Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms

To facilitate genus and species level identification of a broad range of bacteria without the requirement of presumptive identification, we have developed a unified set of primers and polymerase chain reaction conditions to amplify spacer regions between the 16S and 23S genes in the prokaryotic rRNA genetic loci. Spacer regions within these loci show a significant level of length and sequence polymorphism across both genus and species lines. A generic pair of priming sequences was selected for the amplification of these polymorphisms from highly conserved sequences in the 16S and 23S genes occurring adjacent to these polymorphic regions. This single set of primers and reaction conditions was used for the amplification of 16S-23S spacer regions for over 300 strains of bacteria belonging to eight genera and 28 species or serotypes, including Listeria, Staphylococcus, and Salmonella species and additional species related to these pathogenic organisms. When the spacer amplification products were resolved by electrophoresis, the resulting patterns could be used to distinguish all of the species of bacteria within the test group. Unique elements in the amplification product patterns generally clustered at the species level, although some genus-specific characteristics were also observed. On the basis of the results obtained with our test group of 300 bacterial strains, amplification of the 16S-23S ribosomal spacer region is a suitable process for generating a data base for use in a polymerase chain reaction-based identification method, which can be comprehensively applied to the bacterial kingdom.
Will This Video Go Viral: Explaining and Predicting the Popularity of Youtube Videos

What makes content go viral Which videos become popular and why others don't Such questions have elicited significant attention from both researchers and industry, particularly in the context of online media. A range of models have been recently proposed to explain and predict popularity; however, there is a short supply of practical tools, accessible for regular users, that leverage these theoretical results. HIPie--an interactive visualization system--is created to fill this gap, by enabling users to reason about the virality and the popularity of online videos. It retrieves the metadata and the past popularity series of Youtube videos, it employs the Hawkes Intensity Process, a state-of-the-art online popularity model for explaining and predicting video popularity, and it presents videos comparatively in a series of interactive plots. This system will help both content consumers and content producers in a range of data-driven inquiries, such as to comparatively analyze videos and channels, to explain and to predict future popularity, to identify viral videos, and to estimate responses to online promotion.
The use of 16s rDNA methods in soil microbial ecology

New and exciting molecular methods, many using the 16S small sub-unit ribosomal nucleic acid molecule, are opening the microbial "black box" in soil. These studies have added much to our knowledge of microbial diversity in soils, and are beginning to advance our understanding of the relationship between this diversity and its function in soil processes. Over the next few years, the knowledge gained from molecular studies will, we hope, lead to improvements in sustainable land management and sustainable exploitation of soil genetic resources. As we enter the third millenium, it is appropriate to review the application of 16S rDNA methods to soil microbiology. This review examines 16S ribosomal DNA (rDNA) methods and their application to soil. It mentions their limits and suggests how they may be applied in the future.
BENAZEPRIL, AN ANGIOTENSIN‐CONVERTING ENZYME INHIBITOR, ALLEVIATES RENAL INJURY IN SPONTANEOUSLY HYPERTENSIVE RATS BY INHIBITING ADVANCED GLYCATION END‐PRODUCT‐MEDIATED PATHWAYS

1 Advanced glycation end‐products (AGE) and their receptors (RAGE) have been implicated in renal damage in diabetes. The aim of the present study was to investigate the effects of benazepril, an angiotensin‐converting enzyme inhibitor (ACEI), on the formation of AGE, the expression RAGE and other associated components in the oxidative stress pathway in spontaneously hypertensive rats (SHR). 2 Groups of SHR were treated with or without 10 mg/kg per day benazepril for 12 weeks. Systolic blood pressure (SBP) and angiotensin (Ang) II levels were evaluated in SHR and control Wistar‐Kyoto (WKY) rats. Renal function was investigated by determining levels of proteinuria and glomerulosclerosis. Furthermore, reactive oxygen species (ROS) in the rat renal cortex were analysed using an H2O2‐based hydroxyl radical‐detection assay and the renal content of AGE, RAGE, NADPH oxidase p47phox, nuclear factor (NF)‐κB p65, phosphorylated (p‐) NF‐κB p65, vascular cell adhesion molecule (VCAM)‐1 and transforming growth factor (TGF)‐β1 was determined by immunohistochemistry, quantitative real‐time polymerase chain reaction and western blot analysis. 3 Treatment with benazepril inhibited the formation of AngII, reduced SBP and alleviated renal lesions in SHR compared with both untreated SHR and control WKY rats. Benazepril treatment significantly suppressed the accumulation of AGE and expression of RAGE in the kidney of SHR. In addition, benazepril treatment reduced the upregulation of NADPH oxidase p47phox, ROS generation and NF‐κB p65, p‐NF‐κB p65, VCAM‐1 and TGF‐β1 expression in the kidney of SHR compared with both untreated SHR and control WKY rats. 4 The results of the present study provide new insights into the regulation by the renin–angiotensin system of AGE–RAGE, oxidative stress and nephropathy, increasing our understanding of the role of the RAS in nephropathy.
Critical role for a high-affinity chemokine-binding protein in gamma-herpesvirus-induced lethal meningitis.

Chemokines are involved in recruitment and activation of hematopoietic cells in sites of infection and inflammation. The M3 gene of the gamma-herpesvirus gammaHV68 encodes an abundant secreted protein that binds CC chemokines with high affinity. We report here that this gene is essential for efficient induction of lethal meningitis by gammaHV68. An M3 mutant gammaHV68 (gammaHV68-M3.stop) was 100-fold less virulent than wild-type or marker rescue control (gammaHV68-M3.MR) viruses after intracerebral inoculation. After intracerebral inoculation, gammaHV68-M3.stop grew to lower titers than gammaHV68 or gammaHV68-M3.MR in the brain but spread to and grew normally in the spleen and lung. Expression of several CC chemokines was significantly induced in the CNS by gammaHV68 infection. Consistent with M3 acting by blockade of CC chemokine action, gammaHV68 induced a neutrophilic meningeal inflammatory infiltrate, while gammaHV68-M3.stop induced an infiltrate in which lymphocytes and macrophages predominated. In contrast to the important role of M3 in lethal meningitis, M3 was not required for establishment or reactivation from latent infection or induction of chronic arteritis. These data suggest a role for chemokines in the protection of the nervous system from viral infection and that the M3 protein acts in a tissue-specific fashion during acute but not chronic gammaHV68 infection to limit CC chemokine-induced inflammatory responses.
Comparison of Transplacental Treatment of Fetal Supraventricular Tachyarrhythmias With Digoxin, Flecainide, and Sotalol: Results of a Nonrandomized Multicenter Study

Background— Fetal tachyarrhythmia may result in low cardiac output and death. Consequently, antiarrhythmic treatment is offered in most affected pregnancies. We compared 3 drugs commonly used to control supraventricular tachycardia (SVT) and atrial flutter (AF). Methods and Results— We reviewed 159 consecutive referrals with fetal SVT (n=114) and AF (n=45). Of these, 75 fetuses with SVT and 36 with AF were treated nonrandomly with transplacental flecainide (n=35), sotalol (n=52), or digoxin (n=24) as a first-line agent. Prenatal treatment failure was associated with an incessant versus intermittent arrhythmia pattern (n=85; hazard ratio [HR]=3.1; P<0.001) and, for SVT, with fetal hydrops (n=28; HR=1.8; P=0.04). Atrial flutter had a lower rate of conversion to sinus rhythm before delivery than SVT (HR=2.0; P=0.005). Cardioversion at 5 and 10 days occurred in 50% and 63% of treated SVT cases, respectively, but in only 25% and 41% of treated AF cases. Sotalol was associated with higher rates of prenatal AF termination than digoxin (HR=5.4; P=0.05) or flecainide (HR=7.4; P=0.03). If incessant AF/SVT persisted to day 5 (n=45), median ventricular rates declined more with flecainide (−22%) and digoxin (−13%) than with sotalol (−5%; P<0.001). Flecainide (HR=2.1; P=0.02) and digoxin (HR=2.9; P=0.01) were also associated with a higher rate of conversion of fetal SVT to a normal rhythm over time. No serious drug-related adverse events were observed, but arrhythmia-related mortality was 5%. Conclusion— Flecainide and digoxin were superior to sotalol in converting SVT to a normal rhythm and in slowing both AF and SVT to better-tolerated ventricular rates and therefore might be considered first to treat significant fetal tachyarrhythmia.
Histomorphometric classification of postmenopausal osteoporosis: implications for the management of osteoporosis.

AIMS--To define and group static and dynamic iliac crest histomorphometric parameters in women with established osteoporosis. METHODS--Iliac crest biopsy specimens from 146 white women were sectioned undecalcified and examined using image analysis. RESULTS--Five distinct groups were defined on the basis of histomorphometric changes in cell function: group 1, decreased osteoblastic and osteoclastic activity; group 2, decreased osteoblastic and increased osteoclastic activity; group 3, increased osteoblastic and osteoclastic activity; group 4, no bone surface cell activity; and group 5, apparently normal osteoblastic and osteoclastic activity. CONCLUSIONS--Five distinct subgroups of patients with postmenopausal osteoporosis can be defined based on changes in bone cell function. Defining cellular dysfunction in this way may be important for tailoring treatment regimens to the needs of individual patients.
Extreme Learning Machine With Subnetwork Hidden Nodes for Regression and Classification

As demonstrated earlier, the learning effectiveness and learning speed of single-hidden-layer feedforward neural networks are in general far slower than required, which has been a major bottleneck for many applications. Huang et al. proposed extreme learning machine (ELM) which improves the training speed by hundreds of times as compared to its predecessor learning techniques. This paper offers an ELM-based learning method that can grow subnetwork hidden nodes by pulling back residual network error to the hidden layer. Furthermore, the proposed method provides a similar or better generalization performance with remarkably fewer hidden nodes as compared to other ELM methods employing huge number of hidden nodes. Thus, the learning speed of the proposed technique is hundred times faster compared to other ELMs as well as to back propagation and support vector machines. The experimental validations for all methods are carried out on 32 data sets.
A Gaussian Process Model for Inferring the Dynamic Transcription Factor Activity

In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequence. Transcription factors control the flow (or transcription) of genetic information from DNA to mRNA. To develop models of cellular processes quantitative estimation of the regulatory relationship between transcription factors and genes is a basic requirement. It is difficult for a number of reasons: transcription factors' expression levels are often low and noisy, and many transcription factors are post- transcriptionally regulated. So, from the expression levels of their target genes it is functional to infer the activity of the transcription factors.
A prospective study of intake of trans-fatty acids from ruminant fat, partially hydrogenated vegetable oils, and marine oils and mortality from CVD

Trans-fatty acids (TFA) have adverse effects on blood lipids, but whether TFA from different sources are associated with risk of CVD remains unresolved. The objective of the present study was to evaluate the association between TFA intake from partially hydrogenated vegetable oils (PHVO), partially hydrogenated fish oils (PHFO) and ruminant fat (rTFA) and risks of death of CVD, CHD, cerebrovascular diseases and sudden death in the Norwegian Counties Study, a population-based cohort study. Between 1974 and 1988, participants were examined for up to three times. Fat intake was assessed with a semi-quantitative FFQ. A total of 71 464 men and women were followed up through 2007. Hazard ratios (HR) and 95 % CI were estimated with Cox regression. Energy from TFA was compared to energy from all other sources, carbohydrates or unsaturated cis-fatty acids with different multivariable models. During follow-up, 3870 subjects died of CVD, 2383 of CHD, 732 of cerebrovascular diseases and 243 of sudden death. Significant risks, comparing highest to lowest intake category, were found for: TFA from PHVO and CHD (HR 1·23 (95 % CI 1·00, 1·50)) and cerebrovascular diseases (HR 0·65 (95 % CI 0·45, 0·94)); TFA from PHFO and CVD (HR 1·14 (95 % CI 1·03, 1·26)) and cerebrovascular diseases (HR 1·32 (95 % CI 1·04, 1·69)); and rTFA intake and CVD (HR 1·30 (95 % CI 1·05, 1·61)), CHD (HR 1·50 (95 % CI 1·11, 2·03)) and sudden death (HR 2·73 (95 % CI 1·19, 6·25)) in women. These associations with rTFA intake were not significant in men (Pinteraction ≥ 0·01). The present study supports that TFA intake, irrespective of source, increases CVD risk. Whether TFA from PHVO decreases risk of cerebrovascular diseases warrants further investigation.
Fast and Scalable Approximate Spectral Matching for Higher Order Graph Matching

This paper presents a fast and efficient computational approach to higher order spectral graph matching. Exploiting the redundancy in a tensor representing the affinity between feature points, we approximate the affinity tensor with the linear combination of Kronecker products between bases and index tensors. The bases and index tensors are highly compressed representations of the approximated affinity tensor, requiring much smaller memory than in previous methods, which store the full affinity tensor. We compute the principal eigenvector of the approximated affinity tensor using the small bases and index tensors without explicitly storing the approximated tensor. To compensate for the loss of matching accuracy by the approximation, we also adopt and incorporate a marginalization scheme that maps a higher order tensor to matrix as well as a one-to-one mapping constraint into the eigenvector computation process. The experimental results show that the proposed method is faster and requires smaller memory than the existing methods with little or no loss of accuracy.
Population‐based study of antibody to the human polyomaviruses BKV and JCV and the simian polyomavirus SV40

Molecular studies suggest that the simian polyomavirus SV40 is present in the human population, possibly introduced in contaminated polio vaccine. However, no recent seroepidemiological data exist in England on SV40 or on the two human polyomaviruses, BKV and JCV. A comparative age seroprevalence study was undertaken on 2,435 residual sera from 1991 by haemagglutination inhibition (HI) for BKV and JCV, and virus neutralisation for SV40. The overall rates of seropositivity for BKV and JCV were 81% and 35%, respectively, and each was significantly related to age (P < 0.001). BKV seroprevalence reached 91% at 5–9 years of age, but JCV seroprevalence reached only 50% by age 60–69 years. There was a highly significant association between BKV antibody titre and age (P < 0.001), titres decreasing linearly at a rate of 8.7% per 10 years (95% CI = 7.4–10% drop). Significantly more males than females had antibody to JCV (P = 0.013). In individuals under 40 years of age there was a significant negative association between the presence of antibody to BKV and JCV (P < 0.001). By contrast, the antibody prevalence to SV40 remained at 1.3–5% throughout all age groups and titres were low. There was a significant positive association between the presence of antibody to SV40 and antibody to both BKV (P < 0.001) and JCV (P = 0.009), and also to the geometric mean titre (GMT) of BKV antibody (P = 0.011). The results indicate that BKV and JCV are transmitted by different routes. There is no serological evidence that SV40 entered the human population during the past 80 years, and the possibility of cross‐reaction with BKV or JCV antibody must be considered. J. Med. Virol. 71:115–123, 2003. © 2003 Wiley‐Liss, Inc.
Adaptation Method for Level of Detail (LOD) of 3D contents

In this research we present a method for adaptation of 3D contents over ubiquitous environment. The need of contents adaptation and delivery is growing to support multiple target platforms for single source. Since contents base on computer graphics deal with a large data set and a high performance, a service adaptation for context changing is required to manipulate graphics contents with a more complicated method in multiple devices such as desktops, laptops, PDAs, mobile phones, etc. This paper presents some theoretical method for adaptation, which is service rendering middleware, and device-based decision making algorithm for LOD of 3D contents. Service rendering middleware consists of service adaptation (SA) for analyzing environments, service rendering (SR) for reconfiguring customized services and LOD algorithm for generating an adapted service by processing customized data according to the level of detail. Also, the decision-making algorithm, which is based on device capabilities, is used both in LOD algorithm module and method to decide level of 3D contents.
The Incorporation of 5-Fluorouracil into RNA Affects the Ribonucleolytic Activity of the Exosome Subunit Rrp6

5-Fluorouracil (5FU) is a fluoropyrimidine used for the treatment of solid tumors. 5FU is a precursor of dTTP and UTP during biogenesis, and it interferes with both DNA and RNA metabolism. The RNA exosome, a multisubunit complex with ribonucleolytic activity, has been identified as one of the targets of 5FU in yeast. Studies in human cells have shown that the catalytic subunit of the nuclear exosome, Rrp6, is specifically targeted. Here, we have investigated the direct effect of 5FU on the activity of Rrp6 in Drosophila S2 cells, and we have identified two aspects of Rrp6 function that are altered by 5FU. First, gel filtration analysis revealed that the repertoire of multimolecular complexes that contain Rrp6 is modified by exposure to 5FU, which is consistent with the proposal that incorporation of 5FU into RNA leads to the sequestration of Rrp6 in ribonucleoprotein complexes. Second, the incorporation of 5FU into RNA renders the RNA less susceptible to degradation by Rrp6, as shown by Rrp6 activity assays in vitro. Our results imply that aberrant transcripts synthesized in 5FU-treated cells cannot be turned over efficiently by the surveillance machinery. Together with previous results on the mechanisms of action of 5FU, our findings suggest that the cytotoxicity of 5FU at the RNA level is the result of at least three different effects: the increased levels of retroviral transcripts with mutagenic potential, the reduced synthesis of ribosomes, and the inhibition of the nuclear RNA surveillance pathways. Drugs that reinforce any of these effects may boost the cytotoxicity of 5FU. Mol Cancer Res; 9(3); 332–40. ©2011 AACR.
Single-Pass PCA of Large High-Dimensional Data

Principal component analysis (PCA) is a fundamental dimension reduction tool in statistics and machine learning. For large and high-dimensional data, computing the PCA (i.e., the singular vectors corresponding to a number of dominant singular values of the data matrix) becomes a challenging task. In this work, a single-pass randomized algorithm is proposed to compute PCA with only one pass over the data. It is suitable for processing extremely large and high-dimensional data stored in slow memory (hard disk) or the data generated in a streaming fashion. Experiments with synthetic and real data validate the algorithm's accuracy, which has orders of magnitude smaller error than an existing single-pass algorithm. For a set of high-dimensional data stored as a 150 GB file, the proposed algorithm is able to compute the first 50 principal components in just 24 minutes on a typical 24-core computer, with less than 1 GB memory cost.
Usability Comparison of Mouse, Touch and Tangible Inputs for 3D Data Manipulation

We evaluate the performance and usability of mouse-based, touch-based, and tangible interaction for manipulating objects in a 3D virtual environment. This comparison is a step toward a better understanding of the limitations and benefits of these existing interaction techniques, with the ultimate goal of facilitating the integration of different 3D data exploration environments into a single interaction continuum. For this purpose we analyze participants' performance in 3D manipulation using a docking task. We measured completion times, docking precision, as well as subjective criteria such as fatigue, workload, and preference. Our results show that the three input modalities provide similar levels of precision but require different interaction times. We also discuss our qualitative observations as well as people's preferences and put our findings into context of the practical application domain of 3D data analysis environments.
Polymicrobial Bloodstream Infection in Pediatric Patients: Risk Factors, Microbiology, and Antimicrobial Management

Background: Few studies focus on polymicrobial bloodstream infections (PBSIs) in children. In previous reports, children with PBSI frequently had complex underlying medical conditions and a high incidence of specific microorganisms, but systematic evaluation with controls was not performed. We postulated that specific clinical risk factors are associated with an increased risk of PBSI, and that illness may be more severe with these infections. Additionally, we suspected that routine empiric antimicrobial therapy may frequently be inadequate to treat the variety of pathogens in PBSI. Methods: Positive blood cultures from 1998 to 2004 were reviewed. Patients whose cultures grew >1 organism were age-matched with monomicrobial bloodstream infection controls. Records were reviewed to compare their underlying medical conditions, organisms isolated, adequacy of therapy, and clinical characteristics of illness. Results: Twenty-nine episodes of PBSI were identified in 18 subjects. PBSI patients were more likely to have chronic medical conditions, chronic gastrointestinal pathology, central venous catheters, and to be receiving parenteral nutrition than controls. Pathogens found more commonly in PBSI episodes included Enterococcus spp. , coagulase-negative staphylococci, and Candida spp. Empiric antimicrobial therapy was less likely to be adequate in patients with PBSI. PBSI patients were hospitalized longer, required longer intensive care and had prolonged bloodstream infection. Subjects with PBSI had prolonged duration of fever and had higher degrees of sepsis than controls. Conclusions: Chronic medical conditions, particularly gastrointestinal disease, are risk factors for PBSIs. Because clinical illness may be more severe, alteration of the empiric antimicrobial regimen should be considered in some of these patients.