Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiation of Campylobacter jejuni and Campylobacter coli Using Multiplex-PCR and High Resolution Melt Curve Analysis

Campylobacter spp. are important causes of bacterial gastroenteritis in humans in developed countries. Among Campylobacter spp. Campylobacter jejuni (C. jejuni) and C. coli are the most common causes of human infection. In this study, a multiplex PCR (mPCR) and high resolution melt (HRM) curve analysis were optimized for simultaneous detection and differentiation of C. jejuni and C. coli isolates. A segment of the hippuricase gene (hipO) of C. jejuni and putative aspartokinase (asp) gene of C. coli were amplified from 26 Campylobacter isolates and amplicons were subjected to HRM curve analysis. The mPCR-HRM was able to differentiate between C. jejuni and C. coli species. All DNA amplicons generated by mPCR were sequenced. Analysis of the nucleotide sequences from each isolate revealed that the HRM curves were correlated with the nucleotide sequences of the amplicons. Minor variation in melting point temperatures of C. coli or C. jejuni isolates was also observed and enabled some intraspecies differentiation between C. coli and/or C. jejuni isolates. The potential of PCR-HRM curve analysis for the detection and speciation of Campylobacter in additional human clinical specimens and chicken swab samples was also confirmed. The sensitivity and specificity of the test were found to be 100% and 92%, respectively. The results indicated that mPCR followed by HRM curve analysis provides a rapid (8 hours) technique for differentiation between C. jejuni and C. coli isolates.
Infertility in female mice with an oocyte-specific knockout of GPI-anchored proteins

Glycosylphosphatidylinositol-anchored proteins on the egg surface have been proposed to play a role in gamete fusion on the basis of in vitro experiments. We tested this hypothesis by asking if oocyte GPI-anchored proteins are required for fertilization in vivo. Oocyte-specific knockout mice were created using the Cre/loxP system to delete a portion of the Pig-a gene, which encodes an enzyme involved in GPI anchor biosynthesis. Conditional Pig-a-knockout females are infertile, and eggs recovered from the females after mating are unfertilized. In in vitro assays, the knockout eggs are severely deficient in their ability to fuse with sperm. These results demonstrate that GPI-anchored proteins are required for gamete fusion. Loss of the GPI-anchored complement of plasma membrane proteins could prevent fusion by altering the organization and function of GPI-anchored protein-containing lipid domains. Alternatively, a single GPI-anchored protein may be required in the fusion process. To distinguish between these possibilities, we have begun to identify the GPI-anchored proteins on the egg surface. We have identified one egg GPI-anchored protein as CD55, an ∼70 kDa complement regulatory protein. It has previously been found that CD55-knockout mice are fertile, demonstrating that CD55 is not essential for fertilization. This finding also means that the presence of the full complement of egg GPI-anchored proteins is not necessary for gamete fusion. Other egg GPI-anchored proteins acting in the fusion process can now be investigated, with the goal of understanding the mechanism of their function in sperm-egg fusion.
On the H-two norm of switched systems via homogeneous rational Lyapunov functions

This paper addresses the problem of determining the H-two norm of continuous-time switched linear systems in the case of arbitrary switching. A novel class of Lyapunov functions is proposed, called homogeneous rational Lyapunov functions (HRLFs). It is shown that a sufficient condition for establishing upper bounds of the H-two norm can be given in terms of a linear matrix inequality (LMI) feasibility test by searching for an HRLF of any a priori chosen degree. Moreover, it is shown that this condition is also necessary under some assumptions by using HRLF candidates with degree sufficiently large. Some numerical examples illustrate the proposed approach and its advantages with respect to the existing methods.
A Critical Review of the Preetham Skylight Model

The Preetham skylight model is currently one of the most widely used analytic models of skylight luminance in computer graphics. Despite its widespread use, very little work has been carried out to verify the results generated by the model, both in terms of the luminance patterns it generates, and in terms of numerical reliability and stability. In this paper, we show where the model exhibits problematic behaviour, and compare the computed luminance values with the CIE 2003 Standard General Sky, and our own measurements of real, cloudless skies.
Dominant-Negative Activity Activity and Reveals the Critical Role of Nuclear Import in p 53 Lacks Intrinsic Transcriptional ∆ The p 53 Isoform

The transcription factor p53 is one of the most frequently mutated tumor suppressors. Recent progress has unraveled several novel isoforms of p53. Intriguingly, one of the p53 isoform, #p53, which lacks part of the DNA binding domain, was reported to be transcriptionally active toward some p53 target genes and is critical for the intra–S phase checkpoint. Here, we show that, in contrast to full-length p53, ectopically expressed #p53 neither transactivated the promoters of p21 or murine double minute-2 (MDM2) nor repressed the cyclin B1 promoter in unstressed H1299 cells. Due to the deletion of a nuclear localization signal, #p53 was not imported into the nucleus. Engineering of nuclear localization signals to #p53 restored nuclear accumulation. However, the nuclear-targeting #p53 remained inactive, indicating that the lack of intrinsic activity of #p53 was not simply due to subcellular localization but to its incomplete DNA binding domain. Similar to p53, #p53 was subjected to MDM2-mediated ubiquitination/proteolysis. The cytoplasmic localization of #p53 correlated with the instability of the protein because forcing #p53 into the nucleus increased its stability. Although #p53 could form a complex with p53 and stimulated the cytoplasmic retention of p53, it was not a robust inhibitor of p53. Targeting #p53 into the nucleus enhanced the dominant-negative activity of #p53. These observations underscore the critical role of subcellular localization in the dominant-negative action of p53. [Cancer Res 2007;67(5):1959–69]
The role of protein C deficiency in the etiology of Perthes disease.

BACKGROUND Recent reports support the hypothesis that thrombophilia plays an important role in the pathogenesis of Perthes disease (PD) and the objective of this report is to show evidence of the role of protein C deficiency in the etiology of PD, based on a meta-analysis of current scientific literature. MATERIAL AND METHODS Studies were selected in all languages over the last twenty years (1986 to 2006) in MEDLINE, LILACS and EMBASE data bases. The inclusion criteria involved controlled studies, those that presented protein C as a continuous variable, and studies conducted in children with Perthes disease. The fixed effect model for continuous data was used; differences between groups were assessed by the t-test, Z-test and Cochran Q test for independent data and the level of significance was p < 0.05. RESULTS The selected studies involved 175 patients and 193 control subjects. The selected studies were shown to be heterogeneous, but there were no statistically significant differences in protein C levels between groups. CONCLUSION The authors' findings were unable to support the hypothesis that protein C deficiency is associated with Perthes disease and that it may play an important role in the ethiopathogenesis of avascular necrosis of the femoral head in childhood.
Animal Research, Animal Welfare, and the Three R's*

The last 50 years have witnessed a dazzling array of social and ethical revolutions in Western society. Such movements as feminism, civil rights, environmentalism, affirmative action, consumer advocacy, pro-and anti-abortion activism, homosexual rights, children‟s rights, the student movement, antiwar activism and public rejection of biotechnology have changed the way in which governments and public institutions comport themselves. This is equally true for private enterprise: to be successful, businesses and institutions must be seen as operating solidly in harmony with changing and emerging social ethics.
Mechanisms of oscillatory activity in guinea‐pig nucleus reticularis thalami in vitro: a mammalian pacemaker.

1. The ionic mechanisms of rhythmic burst firing and single spike, tonic discharge were investigated with extracellular and intracellular recordings of single neurones in the guinea‐pig nucleus reticularis thalami (NRT) maintained as a slice in vitro. 2. Activation of cortical/thalamic afferents to NRT neurones resulted in a short latency burst of action potentials which could be followed by a rhythmic sequence of oscillatory burst firing. Intracellularly, this oscillatory activity was associated with an alternating sequence of low threshold Ca2+ spikes separated by after‐hyperpolarizing potentials. Intracellular injection of short duration hyperpolarizing current pulses resulted in a similar sequence of oscillatory burst firing, suggesting that this activity is an intrinsic property of NRT cells. The frequency of rhythmic burst firing was highly voltage and temperature dependent and was between 7‐12 Hz at ‐65 to ‐60 mV at 38 degrees C. In addition, at depolarized membrane potentials, oscillatory burst firing was typically followed by a prolonged tail of single spike activity. 3. Application of the Na+ channel poison tetrodotoxin blocked the generation of fast action potentials, but left intact the rhythmic sequence of low threshold Ca2+ spikes separated by after‐hyperpolarizing potentials (AHPs). The reversal potential of the AHPs was ‐94 mV, suggesting that it was mediated by an increase in K+ conductance. Extracellular application of tetraethylammonium or apamin, or intracellular injection of Cs+ or the Ca2+ chelating agent EGTA, blocked the Ca2+ spike AHP, indicating that it is mediated by a Ca(2+)‐activated K+ current. 4. Block of the AHP resulted in the marked enhancement of a slow after‐depolarizing potential (ADP). The slow ADP occurred only following the generation of low threshold Ca2+ spikes. Replacement of extracellular Ca2+ with Mg2+ or Sr2+ resulted in an abolition of the slow ADP. In addition, the increase in [Mg2+]o resulted in an abolition of the low threshold Ca2+ spike. In contrast, replacement of extracellular Ca2+ with Ba2+ did not abolish the slow ADP. These results indicate that the ADP can be activated by either Ca2+ or Ba2+, but not by Mg2+ or Sr2+. 5. Replacement of extracellular Na+ with choline+ did not abolish the slow ADP, while replacement with N‐methyl‐D‐glucamine+ did, indicating that the slow ADP can be supported by choline+, but not by N‐methyl‐D‐glucamine+. Neither chemical affected the low threshold Ca2+ spike. These results are consistent with the slow ADP being mediated by a Ca(2+)‐activated non‐selective cation (CAN) current. (ABSTRACT TRUNCATED AT 400 WORDS)
Decision Making, Value Propositioning, and Project Failures - Reality and Responsibility

This paper outlines reasons for project failures and ties them to value proposition failures. It defines a value proposition as including both the proposed project deliverable values as well as the implementation processes that will assure value is delivered. It shows that an effective value proposition is not so much about the technology being proposed as it is about the problem and value perceptions of the Decision Makers who will sponsor a project; and that it is the project Champion's responsibility to learn the perceptions of decisions makers, and to carefully guide their education of problem issues and solution values.continuously. To this end the bulk of this paper presents two models of how Decision Makers form perceptions from value propositions. One model represents the psychological behavior of individuals as Decision Makers, and the other of group decision making behavior. Both draw from Nobel Prize winning research and show how misperception is the general rule, illuminating the issues that the Champion must address.
Decolonizing Research Paradigms in the Context of Settler Colonialism: An Unsettling, Mutual, and Collaborative Effort

All research is guided by a set of philosophical underpinnings. Indigenous methodologies are in line with an Indigenous paradigm, while critical and liberatory methodologies fit with the transformative paradigm. Yet Indigenous and transformative methodologies share an emancipatory and critical stance and thus are increasingly used in tandem by both Western and Indigenous scholars in an attempt to decolonize methodologies, research, and the academy as a whole. However, these multiparadigmatic spaces only superficially support decolonization which, in the Canadian context of settler colonialism, is a radical and unsettling prospect that is about land, resources, and sovereignty. Applying this definition of decolonization to the decolonization of research paradigms, this article suggests that such paradigms must be developed, from scratch, conjointly between Indigenous and Western researchers.
C-SAW---contextual semantic alignment of ontologies: using negative semantic reinforcement

Understanding the meaning of each term in an ontology is essential for successfully integrating and aligning ontologies. Much ontology integration research to date is focused on syntactic, structural and semantic matching where the actual meaning of the concepts is disregarded. The C-SAW approach to ontology alignment is based on the Contextualizing the concepts by using a set of Semantic Alignment Words (C-SAW). The C-SAW approach is enhanced by Negative Semantic Reinforcement (NSR), where additional semantic meaning can be added to the set of Semantic Alignment Words, by considering words which are unrelated to the concept.
Immuno-Stimulatory Activity of Escherichia coli Mutants Producing Kdo2-Monophosphoryl-Lipid A or Kdo2-Pentaacyl-Monophosphoryl-Lipid A

Lipid A is the active center of lipopolysaccharide which also known as endotoxin. Monophosphoryl-lipid A (MPLA) has less toxicity but retains potent immunoadjuvant activity; therefore, it can be developed as adjuvant for improving the strength and duration of the immune response to antigens. However, MPLA cannot be chemically synthesized and can only be obtained by hydrolyzing lipopolysaccharide (LPS) purified from Gram-negative bacteria. Purifying LPS is difficult and time-consuming and can damage the structure of MPLA. In this study, Escherichia coli mutant strains HWB01 and HWB02 were constructed by deleting several genes and integrating Francisella novicida gene lpxE into the chromosome of E. coli wild type strain W3110. Compared with W3110, HWB01 and HWB02 synthesized very short LPS, Kdo2-monophosphoryl-lipid A (Kdo2-MPLA) and Kdo2-pentaacyl-monophosphoryl-lipid A (Kdo2-pentaacyl-MPLA), respectively. Structural changes of LPS in the outer membranes of HWB01 and HWB02 increased their membrane permeability, surface hydrophobicity, auto-aggregation ability and sensitivity to some antibiotics, but the abilities of these strains to activate the TLR4/MD-2 receptor of HKE-Blue hTLR4 cells were deceased. Importantly, purified Kdo2-MPLA and Kdo2-pentaacyl-MPLA differed from wild type LPS in their ability to stimulate the mammalian cell lines THP-1 and RAW264.7. The purification of Kdo2-MPLA and Kdo2-pentaacyl-MPLA from HWB01 and HWB02, respectively, is much easier than the purification of LPS from W3110, and these lipid A derivatives could be important tools for developing future vaccine adjuvants.
Gene expression changes within Müller glial cells in retinitis pigmentosa

Purpose Retinitis pigmentosa (RP) is a progressive retinal degeneration in which the retina loses nearly all of its photoreceptor cells and undergoes major structural changes. Little is known regarding the role the resident glia, the Müller glia, play in the progression of the disease. In this article, we define gene expression changes in Müller glial cells (MGCs) from two different mouse models of RP, the retinal degeneration 1 (rd1) and rhodopsin knockout (Rhod-ko) models. The RNA repertoire of single MGCs was comprehensively profiled, and a comparison was made between MGCs from wild-type (WT) and mutant retinas. Two time points were chosen for analysis, one at the peak of rod photoreceptor death and one during the period of cone photoreceptor death. Methods Retinas were dissociated, and single MGCs were chosen under a dissecting microscope using a micropipette. Single cell cDNAs were generated and genome-wide profiles were obtained by hybridization to Affymetrix arrays. A comparison was made among all samples to discover the changes in gene expression during the periods of rod and cone photoreceptor death. Results MGCs respond to retinal degeneration by undergoing gliosis, a process marked by the upregulation of glial fibrillary acidic protein (Gfap). Many additional transcripts were found to change. These can be placed into functional clusters, such as retinal remodeling, stress response, and immune-related response. Conclusions A high degree of heterogeneity among the individual cells was observed, possibly due to their different spatial proximities to dying cells and/or inherent heterogeneity among MGCs.
Plasticity of GABAA receptor diffusion dynamics at the axon initial segment

The axon initial segment (AIS), a site of action potential initiation, undergoes activity-dependent homeostatic repositioning to fine-tune neuronal activity. However, little is known about the behavior of GABAA receptors (GABAARs) at synapses made onto the axon and especially the AIS. Here, we study the clustering and lateral diffusion of GABAARs in the AIS under baseline conditions, and find that GABAAR lateral mobility is lower in the AIS than dendrites. We find differences in axonal clustering and lateral mobility between GABAARs containing the α1 or α2 subunits, which are known to localize differentially to the AIS. Interestingly, we find that chronic activity driving AIS repositioning does not alter GABAergic synapse location along the axon, but decreases GABAAR cluster size at the AIS. Moreover, in response to chronic depolarization, GABAAR diffusion is strikingly increased in the AIS, and not in dendrites, and this is coupled with a decrease in synaptic residency time of GABAARs at the AIS. We also demonstrate that activation of L-type voltage-gated calcium channels is important for regulating GABAAR lateral mobility at the AIS during chronic depolarization. Modulation of GABAAR diffusion dynamics at the AIS in response to prolonged activity may be a novel mechanism for regulating GABAergic control of information processing.
Extremely hard GRB spectra prune down the forest of emission models

We consider the evidence for very hard low energy spectra during the prompt phase of Gamma-Ray Bursts (GRB). In particular we examine the spectral evolution of GRB 980306 together with the detailed analysis of some other bursts already presented in the literature (GRB 911118, GRB 910807, GRB 910927 and GRB 970111), and check for the significance of their hardness (i.e. extremely steep spectral slopes below the EFE peak) by applying dierent tests. These bursts, detected by the Burst And Transient Source Experiment (BATSE) in the30 keV-2 MeV energy range, are suciently bright to allow time resolved spectral studies on time intervals of the order of tenths of a second. We discuss the hard spectra of these bursts and their evolution in the context of several non-thermal emission models, which all appear inadequate to account for these cases. The extremely hard spectra, which are detected in the early part of the BATSE light curve, are also compared with a black body spectral model: the resulting fits are remarkably good, except for an excess at high energies (in several cases) which could be simply accounted for by the presence of a supra-thermal component. The findings on the possible thermal character of the evolving spectrum and the implications on the GRB physical scenario are considered in the frameworks of photospheric models for a fireball which is becoming optically thin, and of Compton drag models, in which the fireball boosts "ambient" seed photons by its own bulk motion. Both models, according to simple estimates, appear to be qualitatively and quantitatively consistent with the found spectral characteristics, although their possible caveats are discussed.
Are the Right People Measuring the Right Things? A Lean Path to Achieving Business Objectives

T he effectiveness of the CMMI framework at helping organizations achieve business objectives is currently a hotly debated topic [1]. One of my clients responded to my recent suggestion to consider using the CMMI and Agile techniques together by stating: We do not place much value in the CMMI because we have not seen a difference between Level 4 and 5 organizations and those rated lower. At a recent conference in a presentation about high process-maturity project failures, we also heard some failures were due to non-process effects such as people [2]. To help us understand what might be going on, I would like to share a case study. I have a client who has been using the CMM/CMMI framework for many years to aid process improvement. According to traditional literature, they appear to be doing the right things. They have discussed and captured their business objectives using the Goal-Question-Metric technique, and they have aligned their measures with these objectives. They have standardized their processes and trained their people [3]. This client has multiple product lines. Their processes and training include a strong emphasis on product baseline management with disciplined change approvals. Their established and documented business objectives include increasing off-the-shelf product sales, reducing unique customer customization, and meeting cost and schedule commitments. To help achieve these objectives, the client has been striving to increase management visibility of work through the use of standard product and process metrics. This all seems to make sense. So a natural question arises: Are they achieving their business objectives? While isolated success stories exist, most senior managers – as well as the company metrics – indicate the organization has fallen far short of its goals. While the organization continues to propose and bid off-the-shelf solutions, standard metrics show significant unplanned product changes and cost and schedule overruns. A frequent refrain heard at senior management reviews is the following: " Why are we making all these unplanned and un-bid changes? " So what happened? While this organization appears to have followed the prevailing wisdom in deploying sound processes, why have they failed to achieve their objectives? This case is not unique. Over the past 10 years, I have observed variants of this pattern in multiple organizations. A closer look at this case may provide insight that can help answer why many organizations seeking higher process maturities are failing to enjoy the promised results of their …