chronic renal insufficiency in hemodialysis: nurses educational activities].

The aim of this study is to contribute to the knowledge of the nurse's educative activity with chronic renal patients undergoing an hemodialytic treatment, providing an improvement in the patient's quality of life and using a model called "awareness education". The subjects of this study were eight chronic renal patients--four female patients and four male patients whose age varied from 17 to 63 years old. The methodological approach was the research-action and data collection about significant situations was carried out through participant observation. Data interpretation was related to the referential proposed by PAULO FREIRE, i.e. the analysis of the generating themes. Data were selected and encoded in six generating topics: Chronic Renal Failure (IRC), Causes of IRC, Hemodialytic Treatment, Chronic Renal Patient's Limitations and Possibilities when undergoing an Hemodialytic Treatment, Renal Transplantation and Family Support. The Discussion Groups were developed according to the Pedagogical Method by PAULO FREIRE. After that stage, satisfactory changes in the chronic renal patients' quality of life who participated in the teaching-learning process have been observed. This has enabled us to conclude that there has been a development of the naïve consciousness for the criticism about their situation, owing to some changes in their reality.
A Division III Student-Athlete Academic Support Program Model.

Varsity student-athletes (SAs) in National Collegiate Athletic Association member institutions encounter obstacles to their academic achievement that non-athletes do not, such as time for physical training and practice, and travel away from campus for games. A program is described that provides support for SAs. The Student-Athlete Academic Support Program (SAASP) originated in 1994 and is based on a single goal: that all of the institution's SAs "graduate prepared. " The program content includes: (1) "career maturity" or knowing what careers are available, knowing the academic prerequisites for careers of interest, and spending time with someone in the target career; (2) a grade point average sufficiently high for competitive graduate admission, and study skills competence; and (3) developing a self-image as a student-scholar. The objective of the SAASP is to improve the academic performance, retention, and graduation rate of all SAs. Existing staff, academic coordinators for each sport, are part of the program team. They are immediate role models for the SAs and enhance the SAs internalization of an academic identity. A close relationship is also maintained with the college career planning ,office through regular meetings with its staff and SAs. Mandated study-time, study skills workshops, and tutoring services are additional components of the program. (.TLS) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. *********************************************************************** A Division III Student-Athlete Academic Support Program Model David A. Smith and William E. Herman SUNY Potsdam Psychology Department Potsdam, NY 13676 Ph. (315)267-2018 e-mail: smithda@potsdam.edu "PERMISSION TO REPRODUCE THIS MATERIAL HAS BEEN GRANTED BY TO THE EDUCATIONAL RESOURCES INFORMATION CENTER (ERIC). " U.S. DEPARTMENT OF EDUCATION Office of Educational Research and Improvement EDUCATIONAL RESOURCES INFORMATION CENTER (ERIC) 0 This document has been reprodUced as received from the person or organization originating it O Minor changes have been made to improve reproduction quality. Points of view or opinions stated in this docu ment do not necessarily represent official OERI position or policy. Presented at the 104th Annual Convention of the American Psychological Association Toronto, Ontario, Canada August 9, 1996 ct NN, BEST COPY AVAILABLE 2
Genetic mutations in epigenetic modifiers as therapeutic targets in acute myeloid leukemia

Introduction: Despite enormous insights into the molecular mechanisms of acute myeloid leukemia (AML) pathophysiology, this disease is still fatal in the majority of patients, highlighting the urgent need for novel biomarkers useful in AML prognosis and therapy. Areas covered: The advent of modern sequencing technologies has allowed the identification of genetic mutations in genes encoding for specific enzymes involved in the epigenetic regulation of gene expression. The authors review recent data demonstrating the involvement of mutations in genes encoding for epigenetic players and their complex combination with somatic genetic mutations in the pathogenesis of AML. They also discuss the prognostic and therapeutic implications of these findings. Expert opinion: Current clinical and preclinical studies are underscoring the importance of targeting epigenetic modifiers as new biomarkers for a better prognostic risk stratification and therapeutic evaluation of intermediate-risk patients. Combining data from traditional and modern methodologies will allow a definition of the complex networks of epigenetic changes and molecular interactions between candidate epitargets and key regulators of hematopoiesis. It will thus be possible to achieve an overview of potential aberrant mechanisms driving leukemogenesis in different classes of AML patients. Such an improved approach could pave the way towards ‘personalized’ therapies.
Feline toxoplasmosis in Finland

Three subgroups of the Finnish cat population underwent investigation for different aspects of feline toxoplasmosis. Blood samples of 445 purebred pet cats and 45 shelter cats were screened for Toxoplasma gondii–specific immunoglobulin G antibodies with a direct agglutination test. The overall seroprevalence was 48.4%; older cats and cats receiving raw meat in their diet were more often seropositive. Fecal samples were obtained from 131 shelters cats; 2 of the cats were found shedding T. gondii–like oocysts, and the oocysts shed by 1 of the 2 were confirmed as T. gondii with polymerase chain reaction. Among 193 cats submitted for necropsy during a 3.5-year period, 6 (3.1%) had been diagnosed with generalized toxoplasmosis and were retrospectively further investigated. The main pathological lesions included acute interstitial pneumonia, acute necrotizing hepatitis, and nonsuppurative meningoencephalitis with glial granulomas. Immunohistochemical staining demonstrated a mild to massive parasite burden in tissues with pathological lesions as well as in unaffected tissues. The results of the direct multilocus genotyping of T. gondii parasites detected were consistent with endemic genotype II, and the causative parasite strains were isolated from 2 of the generalized toxoplasmosis cases. The results indicate that cats in Finland commonly encounter T. gondii and contribute to the environmental oocyst burden, while the endemic genotype II can also prove fatal to the parasite’s definitive host. Preventing feline T. gondii infections is not only of public health importance but also a welfare issue for the cats themselves.