Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Applications in Genetics and Molecular Biology Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis : Is it Worth a Risk ?

One of the prevailing ideas in the literature on microarray data analysis is to pool the expression measures across genes and treat them as a sample drawn from some distribution. Several universal laws were proposed to analytically describe this distribution. This idea raises a number of concerns. The expression levels of genes are not identically distributed random variables so that treating them as a sample amounts to sampling from a mixture of equally weighted distributions, each being associated with a different gene. The expression levels of different genes are heavily dependent random variables so that the law of large numbers and statistical goodness-of-fit tests are normally inapplicable to this kind of data. This dependence represents a very serious pitfall in microarray data analysis.
Decoupling Control of MSM Rotor with Heavy Self-weight and Great Moment of Inertia Based on Internal Model Control

The control performance of magnetically suspended motor (MSM) with heavy self-weight and great moment of inertia is affected by parameter uncertainty and external disturbances, and the coupling effect in radial tilting of MSM becomes serious with the increase of rotational speed and moment of inertia, and then the robustness would be reduced. Therefore, an internal model control (IMC) model is proposed to adjust the robustness of MSM. Based on the IMC model, a decoupling IMC model is designed for MSM on four degrees of freedom. Simulation and experiment are conducted to verify that the IMC model improves the robust stability of MSM, and the decoupling IMC model effectively realizes the decoupling control of MSM on four degrees of freedom.
Adaptabilidade e estabilidade de milho no Nordeste brasileiro.

The adaptability and stability of fifteen varieties and two hybrids of corn were evaluated at ninety one environments of the Brazilian Northeast, during the period of 1999 to 2003 in a randomized block design, with three replications, aiming their recommendation to the prevalent agricultural systems. The aggregated variance analysis detected significant differences among environments and materials, but also detected an inconsistent behavior of the materials face the environmental oscillations. The Pioneer 3021 and BRS 3123 hybrids, used as controls, showed better adaptation than the varieties with superior grain yield either under favorable as unfavorable environment. The Sertanejo, AL 25, AL 34, AL 30, and Asa Branca varieties, which have better adaptation shown to be more demanding under unfavorable conditions, justifying their recommendation to favorable environments. The Assum Preto and Caatingueiro varieties, despite their low adaptation and demanding characteristics under unfavorable conditions, have in their high precocity strong reasons for their recommendation to semiarid environments
A Systematic Review and Pooled Analysis of Studies of Oral Etoposide in Metastatic Breast Cancer.

Objective Oral etoposide has been used as a later line therapy for metastatic breast cancer for more than twenty years. Its efficacy and clinical usefulness has been suggested in small phase II studies in the metastatic breast cancer population and the drug has also the added advantage of convenient oral administration. Despite these advantages, the place of oral etoposide in treatment of metastatic breast cancer has been challenged in the last decade due to introduction of several other chemotherapeutics, including options available orally, as well as novel targeted therapies. This report pools the data on response rates and survival from all available oral etoposide studies in order to reach a more precise estimate of the clinical benefit of the drug. Materials and methods A review of the literature was performed for studies of oral etoposide in metastatic breast cancer. Data were extracted from eligible studies and summary statistics derived. Calculations of pooled response rates and survival estimates were performed according to a random or fixed effect model as appropriate. Results The pooled estimate of Response Rate derived from twelve studies found in the English literature was 18.5% (95% CI 11.5-25.5%). The pooled estimate of Clinical Benefit Rate (CBR) was 45.8% (95% CI 38.6-53.0%) and median Overall Survival (OS) approached 1 year. Summarized adverse effects profile data show an overall manageable toxicity. Conclusion This pooled analysis provides evidence of a moderate clinical effectiveness of oral etoposide in metastatic breast cancer that could be useful in situations that options are limited but active treatment still appropriate.
Rapid Turnover of Hyphae of Mycorrhizal Fungi Determined by AMS Microanalysis of 14C

Processes in the soil remain among the least well-characterized components of the carbon cycle. Arbuscular mycorrhizal (AM) fungi are ubiquitous root symbionts in many terrestrial ecosystems and account for a large fraction of photosynthate in a wide range of ecosystems; they therefore play a key role in the terrestrial carbon cycle. A large part of the fungal mycelium is outside the root (the extraradical mycelium, ERM) and, because of the dispersed growth pattern and the small diameter of the hyphae (<5 micrometers), exceptionally difficult to study quantitatively. Critically, the longevity of these fine hyphae has never been measured, although it is assumed to be short. To quantify carbon turnover in these hyphae, we exposed mycorrhizal plants to fossil (“carbon-14–dead”) carbon dioxide and collected samples of ERM hyphae (up to 116 micrograms) over the following 29 days. Analyses of their carbon-14 content by accelerator mass spectrometry (AMS) showed that most ERM hyphae of AM fungi live, on average, 5 to 6 days. This high turnover rate reveals a large and rapid mycorrhizal pathway of carbon in the soil carbon cycle.
A comparison of methods for determining genotypes at the tumour necrosis factor‐α−308, interleukin (IL)‐1β+3953, IL‐6 −174 and IL‐10 −1082/−819/−592 polymorphic loci

Induced heteroduplex genotyping (IHG) is one of many methods that can be used to determine single nucleotide polymorphisms (SNPs). It is relatively new in comparison to other polymerase chain reaction (PCR)‐based techniques. The aim of this study was to compare the results of genotyping using IHG with the results of genotyping using either polymerase chain reaction–sequence‐specific primers (PCR‐SSP) or polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) for SNPs in the tumour necrosis factor (TNF)‐α, interleukin (IL)‐1β, IL‐6 and IL‐10 genes. Ninety patients who consented to participate in the study had their genotypes determined by IHG and either PCR‐SSP (TNF‐α−308 and IL‐10 −1082/−819/−592) or PCR‐RFLP (IL‐1β+3953 and IL‐6 −174). Results for each locus were compared between techniques by calculating the Kappa statistic as a measure of agreement. The IHG and more traditional genotyping methods produced very similar results at all loci. The Kappa statistics for each locus were as follows: TNF‐α−308, K = 0.727; IL‐1β+3953, K = 0.886; IL‐6 −174, K = 0.909; IL‐10 −1082, K = 0.876; IL‐10 −592, K = 0.920. IHG is a valid method for the determination of genotypes at the loci examined in this study and produces comparable results to those of more traditional methods of genotyping.
Beyond Binarism: Exploring a Model of Living Cultural Heritage for Dance

This essay, inspired by the 2003 UNESCO Convention for the Safeguarding of Intangible Cultural Heritage, explores meanings and definitions of the term ‘cultural heritage’ as it may be applied to dance. UNESCO's effort to include many different types of human expressions in its lists is commendable and an important attempt to safeguard the aspects of the world's cultural heritage. However, the binary oppositions of ‘tangible’/’intangible’, frequently used to describe material and immaterial elements of culture and heritage create a false dichotomy. This label is particularly problematic for dance, given its complex, multi-dimensional nature in which intangible and tangible elements are indissolubly linked. Instead, we suggest an alternative perspective of ‘living cultural heritage’ which is informed by three post-dualist conceptions contained within Giddens' Structuration theory (structure-agency), Merleau-Ponty's phenomenology (mind-body) and Bourdieu's theory of cultural practice (field-practice-habitus).
A Qualitative Study on the Influence of Quality Systems in Meeting Performance Funding Criteria in Wisconsin Technical College System Institutions

This case study investigated the influence of quality systems on meeting performance funding criteria in Wisconsin Technical College System institutions. Using qualitative text-analysis methodology, the case study identified the common processes, systems, values, and culture of three Wisconsin Forward Award-recognized technical colleges, looking for ways these characteristics were used for attaining performance-based funding goals. Sources analyzed included the colleges’ Wisconsin Forward Award application documents and evaluator feedback reports, and the transcripts of six interviews conducted with professionals with expertise in organizational effectiveness and performance funding at these institutions. Findings indicated that the entities shared quality, benchmarking, feedback, strategic planning, and budgeting processes and systems, as well as student-focused values and culture. The case study conclusions suggested that these commonalities were not aligned with performance-based funding goals. Interviewees felt that it was too early to draw conclusions on the effectiveness of these goals. The researcher recommends consideration of the processes, systems, values, and culture shared by these colleges by other technical colleges, and improved alignment of organizational practices with performance-based funding expectations. Suggestions also include improving the convergence of various state accountability and quality improvement initiatives to reduce leading institutions in divergent directions.
Reliability and Usefulness of a New In Vivo Measurement System of the Pivot Shift

Residual pivot shift after ACL reconstruction is a crucial factor related to poor clinical outcome. However, no method exists that is able to evaluate pivot shift quantitatively and noninvasively. We propose a new measurement system for the pivot shift test using an electromagnetic device and have evaluated its reliability and clinical usefulness. Posterior translation, lateral translation and maximum velocity during the reduction phase of pivot shift were calculated and used as parameters for evaluation. In measurement system analysis, discrepancies of motion between the bones and the sensors were minimal, while reproducibility in repeated measurement was acceptable. Next, clinical usefulness was evaluated by correlating the values obtained by kinematic measurement with the clinical grade. We found differences in each of the measured parameters among clinical grades. These data suggest the system is a valuable measurement tool for clinical evaluation of the pivot shift test.Level of Evidence: Level II, diagnostic study. See Guidelines for Authors for a complete description of levels of evidence.
Effect of Luminance on Visual Evoked Potential Amplitudes in Normal and Disabled Readers

Background. Considerable evidence exists that some reading-disabled children have disordered visual processing, specifically in the fast processing magnocellular (M) pathway. Methods. The extent that varying luminance and temporal frequency affect amplitude and latency of visual evoked potentials (VEPs) in normally achieving and reading-disabled children grades 4 to 6 was measured. Each group consisted of approximately 30 subjects. Monocular and binocular single channel VEPs were recorded using a sinusoidal checkerboard pattern of spatial frequency 14 min arc at 3 different temporal frequencies (1, 4, and 8 Hz), and an 8 Hz flicker fusion stimulus. Stimuli were presented under high and low luminance conditions. The peak of the major positive wave component (P1Oo) of each waveform and the trough of the previous major negative wave component were identified, and the peak to trough amplitude was measured. Results. Statistical analysis of the VEP amplitudes and latencies in response to different experimental conditions was performed using a repeated measure analysis of variance (MANOVA). VEP amplitudes were significantly higher for normal readers across all conditions. Within all subjects, significant effects were found for monocular vs. binocular viewing, temporal frequencies, and high vs. low luminance. Similar analysis of latencies revealed no significant differences. Conclusions. The presence of a weaker VEP response in reading-disabled children suggests a deficit early in visual processing. The significant difference in VEP amplitudes between the two reading groups provides an objective measure of a deficit in the M pathway that has been implicated in this condition. Whether serial VEP recordings might help to assess the effects of optometric therapy by providing an independent index of therapeutic efficiency is of special interest.
Abnormal microglial activation in the Cstb−/− mouse, a model for progressive myoclonus epilepsy, EPM1

Progressive myoclonus epilepsy of Unverricht–Lundborg type (EPM1) is an autosomal‐recessively inherited neurodegenerative disorder characterized by severely incapacitating myoclonus, seizures, and ataxia, and caused by loss‐of‐function mutations in the cystatin B gene (CSTB). A central neuropathological finding in the Cstb−/− mouse, an animal model for EPM1, is early microglial activation, which precedes astroglial activation, neuronal loss, and onset of myoclonus, thus implying a critical role for microglia in EPM1 pathogenesis. Here, we characterized phenotypic and functional properties of microglia from Cstb−/− mice utilizing brain tissue, microglia directly isolated from the brain, and primary microglial cultures. Our results show significantly higher Cstb mRNA expression in microglia than in neurons and astrocytes. In Cstb−/− mouse brain, expression of the inflammatory marker p‐p38 MAPK and the proportion of both pro‐inflammatory M1 and anti‐inflammatory M2 microglia is higher than in control mice. Moreover, M1/M2 polarization of microglia in presymptomatic Cstb−/− mice is, compared to control mice, skewed towards M2 type at postnatal day 14 (P14), but towards M1 type at P30, a time point associated with onset of myoclonus. At this age, the high expression of both pro‐inflammatory inducible nitric oxide synthase (iNOS) and anti‐inflammatory arginase 1 (ARG1) in Cstb−/− mouse cortex is accompanied by the presence of peripheral immune cells. Consistently, activated Cstb−/− microglia show elevated chemokine release and chemotaxis. However, their MHCII surface expression is suppressed. Taken together, our results link CSTB deficiency to neuroinflammation with early activation and dysfunction of microglia and will open new avenues for therapeutic interventions for EPM1. GLIA 2015;63:400–411
The complexity of minimal inference problem for conservative constraint languages

We study the complexity of the inference problem for propositional circumscription (the minimal inference problem) over arbitrary finite domains. The problem is of fundamental importance in nonmonotonic logics and commonsense reasoning. The complexity of the problem for the two-element domain has been completely classified [Durand, Hermann, and Nordh, Trichotomy in the complexity of minimal inference, LICS 2009]. In this paper, we classify the complexity of the problem over all conservative languages. We consider a version of the problem parameterized by a set of relations (a constraint language), from which we are allowed to build a knowledge base, and where a linear order used to compare models is a part of an input. We show that in this setting the problem is either Π2P-complete, coNP-complete, or in P. The classification is based on a coNP-hardness proof for a new class of languages, an analysis of languages that do not express any member of the class and a new general polynomial-time algorithm solving the minimal inference problem for a large class of languages.
Technology substitution and standardization in telecommunication services

Traditional studies on information technology (IT) substitution and standardization have focused mostly on products, standalone components or equipment interfaces. The dynamics of technology life cycle have rarely been considered and innovation has tended to be viewed mostly as a competitive tool or as an opportunity for new entrants. However, the context of interactions among markets, technologies and standards provides many clues regarding the evolution of service innovations in public telecommunication networks. In particular, by combining marketing and technological perspectives, it is possible to consider the discontinuities that the evolution of technologies can provoke, as well as the changes in the attributes used to rank services. With this approach, an innovation can be categorized in four ways: incremental, architectural, platform, and radical. Process and architectural innovations are more readily integrated within the existing framework, both from the technological and financial viewpoints. For platform innovations, sales of network equipment can be a useful leading indicator for service evolution. This has several consequences. As a consequence, telecommunication carriers are now obliged to develop their own custom solutions to integrate the various proprietary OSSs that are used to operate modern networks. We illustrate these ideas with historical data for networks using the following protocols: X.25, frame relay and ATM (asynchronous transfer mode).
A Drug–Perfluorocarbon Nanoemulsion with an Ultrathin Silica Coating for the Synergistic Effect of Chemotherapy and Ablation by High‐Intensity Focused Ultrasound

The synergistic effect of chemotherapy and ablation using high-intensity focused ultrasound (HIFU) is realized with a newly developed drug-delivery system. The system comprises an ultrathin silica shell surrounding a poly(lactic-co-glycolic acid) nanoemulsion core containing the drug (CPT) and a perfluorocarbon (PFOB). This nanosystem presents many advantages in drug delivery, such as excellent structural stability, high drug-loading capacity, and rapid HIFU-mediated drug release.
Intergeneric natural plasmid transformation between E. coli and a marine Vibrio species

Natural transformation is the mechanism of procaryotic gene transfer that involves the uptake and expression of genetic information encoded in extracellular DNA. This process has been regarded as a mechanism to transfer genes (primarily chromosomal markers) between closely related strains or species. Here we demonstrate the cell–contact–dependent transfer of a non–conjugative plasmid from a laboratory E. coli strain to a marine Vibrio species, the first report of intergeneric natural plasmid transformation involving a marine bacterium. The nucleic acid synthesis inhibitors nalidixic acid and rifampicin inhibited the ability of the E. coli to function as a donor. However, dead cells also served as efficient donors. There was an obligate requirement for cell contact. No transfer occurred in the presence of DNase I, when donors and recipients were separated by a 0.2–μm filter, or when spent medium alone was used as a source of transforming DNA. These results indicate that contact–mediated intergeneric plasmid exchange can occur in the absence of detectable viable donor cells and that small non–conjugative plasmids can be spread through heterogeneous microbial communities by a process previously not recognized, natural plasmid transformation. These findings are important in the assessment of genetic risk to the environment, particularly from wastewater treatment systems and the use of genetically engineered organisms in the environment.
Modulation of the heat shock response by one-carbon metabolism in Escherichia coli

A genetic screen designed to isolate mutants of Escherichia coli W3110 altered in the ability to induce the heat shock response identified a strain unable to induce the heat shock proteins in a rich, defined medium lacking methionine after exposure to 2,4-dinitrophenol. This strain also grew slowly at 28 degrees C and linearly at 42 degrees C in this medium. The abnormal induction of the heat shock proteins and abnormal growth at both high and low temperatures were reversed when methionine was included in the growth medium. The mutation responsible for these phenotypes mapped to the glyA gene, a biosynthetic gene encoding the enzyme that converts serine and tetrahydrofolate to glycine and 5,10-methylenetetrahydrofolate. This reaction is the major source of glycine and one-carbon units in the cell. Because fixed one-carbon units, in the form of methionine, allowed mutant cells to induce the heat shock response after exposure to 2,4-dinitrophenol, a one-carbon restriction may be responsible for the phenotypes described above.
Rescue angioplasty during myocardial infarction has a beneficial effect on mortality: a tenable hypothesis.

HYPOTHESIS Rescue percutaneous transluminal coronary angioplasty (PTCA) reduces mortality during myocardial infarction. OBJECTIVE To determine if PTCA after failed thrombolytic therapy results in reduced mortality. DESIGN Twenty-eight patients with a persistently occluded infarct artery following thrombolytic therapy more than 3 h after symptom onset were randomized to rescue PTCA (n = 16) or conservative treatment (n = 12) as part of a prospective randomized trial of reperfusion therapy during myocardial infarction in 184 patients. Hospital mortality was assessed in these groups as well as in the 177 patients with known infarct artery status after initial attempts at reperfusion. MAIN RESULTS There was one death among the 16 patients in the rescue PTCA group versus four deaths in the 12 patients treated conservatively (P = 0.13). Moreover, the death in the rescue PTCA group occurred in one of three patients in whom the procedure failed. Mortality in the entire study group was 10.3% (19 of 184); 4.2% (six of 142) in patients in whom patency was achieved after thrombolysis and/or PTCA and 34.3% (12 of 35) in those in whom reperfusion was not achieved (P less than 0.001). In patients with anterior myocardial infarction, mortality was 6.7% (four of 60) in those with reperfusion and 47.1% (eight of 17) in those with a persistently occluded artery (P less than 0.001). In patients with inferior myocardial infarction, 2.4% (two of 82) with reperfusion and 22.2% (four of 18) with a persistently occluded artery died (P less than 0.01). CONCLUSIONS Although the number of patients in the randomized groups was small, the trend toward a lower mortality after rescue PTCA supports the hypothesis that rescue PTCA may be beneficial. The mortality results in relation to presence or absence of reperfusion from the entire study population underscores the importance of achieving patency during myocardial infarction.