Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity through the Looking Glass: Effect of Enrichment Bias

The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D(sup+)) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of the direct-plating isolates hybridized with the tfdA and tfdB genes from Alcaligenes eutrophus JMP134(pJP4), 27% hybridized with the tfdA and tfdB genes from Burkholderia sp. strain RASC, and 30% hybridized with none of the probes. In contrast, the enrichment isolates not only represented fewer populations than the isolates obtained by direct plating but also exhibited, almost exclusively, a single hybridization pattern with 2,4-D catabolic gene probes. Approximately 98% of the enrichment isolates possessed pJP4-type tfdA and tfdB genes, whereas isolates containing RASC-type tfdA and tfdB genes were obtained from only 2 of the 85 enrichment cultures. The skewed occurrence of the pJP4-type genes among the isolates obtained by enrichment suggests that the competitive fitness of 2,4-D(sup+) populations during growth with 2,4-D may be influenced either by specific tfd alleles or by genetic factors linked to these alleles. Moreover, the results indicate that evaluation of the diversity and distribution of catabolic pathways in nature can be highly distorted by the use of enrichment culture techniques.
AdCD40L—Crossing the Valley of Death?

CD40-mediated cancer therapy has been under development since it became clear that CD40 plays a profound role in the stimulation of adaptive immune responses. Further, CD40 signaling on tumor cells may lead to growth arrest or even apoptosis that improves therapy outcome. The therapeutic window is appealing since the immune system is selective and normal cells do not apoptose upon CD40 signaling. AdCD40L is an adenoviral-based immunostimulatory gene therapy under evaluation for its efficacy to treat cancer. Because of its nature, the adenoviral backbone will stimulate TLRs while CD40L potentiates the shifts toward Th1 type of immunity. AdCD40L has shown efficacy in various murine models, and safety studies have been performed on dog patients and in human clinical trials. AdCD40L has been used for both ex vivo gene modification of tumor cell vaccines as well as for direct intratumoral injections. Lately, an oncolytic vector has been used to further increase the eradication of solid tumors that as a consequence further boosts the release of tumor antigens and creates danger signaling in the tumor micro milieu. This review discusses the currently unfolding mechanisms of action of AdCD40L gene therapy and its possibilities to reach clinical care.
Students' perception of community disapproval, perceived enforcement of school antismoking policies, personal beliefs, and their cigarette smoking behaviors: results from a structural equation modeling analysis.

INTRODUCTION School tobacco use policies are often considered to be part of a comprehensive approach to preventing or reducing adolescent cigarette smoking. However, little is known about the relationships between such policies and adolescents' smoking behaviors or the mechanisms by which any such influence may occur. The present study tested a conceptual model that specifies possible direct and indirect relationships among community norms, school antismoking policies, adolescents' personal smoking beliefs, and cigarette smoking behaviors. METHODS This study used data from 17,256 middle and high school students who participated in the 2006 Oregon Health Teens Survey. RESULTS Structural equation modeling indicated that perceived enforcement of school policy was directly and positively related to perceived community norms. In addition, adolescents' personal beliefs appeared to mediate the relationship between perceived enforcement of school antismoking policies and past-30-day cigarette smoking. School policies, in turn, partially mediated the relationship between community norms and smoking beliefs. DISCUSSION The results of this study provide a better understanding of how community norms and school antismoking policies may affect adolescents' cigarette smoking.
Subcellular distribution of viral structural proteins during simian virus 40 infection

The amounts of simian virus 40 structural polypeptides Vp1, Vp2, and Vp3 in different subcellular fractions at various times after lytic infection were determined by a quantitative immunoblotting procedure. Simian virus 40-infected cells were lysed with a buffer containing Nonidet P-40 to yield a soluble fraction. The Nonidet P-40-insoluble fraction was further fractionated in the presence of deoxycholate and Tween 40 to yield a soluble fraction (cytoskeletal) and an insoluble fraction (Nuc), which is primarily cell nuclei. At 33 h postinfection, the majority of viral structural proteins was found in the cell nucleus, whereas, at 48 to 65 h postinfection, Vp1 was distributed evenly among all cell fractions and Vp2 and Vp3 were found predominantly in the cytoskeletal and Nuc fractions. Thus, not all of the viral polypeptides synthesized in the cytoplasm migrated into the cell nucleus. Throughout infection, the molar ratio (Vp3/Vp2) was rather constant in all subcellular fractions, indicating that the synthesis or processing or both of Vp2 and Vp3 are coordinately regulated. The molar ratio of Vp1/(Vp2 + Vp3) varied among the fractions. The Vp1/(Vp2 + Vp3) molar ratio in the soluble fraction varied during the course of infection; however, constant ratios were maintained in the cytoskeletal and Nuc fractions. Thus, the mechanism which controls the movement of Vp1 to different compartments of the cell appears to be different from that of Vp2 and Vp3. The Vp1/(Vp2 + Vp3) value in the Nuc fraction was similar to the ratio found in virus particles. The constant molar distribution of Vp1, Vp2, and Vp3 in the Nuc fraction throughout infection suggests that there is a specific mechanism which regulates the transport of viral structural proteins. These results support the hypothesis that the structural proteins of simian virus 40 are transported into the cell nucleus in precise proportions.
CoD: inferring immune-cell quantities related to disease states

MOTIVATION The immune system comprises a complex network of genes, cells and tissues, coordinated through signaling pathways and cell-cell communications. However, the orchestrated role of the multiple immunological components in disease is still poorly understood. Classifications based on gene-expression data have revealed immune-related signaling pathways in various diseases, but how such pathways describe the immune cellular physiology remains largely unknown. RESULTS We identify alterations in cell quantities discriminating between disease states using ' Cell type of Disease' (CoD), a classification-based approach that relies on computational immune-cell decomposition in gene-expression datasets. CoD attains significantly higher accuracy than alternative state-of-the-art methods. Our approach is shown to recapitulate and extend previous knowledge acquired with experimental cell-quantification technologies. CONCLUSIONS The results suggest that CoD can reveal disease-relevant cell types in an unbiased manner, potentially heralding improved diagnostics and treatment. AVAILABILITY AND IMPLEMENTATION The software described in this article is available at http://www.csgi. tau.ac. il/CoD/.
The impact of viral tropism and housing conditions on the transmission of three H5/H7 low pathogenic avian influenza viruses in chickens

SUMMARY In this study, shedding and transmission of three H5/H7 low pathogenic avian influenza viruses (LPAIVs) in poultry was characterized and the impact of floor system on transmission was assessed. Transmission experiments were simultaneously conducted with two groups of animals housed on either a grid or a floor covered with litter. Transmission was observed for H5N2 A/Ch/Belgium/150VB/99 LPAIV. This virus was shed almost exclusively via the oropharynx and no impact of floor system was seen. Transmission was also seen for H7N1 A/Ch/Italy/1067/v99 LPAIV, which was shed via both the oropharynx and cloaca. A slight increase in transmission was seen for animals housed on litter. H5N3 A/Anas Platyrhynchos/Belgium/09-884/2008 LPAIV did not spread to susceptible animals, regardless of the floor system. This study shows that environmental factors such as floor systems used in poultry barns may act upon the transmission of LPAIVs. However, the level of influence depends on the virus under consideration and, more specifically, its principal replication sites.
Comparison of supraglottic devices i-gel® and LMA Fastrach® as conduit for endotracheal intubation

There is no mention of the technique used for randomization that is considered the heart of any randomized controlled trial. The ‘chit’ method as highlighted by the authors seems to be a surrogate of ‘closed envelope technique’ and is meant for allocation concealment but not for randomization. [2] The basis of the sample size calculation is not clear. The authors have only mentioned the effect size (10%), the alpha error and the power of the study without describing the presumed baseline success rate of intubation with LMA Fastrach®. It is difficult to calculate the sample size in the absence of the baseline success rate of intubation with LMA Fastrach®. If one assumes, the baseline success rate to be 74% (as per the final result of this study), with an effect size of 10% and keeping the power and the alpha error same, then the desired sample size turns out to be 1318 subjects with 659 in each arm. If one tries to calculate the power of the current study with a sample size of 100 patients, then it turns out to be 23%. [3] The power further reduces to only 14% with the sample size of 50 subjects as estimated by the authors. There is no mention about the principle used for the analysis that is, whether it was ‘intention to treat’ or not.
Defining locality in genetic programming to predict performance

A key indicator of problem difficulty in evolutionary computation problems is the landscape's locality, that is whether the genotype-phenotype mapping preserves neighbourhood. In genetic programming the genotype and phenotype are not distinct, but the locality of the genotype-fitness mapping is of interest. In this paper we extend the original standard quantitative definition of locality to cover the genotype-fitness case, considering three possible definitions. By relating the values given by these definitions with the results of evolutionary runs, we investigate which definition is the most useful as a predictor of performance.
PRES: a score metric for evaluating recall-oriented information retrieval applications

Information retrieval (IR) evaluation scores are generally designed to measure the effectiveness with which relevant documents are identified and retrieved. Many scores have been proposed for this purpose over the years. These have primarily focused on aspects of precision and recall, and while these are often discussed with equal importance, in practice most attention has been given to precision focused metrics. Even for recall-oriented IR tasks of growing importance, such as patent retrieval, these precision based scores remain the primary evaluation measures. Our study examines different evaluation measures for a recall-oriented patent retrieval task and demonstrates the limitations of the current scores in comparing different IR systems for this task. We introduce PRES, a novel evaluation metric for this type of application taking account of recall and the user's search effort. The behaviour of PRES is demonstrated on 48 runs from the CLEF-IP 2009 patent retrieval track. A full analysis of the performance of PRES shows its suitability for measuring the retrieval effectiveness of systems from a recall focused perspective taking into account the user's expected search effort.
Tissue acidosis induces neuronal necroptosis via ASIC1a channel independent of its ionic conduction

Acidotoxicity is common among neurological disorders, such as ischemic stroke. Traditionally, Ca2+ influx via homomeric acid-sensing ion channel 1a (ASIC1a) was considered to be the leading cause of ischemic acidotoxicity. Here we show that extracellular protons trigger a novel form of neuronal necroptosis via ASIC1a, but independent of its ion-conducting function. We identified serine/threonine kinase receptor interaction protein 1 (RIP1) as a critical component of this form of neuronal necroptosis. Acid stimulation recruits RIP1 to the ASIC1a C-terminus, causing RIP1 phosphorylation and subsequent neuronal death. In a mouse model of focal ischemia, middle cerebral artery occlusion causes ASIC1a-RIP1 association and RIP1 phosphorylation in affected brain areas. Deletion of the Asic1a gene significantly prevents RIP1 phosphorylation and brain damage, suggesting ASIC1a-mediated RIP1 activation has an important role in ischemic neuronal injury. Our findings indicate that extracellular protons function as a novel endogenous ligand that triggers neuronal necroptosis during ischemia via ASIC1a independent of its channel function. DOI: http://dx.doi. org/10.7554/eLife.05682. 001
Learning both Weights and Connections for Efficient Neural Network

Neural networks are both computationally intensive and memory intensive, making them difficult to deploy on embedded systems. Also, conventional networks fix the architecture before training starts; as a result, training cannot improve the architecture. To address these limitations, we describe a method to reduce the storage and computation required by neural networks by an order of magnitude without affecting their accuracy by learning only the important connections. Our method prunes redundant connections using a three-step method. First, we train the network to learn which connections are important. Next, we prune the unimportant connections. Finally, we retrain the network to fine tune the weights of the remaining connections. On the ImageNet dataset, our method reduced the number of parameters of AlexNet by a factor of 9x, from 61 million to 6.7 million, without incurring accuracy loss. Similar experiments with VGG-16 found that the number of parameters can be reduced by 13x, from 138 million to 10.3 million, again with no loss of accuracy.
Sequence of nifL from Klebsiella pneumoniae: mode of action and relationship to two families of regulatory proteins

We present the nucleotide sequence of K. pneumoniae nifL, which negatively regulates nif transcription in response to oxygen and fixed nitrogen. It shows partial sequence homology to the general nitrogen regulatory proteins NtrB of K. pneumoniae and Bradyrhizobium parasponiae. This homology is weaker than that shown between the NifA and NtrC activator components of the nif and general nitrogen control systems. The N‐terminal section of the NifL protein includes a structural duplication sharing sequence homology with part of NtrB, and a region containing a cysteine pair which might be implicated in redox control. Unlike NtrB, NifL appears to lack a DNA‐binding motif, consistent with evidence that NifL represses by interacting directiy with NifA. The C‐terminal section of NifL shows clear homology to NtrB and to a family of proteins involved in transcriptional control or chemotaxis, each of which probably interacts with a member of the family of regulatory proteins showing homology to NtrC.
Early angiosperm ecology: evidence from the Albian-Cenomanian of Europe.

BACKGROUND AND AIMS The mid-Cretaceous is a period of sudden turnover from gymnosperm to angiosperm-dominated floras. The aim was to investigate the fossil plant ecology in order to follow the spread of angiosperm taxa. METHODS Floristic lists and localities from the latest Albian-Cenomanian of Europe are analysed with Wagner's Parsimony Method, a clustering method currently used in phylogeny (cladistics). KEY RESULTS Wagner's Parsimony Method points out that (a) gymnosperms dominated brackish water-related environments while angiosperms dominated freshwater-related environments (e.g. swamps, floodplains, levees, channels), (b) angiosperms showed the highest diversity in stable, freshwater-related environments, (c) a single angiosperm, 'Diospyros' cretacea, is restricted to brackish water-related environments and (d) the families Lauraceae and Platanaceae were exclusive to disturbed, braided river environments, implying a opportunist strategy for early tree angiosperms. CONCLUSIONS During the Mid-Cretaceous, European floras were characterized by (a) coastal gymnosperms, (b) highly diversified fluvial angiosperms and (c) the first European brackish water-related angiosperm.
Optimal Selective Harmonic Control for Power Harmonics Mitigation

— This paper proposes an Internal Model Principle (IMP) based optimal Selective Harmonic Controller (SHC) for power converters to mitigate power harmonics. According to the harmonics distribution caused by power converters, a universal recursive SHC module is developed to deal with a featured group of power harmonics. The proposed optimal SHC is of hybrid structure: all recursive SHC modules with weighted gains are connected in parallel. It bridges the real “ nk  m order RC ” and the complex “parallel structure RC”. Compared to other IMP based control solutions, it offers an optimal trade-off among the cost, the complexity and the performance: high accuracy, fast transient response, easy-implementation, cost-effective, and also easy-to-design. The analysis and synthesis of the optimal SHC system are addressed. The proposed SHC offers power converters a tailor-made optimal control solution for compensating selected harmonic frequencies. Application examples of grid-connected inverters confirm the effectiveness of the proposed control scheme.
Home Safety with Families Being Treated for Child Abuse and Neglect

Home safety is a problem associated with child neglect. Previous attempts to remediate home safety problems within the context of an ecobehavioral approach to treating child abuse and neglect involved considerable counselor involvement. The present research demonstrates the effect of a less cumbersome intervention to reduce home safety hazards in three families being treated for child abuse and neglect. A multiple-baseline design across safety hazards within families and across each family was used to evaluate the effects of the treatment program. Social validation data from two of the families indicated satisfaction with the program.
Evaluation of the Indirect Hemagglutination Assay for Diagnosis of Acute Leptospirosis

ABSTRACT Serology plays an important role in the diagnosis of leptospirosis. Few laboratories have the resources and expertise to perform the microscopic agglutination test. There is a need for rapid and simple serological tests which facilitate the early diagnosis of leptospirosis, while antibiotic therapy may be most effective. A commercially available indirect hemagglutination assay (IHA; MRL Diagnostics, Cypress, Calif.) was evaluated with multiple serum specimens from 107 patients being investigated for leptospirosis. By using a combination of enzyme-linked immunosorbent assay (ELISA) methods for immunoglobulin M (IgM) and IgG antibodies and the microscopic agglutination test, 54 patients were found to have leptospirosis and 53 were found not to have leptospirosis. The sensitivity of IHA for the detection of acute leptospirosis was 100%, the specificity was 94%, the positive predictive value was 95%, and the negative predictive value was 100%. IHA was negative when 13 antinuclear antibody-positive sera, 24 serum specimens from patients with syphilis, and 16 serum specimens false positive by the Venereal Disease Research Laboratory test were tested. IHA was shown to detect both IgM and IgG classes of antibodies in human sera. Serum specimens from 27 dogs investigated for leptospirosis were studied: 3 samples gave nonspecific hemagglutination, but for all remaining samples, the results of IHA and an IgM ELISA were concordant. Performance of IHA was simple, and IHA requires no specialized equipment. It represents a useful assay for laboratories which require a leptospiral diagnostic capability but lack the expertise to perform specialist investigations.
Neuronal correlates of spontaneous fluctuations in fMRI signals in monkey visual cortex: Implications for functional connectivity at rest

Recent studies have demonstrated large amplitude spontaneous fluctuations in functional‐MRI (fMRI) signals in humans in the resting state. Importantly, these spontaneous fluctuations in blood‐oxygenation‐level‐dependent (BOLD) signal are often synchronized over distant parts of the brain, a phenomenon termed functional‐connectivity. Functional‐connectivity is widely assumed to reflect interregional coherence of fluctuations in activity of the underlying neuronal networks. Despite the large body of human imaging literature on spontaneous activity and functional‐connectivity in the resting state, the link to underlying neural activity remains tenuous. Through simultaneous fMRI and intracortical neurophysiological recording, we demonstrate correlation between slow fluctuations in BOLD signals and concurrent fluctuations in the underlying locally measured neuronal activity. This correlation varied with time‐lag of BOLD relative to neuronal activity, resembling a traditional hemodynamic response function with peaks at ∼6 s lag of BOLD signal. The correlations were reliably detected when the neuronal signal consisted of either the spiking rate of a small group of neurons, or relative power changes in the multi‐unit activity band, and particularly in the local field potential gamma band. Analysis of correlation between the voxel‐by‐voxel fMRI time‐series and the neuronal activity measured within one cortical site showed patterns of correlation that slowly traversed cortex. BOLD fluctuations in widespread areas in visual cortex of both hemispheres were significantly correlated with neuronal activity from a single recording site in V1. To the extent that our V1 findings can be generalized to other cortical areas, fMRI‐based functional‐connectivity between remote regions in the resting state can be linked to synchronization of slow fluctuations in the underlying neuronal signals. Hum Brain Mapp 2008. © 2008 Wiley‐Liss, Inc.
Relative Carrying Capacity of Resources and Problems of Sustainable Develop in Xiangxi Autonomous

The ideas and research methods about the relative carrying capacity of resources were used by the author in this paper. The relative carrying capacity of natural, economic resources and synthetic resources capacity of Xiangxi have been calculated, the evolution have been described and from 2001 to 2012, compared with the whole country and Hunan respectively. The research results indicated that Xiangxi relative economic resources capacity and relatively comprehensive resource capacity is always in overload condition from 2001 to 2004, Carrying capacity of natural resources as a reference area in Hunan, from 2005 to 2012 the carrying capacity of natural resources in a surplus state, and the amount of surplus rising. Land resources relative to the contribution of integrated resource carrying capacity is far greater than the contribution of economic resources.
Principle of Mach, the Equivalence Principle and concepts of inertial mass

A study of kinematics of a 2-body system is used to show that the Mach principle, previously rejected by general relativity, can still serve as an alternative to the concept of absolute space, if one takes into account that the background of distant stars (galaxies) determines {\it both} the inertial and the gravitational masses of a body.