Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies of extracellular and intracellular bacterial deoxyribonucleic acids.

Highly polymerized bacterial deoxyribonucleic acids (DNAs) obtained from extracellular and from intracellular locations were analysed. DNAs from two strains (Staphylococcus aureus and S. epidermidis) were of the type having high adenine and thymine contents; two others (Alcaligenes faecalis and Pseudomonas fluorescens) had a high content of guanine and cytosine. For each micro-organism the composition of extracellular DNA was essentially the same as that of the intracellular DNA. Conditions associated with the extracellular accumulation of DNA in cultures of 3 strains were investigated. S. aureus elaborated a deoxyribonuclease (DNase) which required calcium ion and high pH for activity. In a culture medium of c. pH 6 and insufficient calcium, the DNase was inactive and DNA slime accumulated. In cultures of P. fluorescens a specific ribonuclease-sensitive DNase inhibitor protected slime DNA from depolymerization by culture DNase. In cultures of A. faecalis, also, both a DNA slime and a low concentration of DNase may occur. This enzyme, detected by studying its action against solutions of calf thymus DNA prepared from dried fibres, was activated by various cations within the pH range of cultures. Unlike other DNases, however, it has little capacity to attack the slime-layer DNA, which presumably is more nearly native.
Adenoviral infections in children: the impact of rapid diagnosis.

BACKGROUND Adenovirus (ADV) infections were difficult to diagnose in the past, and many infections were unrecognized. Direct fluorescent assay (DFA) for the rapid diagnosis of ADV infection, as part of a viral respiratory panel, became available at Primary Children's Medical Center (Salt Lake City, UT) in December 2000. OBJECTIVE To describe children with ADV infection diagnosed by DFA and viral culture and document the impact of rapid ADV testing on patient care. METHODS DFA testing for respiratory viruses including ADV was performed on nasal wash specimens with parallel viral culture. Chart review was performed for all ADV-positive patients identified from microbiology records between December 2000 and May 2002. RESULTS Of 1901 patients positive for respiratory viruses, 143 (7.5%) were ADV-positive by DFA or culture. The mean age of ADV-positive children was 23 months; 90% were <or=60 months old. Eighty percent were previously healthy, and 56% required admission with a mean length of stay of 3.4 days. The most common diagnoses included fever (31%), bronchiolitis (24%), and pneumonia (14%). Other conditions included suspected Kawasaki disease (KD) and hepatitis. Forty-six percent of ADV-positive children were given antibiotics at presentation, but only 2 (1.4%) had documented bacterial infection (one had Escherichia coli urinary tract infection and one had Moraxella catarrhalis bacteremia). Thirty-six percent of children had a change in management based on positive ADV DFA. In children with suspected KD (n = 5), 100% had positive ADV DFA, and immune globulin was withheld in 4. One immunocompetent patient with fulminant liver failure received cidofovir treatment after a positive ADV DFA and recovered before liver transplant. CONCLUSIONS ADV is a common infection in young children and often results in admission and unnecessary antibiotic therapy. Identifying ADV as the cause of illness can favorably impact care and in some instances may be life-saving. DFA testing for ADV should be considered for infants and children requiring admission for fever, respiratory illness, suspected KD, and hepatitis.
Orchestra: Robust Mesh Networks Through Autonomously Scheduled TSCH

Time slotted operation is a well-proven approach to achieve highly reliable low-power networking through scheduling and channel hopping. It is, however, difficult to apply time slotting to dynamic networks as envisioned in the Internet of Things. Commonly, these applications do not have pre-defined periodic traffic patterns and nodes can be added or removed dynamically. This paper addresses the challenge of bringing TSCH (Time Slotted Channel Hopping MAC) to such dynamic networks. We focus on low-power IPv6 and RPL networks, and introduce Orchestra. In Orchestra, nodes autonomously compute their own, local schedules. They maintain multiple schedules, each allocated to a particular traffic plane (application, routing, MAC), and updated automatically as the topology evolves. Orchestra (re)computes local schedules without signaling overhead, and does not require any central or distributed scheduler. Instead, it relies on the existing network stack information to maintain the schedules. This scheme allows Orchestra to build non-deterministic networks while exploiting the robustness of TSCH. We demonstrate the practicality of Orchestra and quantify its benefits through extensive evaluation in two testbeds, on two hardware platforms. Orchestra reduces, or even eliminates, network contention. In long running experiments of up to 72~h we show that Orchestra achieves end-to-end delivery ratios of over 99.99%. Compared to RPL in asynchronous low-power listening networks, Orchestra improves reliability by two orders of magnitude, while achieving a similar latency-energy balance.
Analysis of web caching architectures: hierarchical and distributed caching

Cache cooperation improves the performance of isolated caches, especially for caches with small cache populations. To make caches cooperate on a large scale and effectively increase the cache population, several caches are usually federated in caching architectures. In this paper, we discuss and compare the performance of different caching architectures. In particular, we consider hierarchical and distributed caching. We derive analytical models to study important performance parameters of hierarchical and distributed caching, i.e., client's perceived latency, bandwidth usage, load in the caches, and disk space usage. Additionally, we consider a hybrid caching architecture that combines hierarchical caching with distributed caching at every level of a caching hierarchy. We evaluate the performance of a hybrid scheme and determine the optimal number of caches that should cooperate at each caching level to minimize client's retrieval latency.
Tenascin‐C Aggravates Autoimmune Myocarditis via Dendritic Cell Activation and Th17 Cell Differentiation

Background Tenascin‐C (TN‐C), an extracellular matrix glycoprotein, appears at several important steps of cardiac development in the embryo, but is sparse in the normal adult heart. TN‐C re‐expresses under pathological conditions including myocarditis, and is closely associated with tissue injury and inflammation in both experimental and clinical settings. However, the pathophysiological role of TN‐C in the development of myocarditis is not clear. We examined how TN‐C affects the initiation of experimental autoimmune myocarditis, immunologically. Methods and Results A model of experimental autoimmune myocarditis was established in BALB/c mice by immunization with murine α‐myosin heavy chains. We found that TN‐C knockout mice were protected from severe myocarditis compared to wild‐type mice. TN‐C induced synthesis of proinflammatory cytokines, including interleukin (IL)‐6, in dendritic cells via activation of a Toll‐like receptor 4, which led to T‐helper (Th)17 cell differentiation and exacerbated the myocardial inflammation. In the transfer experiment, dendritic cells loaded with cardiac myosin peptide acquired the functional capacity to induce myocarditis when stimulated with TN‐C; however, TN‐C‐stimulated dendritic cells generated from Toll‐like receptor 4 knockout mice did not induce myocarditis in recipients. Conclusions Our results demonstrated that TN‐C aggravates autoimmune myocarditis by driving the dendritic cell activation and Th17 differentiation via Toll‐like receptor 4. The blockade of Toll‐like receptor 4‐mediated signaling to inhibit the proinflammatory effects of TN‐C could be a promising therapeutic strategy against autoimmune myocarditis.
Participación electoralen nuevas democracias:la elección presidencialde 2000 en México

Turnout in Mexico has two faces. On the one hand, citizens go to the polls for the same reasons as voters from established democracies do: individual resources and group attachments increase their likelihood of voting. On the other, citizens are distrustful of voting as a result of many decades of fraudulent elections. Mexicans come to the polls with a set of political attitudes and behaviour learned under an authoritarian regime and this legacy influences how they evaluate and react to parties and elections. In this context, perceptions of the political system have a larger than expected influence on turnout. Individuals who share the perception that parties and congressmen do not care about citizens needs and who have negative evaluations about democracy and elections tend to vote less than those who have opposite views. Further, non-electoral modes of participation are negatively correlated with turnout, suggesting that abstention is a protest against a traditionally ineffective political system such as the Mexican. One of the challenges of Mexicos democratic consolidation will be to modify these political attitudes which developed under the ancien rgime, and that today play such an important role in leading people to the polls.
Factors Influencing the Underreporting of Concussion in Sports: A Qualitative Study of Minor Hockey Participants

Objective: The present study is to identify factors contributing to underreporting of concussion in adolescent athletes. Design: Qualitative interviews. Setting: Participants were interviewed in an office environment. Participants: Interviews were conducted with 31 minor hockey players, 10 parents, 6 coaches, 4 trainers, 2 managers, and one game official. Players were 13 to 15 year old. With selective sampling, an inductive approach of analyzing the interviews was undertaken and themes were identified and analyzed. Assessment of Risk Factors: Underreporting is a complex phenomenon. A number of risk factors related to hockey culture, players, reference others, and rules of play were assessed. Main Outcome Measures: Reasons not reporting concussion is accepted in minor hockey. Results: Aspects of hockey culture such as an overemphasis on winning games and upheld misperceptions about the risks associated with concussion were identified as relevant to the underreporting of concussions. Various factors relevant to the underreporting of concussions include player's motivation to win, group membership dynamics such as a player's role as the team's “enforcer,” coaches' own motivation to win to further their own opportunities in the sport, and parents' personal financial interest or alternative agenda in terms of time commitments and their child's future career prospects. Conclusions: Our findings indicate that underreporting of concussion among those players interviewed appears to be prevalent and associated with misconceptions about injury risk, and a culture that both reinforces and encourages underreporting with tacit or overt complicity of parents and coaches. Our findings support the need to alter the culture of violence and tough play in hockey by education, rule changes, economic measures, and changes in governance of the sport. Interviewing more stakeholders and policy makers would shed light on such potential interventions.
ESTIMATING THE TRUE PREVALENCE OF MYCOBACTERIUM BOVIS IN HUNTER-HARVESTED WHITE-TAILED DEER IN MICHIGAN

Apparent prevalence, although useful as a consistent index, may underestimate the true prevalence of disease. In Michigan, the ability to estimate the true prevalence of bovine tuberculosis (TB; caused by Mycobacterium bovis) in free-ranging white-tailed deer (Odocoileus virginianus) will become increasingly important to accurately assess progress towards eradication. Our objectives were threefold: to estimate the true prevalence of M. bovis in free-ranging deer in Michigan, to evaluate the effectiveness of existing TB surveillance methods, and to indirectly assess whether TB epidemiologic data from captive cervid herds can be meaningfully extrapolated to free-ranging populations. The study population consisted of all free-ranging deer submitted for TB testing in 2001 from six townships in northeastern Lower Michigan. Tissue samples of tonsil and cranial lymph nodes were collected bilaterally from all deer eligible for the study that did not have gross lesions suggestive of TB (n = 701). Samples were subjected to histopathologic, acid-fast (AF) staining, mycobacterial culture, and polymerase chain reaction (PCR) testing. Seven deer cultured positive for M. bovis that would not have been detected by current surveillance, yielding apparent and true prevalence estimates (95% confidence limits) of 2.7% (1.6, 3.8) and 3.6% (2.3, 4.9), respectively. The sensitivity, specificity, and positive and negative predictive values of the current surveillance protocol were 75, 100, 100, and 99%, respectively. Histologic lesions were present only in tonsils, and ranged from simple necrosis to caseation, suppuration, and granuloma formation. Acid-fast staining and PCR detected M. bovis in only one of the seven culture-positive deer. Our study provides the first estimate of the true prevalence of M. bovis in Michigan's free-ranging deer population and suggests modest underestimation of that prevalence by current surveillance. This study also suggests that caution is warranted when extrapolating epidemiologic data on TB in captive cervids to free-ranging populations and confirms the pivotal role of the tonsil in early infections.
Genes and behavior.

When we think of behavior, we generally tend to think of some complex human traits such as criminality, extovertedness, and similar traits that are likely to be affected by many genes interacting with the environment. Lets look at some simple examples in several organisms where it is possible to show that behavioral differences can be simply inherited, including some cases in man. Several traits that we are all familiar with seem to be controlled by a single gene, at least in some studies. Natural in horses is said to be simply inherited, with trotting (left front and right rear legs go forward together) versus pacing where both legs on the same side advance together) being dominant. Though this is no proof at all of dominance, trotters are much more prevalent than pacers. trotting gait versus pacing in bird dogs is also reported to show simple inheritance, and I think pointing is supposed to be dominant. Pointing versus setting The simple act of in humans may also have a genetic factor. Clasp your hands, and note whether your left or right thumb is on top. Now try it the other way, and you will see how "unnatural" it feels. Again there are reports that this behavior is determined by a single gene, but I have not seen the kinds of pedigrees that would confirm it. hand clasping The same goes for Some can roll the tongue and other people simply cannot. I don't know which is dominant if it is a single gene trait. tongue rolling versus 'squashing' One place that progress is being made on genetic analysis of behavior is in work with These flies have courtship rituals that are similar to what we see in birds, ie displays, of ducking turning etc. where the action of one sex leads to an "appropriate response in the other. When a mutant is detected, say a male doesn't turn around three times after the female brushes him with her antennae, she will not allow him to mate. In natural populations this would be a dead end, but in the lab where no other males are around, he may eventually be accepted, and the inheritance of the trait can be analyzed. Many individual steps in the courtship ritual have been shown to be regulated by single genes. Drosophila. A lot of folks have thought of neat tricks to identify unusual behavior patterns, capture …
Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe

ABSTRACT The environmental distribution of Dehalococcoides group organisms and their association with chloroethene-contaminated sites were examined. Samples from 24 chloroethene-dechlorinating sites scattered throughout North America and Europe were tested for the presence of members of the Dehalococcoides group by using a PCR assay developed to detect Dehalococcoides 16S rRNA gene (rDNA) sequences. Sequences identified by sequence analysis as sequences of members of the Dehalococcoides group were detected at 21 sites. Full dechlorination of chloroethenes to ethene occurred at these sites. Dehalococcoides sequences were not detected in samples from three sites at which partial dechlorination of chloroethenes occurred, where dechlorination appeared to stop at 1,2-cis-dichloroethene. Phylogenetic analysis of the 16S rDNA amplicons confirmed that Dehalococcoides sequences formed a unique 16S rDNA group. These 16S rDNA sequences were divided into three subgroups based on specific base substitution patterns in variable regions 2 and 6 of the Dehalococcoides 16S rDNA sequence. Analyses also demonstrated that specific base substitution patterns were signature patterns. The specific base substitutions distinguished the three sequence subgroups phylogenetically. These results demonstrated that members of the Dehalococcoides group are widely distributed in nature and can be found in a variety of geological formations and in different climatic zones. Furthermore, the association of these organisms with full dechlorination of chloroethenes suggests that they are promising candidates for engineered bioremediation and may be important contributors to natural attenuation of chloroethenes.
Inference on Recombination and Block Structure Using Unphased Data

In this study compatibility with a tree for unphased genotype data is discussed. If the data are compatible with a tree, the data are consistent with an assumption of no recombination in its evolutionary history. Further, it is said that there is a solution to the perfect phylogeny problem; i.e., for each individual a pair of haplotypes can be defined and the set of all haplotypes can be explained without invoking recombination. A new algorithm to decide whether or not a sample is compatible with a tree is derived. The new algorithm relies on an equivalence relation between sites that mutually determine the phase of each other. (The previous algorithm was based on advanced graph theoretical tools.) The equivalence relation is used to derive the number of solutions to the perfect phylogeny problem. Further, a series of statistics, RjM, j ≥ 2, are defined. These can be used to detect recombination events in the sample's history and to divide the sample into regions that are compatible with a tree. The new statistics are applied to real data from human genes. The results from this application are discussed with reference to recent suggestions that recombination in the human genome is highly heterogeneous.
Independently recruited oxidases from the glucose-methanol-choline oxidoreductase family enabled chemical defences in leaf beetle larvae (subtribe Chrysomelina) to evolve

Larvae of the leaf beetle subtribe Chrysomelina sensu stricto repel their enemies by displaying glandular secretions that contain defensive compounds. These repellents can be produced either de novo (iridoids) or by using plant-derived precursors (e.g. salicylaldehyde). The autonomous production of iridoids, as in Phaedon cochleariae, is the ancestral chrysomeline chemical defence and predates the evolution of salicylaldehyde-based defence. Both biosynthesis strategies include an oxidative step of an alcohol intermediate. In salicylaldehyde-producing species, this step is catalysed by salicyl alcohol oxidases (SAOs) of the glucose-methanol-choline (GMC) oxidoreductase superfamily, but the enzyme oxidizing the iridoid precursor is unknown. Here, we show by in vitro as well as in vivo experiments that P. cochleariae also uses an oxidase from the GMC superfamily for defensive purposes. However, our phylogenetic analysis of chrysomeline GMC oxidoreductases revealed that the oxidase of the iridoid pathway originated from a GMC clade different from that of the SAOs. Thus, the evolution of a host-independent chemical defence followed by a shift to a host-dependent chemical defence in chrysomeline beetles coincided with the utilization of genes from different GMC subfamilies. These findings illustrate the importance of the GMC multi-gene family for adaptive processes in plant–insect interactions.
Comparison of transient elastography (FibroScan), FibroTest, APRI and two algorithms combining these non‐invasive tests for liver fibrosis staging in HIV/HCV coinfected patients: ANRS CO13 HEPAVIH and FIBROSTIC collaboration

Combining noninvasive tests increases diagnostic accuracy for staging liver fibrosis in hepatitis C virus (HCV)‐infected patients, but this strategy remains to be validated in HIV/HCV coinfection. We compared the performances of transient elastography (TE), Fibrotest (FT), the aspartate aminotransferase‐to‐platelet ratio index (APRI) and two algorithms combining TE and FT (Castera) or APRI and FT (SAFE) in HIV/HCV coinfection.
Two DNA polymerases may be required for synthesis of the lagging DNA strand of simian virus 40

Agents discriminating between DNA polymerase alpha and DNA polymerases of class delta (polymerase delta or epsilon) were used to characterize steps in the synthesis of the lagging DNA strand of simian virus 40 during DNA replication in isolated nuclei. The synthesis of lagging-strand intermediates below 40 nucleotides, termed DNA primers (T. Nethanel, S. Reisfeld, G. Dinter-Gottlieb, and G. Kaufmann, J. Virol. 62:2867-2873, 1988), was selectively inhibited by butylphenyl dGTP or by neutralizing DNA polymerase alpha monoclonal antibodies. The synthesis of longer lagging chains of up to 250 nucleotides (Okazaki pieces) was affected to a lesser extent, possibly indirectly, by these agents. Aphidicolin, which inhibits both alpha- and delta-class enzymes, elicited the opposite pattern: DNA primers accumulated in its presence and were not converted into Okazaki pieces. These and previous data suggest that DNA polymerase alpha primase synthesizes DNA primers, whereas another DNA polymerase, presumably DNA polymerase delta or epsilon, mediates the conversion of DNA primers into Okazaki pieces.
Real-time 3D segmentation of the left ventricle using deformable subdivision surfaces

In this paper, we extend a computationally efficient framework for real-time 3D tracking and segmentation to support deformable subdivision surfaces. Segmentation is performed in a sequential state-estimation fashion, using an extended Kalman filter to estimate shape and pose parameters for the subdivision surface. As an example, we have integrated Doo-Sabin subdivision surfaces into the framework. Furthermore, we provide a method for evaluating basis functions for Doo-Sabin surfaces at arbitrary parameter values. These basis functions are precomputed during initialization, and later used during segmentation to quickly evaluate surface points used for edge detection. Fully automatic tracking and segmentation of the left ventricle is demonstrated in a dataset of 21 3D echocardiography recordings. Successful segmentation was achieved in all cases, with limits of agreement (mean plusmn1.96SD) for point to surface distance of 2.2 plusmn 0.8 mm compared to manually verified segmentations. Real-time segmentation at a rate of 25 frames per second consumed a CPU load of 8%.