Miracle-dz/UniFAR-FTUs huggingface dataset:
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Background: Dynamic Bayesian Network (DBN) is an approach widely used for reconstruction of gene regulatory networks from time-series microarray data. Its performance in network reconstruction depends on a structure learning algorithm. REVEAL (REVerse Engineering ALgorithm) is one of the algorithms implemented for learning DBN structure and used to reconstruct gene regulatory networks (GRN). However, the two-stage temporal Bayes network (2TBN) structure of DBN that specifies correlation between time slices cannot be obtained by score metrics used in REVEAL. Methods: In this paper, we study a more sophisticated score function for DBN first proposed by Nir Friedman for stationary DBNs structure learning of both initial and transition networks but has not yet been used for reconstruction of GRNs. We implemented Friedman ’ s Bayesian Information Criterion (BIC) score function, modified K2 algorithm to learn Dynamic Bayesian Network structure with the score function and tested the performance of the algorithm for GRN reconstruction with synthetic time series gene expression data generated by GeneNetWeaver and real yeast benchmark experiment data. Results: We implemented an algorithm for DBN structure learning with Friedman ’ s score function, tested it on reconstruction of both synthetic networks and real yeast networks and compared it with REVEAL in the absence or presence of preprocessed network generated by Zou&Conzen ’ s algorithm. By introducing a stationary correlation between two consecutive time slices, Friedman ’ s score function showed a higher precision and recall than the naive REVEAL algorithm. Conclusions: Friedman ’ s score metrics for DBN can be used to reconstruct transition networks and has a great potential to improve the accuracy of gene regulatory network structure prediction with time series gene expression datasets.
The Centrosomal Kinase Plk1 Localizes to the Transition Zone of Primary Cilia and Induces Phosphorylation of Nephrocystin-1

Polo-like kinase (Plk1) plays a central role in regulating the cell cycle. Plk1-mediated phosphorylation is essential for centrosome maturation, and for numerous mitotic events. Although Plk1 localizes to multiple subcellular sites, a major site of action is the centrosomes, which supports mitotic functions in control of bipolar spindle formation. In G0 or G1 untransformed cells, the centriolar core of the centrosome differentiates into the basal body of the primary cilium. Primary cilia are antenna-like sensory organelles dynamically regulated during the cell cycle. Whether Plk1 has a role in ciliary biology has never been studied. Nephrocystin-1 (NPHP1) is a ciliary protein; loss of NPHP1 in humans causes nephronophthisis (NPH), an autosomal-recessive cystic kidney disease. We here demonstrate that Plk1 colocalizes with nephrocystin-1 to the transition zone of primary cilia in epithelial cells. Plk1 co-immunoprecipitates with NPHP1, suggesting it is part of the nephrocystin protein complex. We identified a candidate Plk1 phosphorylation motif (D/E-X-S/T-φ-X-D/E) in nephrocystin-1, and demonstrated in vitro that Plk1 phosphorylates the nephrocystin N-terminus, which includes the specific PLK1 phosphorylation motif. Further, induced disassembly of primary cilia rapidly evoked Plk1 kinase activity, while small molecule inhibition of Plk1 activity or RNAi-mediated downregulation of Plk1 limited the first and second phase of ciliary disassembly. These data identify Plk1 as a novel transition zone signaling protein, suggest a function of Plk1 in cilia dynamics, and link Plk1 to the pathogenesis of NPH and potentially other cystic kidney diseases.
Steroid avoidance or withdrawal in kidney transplantation

Purpose of reviewSteroid avoidance or early withdrawal in kidney transplantation is supported by recent guidelines, but late steroid withdrawal after the first posttransplant months has been recently discouraged in those guidelines. We have assessed the recent data trying to confirm whether or not these different steroid-sparing strategies are well tolerated. Recent findingsReversible, mild acute rejection rates are increased after steroid avoidance or withdrawal. However, steroid avoidance or early withdrawal is well tolerated in low immunological risk kidney transplant recipients receiving induction with anti-IL2 receptor antibodies or thymoglobulin and a drug regimen based on calcineurin inhibitor and mycophenolate mofetil, at least during 5 years, the longest follow-up reported. In addition, steroid withdrawal after 3–6 months is associated with stable graft function and survival stable up to 3 years after transplantation, the longest follow-up reported. Although clear benefits (cardiovascular and others) are obvious in some observational studies, true benefits in randomized controlled trials remain unclear. SummaryBoth early and late steroid withdrawals are well tolerated in selected low-risk renal allograft recipients treated with modern potent immunosuppression. More trials with carefully designed outcome measures are needed, especially with other modern combinations, including mTOR inhibitors and/or belatacept.
Security policies and trust in ubiquitous computing

Ubiquitous environments comprise resource-constrained mobile and wearable devices and computational elements embedded in everyday artefacts. These are connected to each other using both infrastructure-based as well as short-range ad hoc networks. Limited Internet connectivity limits the use of conventional security mechanisms such as public key infrastructures and other forms of server-centric authentication. Under these circumstances, peer-to-peer interactions are well suited for not just information interchange, but also managing security and privacy. However, practical solutions for protecting mobile devices, preserving privacy, evaluating trust and determining the reliability and accuracy of peer-provided data in such interactions are still in their infancy. Our research is directed towards providing stronger assurances of the reliability and trustworthiness of information and services, and the use of declarative policy-driven approaches to handle the open and dynamic nature of such systems. This paper provides an overview of some of the challenges and issues, and points out directions for progress.
Differentiation and Characterization of Myeloid Cells

Recent molecular studies of myeloid differentiation have utilized several in vitro models of myelopoiesis. Hematopoietic progenitors expressing the CD34+ antigen can be induced in vitro in a process that recapitulates the normal myeloid development. Two human leukemic cell lines, NB‐4 and HL‐60, have been demonstrated to undergo retinoic acid–induced myeloid development, however, both cell lines exhibit defects in the upregulation of late‐expressed neutrophil‐specific genes. In contrast, two murine factor–dependent cell models of myelopoiesis express the full range of neutrophil maturation markers: 32Dcl3 cells, which undergo G‐CSF‐induced myeloid maturation, and EML/EPRO cells, which develop into mature neutrophils in response to cytokines and retinoic acid. In this unit, the induction of myeloid maturation in each of these model systems is described. Commonly used techniques to test for myeloid characteristics of developing cells are also described. Together, these assays provide a solid foundation for in vitro investigations of myeloid development.
A mischief of mice: examining children's performance in single display groupware systems with 1 to 32 mice

Mischief is a system for classroom interaction that allows multiple children to use individual mice and cursors to interact with a single large display [20]. While the system can support large groups of children, it is unclear how children's performance is affected as group size increases. We explore this question via a study involving two tasks, with children working in group sizes ranging from 1 to 32. The first required reciprocal selection of two on-screen targets, resembling a swarm pointing scenario that might be used in educational applications. The second, a more temporally and spatially distributed pointing task, had children entering different words by selecting characters on an on-screen keyboard. Results indicate that performance is significantly affected by group size only when targets are small. Further, group size had a smaller effect when pointing was spatially and temporally distributed than when everyone was concurrently aiming at the same targets.
How Many Countries for Multilevel Modeling? A Comparison of Frequentist and Bayesian Approaches

Researchers in comparative research increasingly use multilevel models to test effects of country-level factors on individual behavior and preferences. However, the asymptotic justification of widely employed estimation strategies presumes large samples and applications in comparative politics routinely involve only a small number of countries. Thus, researchers and reviewers often wonder if these models are applicable at all. In other words, how many countries do we need for multilevel modeling? I present results from a large-scale Monte Carlo experiment comparing the performance of multilevel models when few countries are available. I find that maximum likelihood estimates and confidence intervals can be severely biased, especially in models including cross-level interactions. In contrast, the Bayesian approach proves to be far more robust and yields considerably more conservative tests.
In Vivo Visualization of Endoplasmic Reticulum Stress in the Retina Using the ERAI Reporter Mouse.

PURPOSE Endoplasmic reticulum (ER) stress activates inositol requiring enzyme 1 (IRE1), a key regulator of the unfolded protein response. The ER stress activated indicator (ERAI) transgenic mouse expresses a yellow fluorescent GFP variant (Venus) when IRE1 is activated by ER stress. We tested whether ERAI mice would allow for real-time longitudinal studies of ER stress in living mouse eyes. METHODS We chemically and genetically induced ER stress, and qualitatively and quantitatively studied the Venus signal by fluorescence ophthalmoscopy. We determined retinal cell types that contribute to the signal by immunohistology, and we performed molecular and biochemical assays using whole retinal lysates to assess activity of the IRE1 pathway. RESULTS We found qualitative increase in vivo in fluorescence signal at sites of intravitreal tunicamycin injection in ERAI eyes, and quantitative increase in ERAI mice mated to RhoP23H mice expressing ER stress-inducing misfolded rhodopsin protein. As expected, we found that increased Venus signal arose primarily from photoreceptors in RhoP23H/+;ERAI mice. We found increased Xbp1S and XBP1s transcriptional target mRNA levels in RhoP23H/+;ERAI retinas compared to Rho+/+;ERAI retinas, and that Venus signal increased in ERAI retinas as a function of age. CONCLUSIONS Fluorescence ophthalmoscopy of ERAI mice enables in vivo visualization of retinas undergoing ER stress. ER stress activated indicator mice enable identification of individual retinal cells undergoing ER stress by immunohistochemistry. ER stress activated indicator mice show higher Venus signal at older ages, likely arising from amplification of basal retinal ER stress levels by GFP's inherent stability.
The specific NH2-terminal sequence Ac-EEED of alpha-smooth muscle actin plays a role in polymerization in vitro and in vivo

The blocking effect of the NH2-terminal decapeptide of alpha-smooth muscle (SM) actin AcEEED-STALVC on the binding of the specific monoclonal antibody anti-alpha SM-1 (Skalli, O., P. Ropraz, A. Trzeviak, G. Benzonana, D. Gillessen, and G. Gabbiani. 1986. J. Cell Biol. 103:2787-2796) was compared with that of synthetic peptides modified by changing the acetyl group or by substituting an amino acid in positions 1 to 5. Using immunofluorescence and immunoblotting techniques, anti-alpha SM-1 binding was abolished by the native peptide and by peptides with a substitution in position 5, indicating that AcEEED is the epitope for anti-alpha SM-1. Incubation of anti-alpha SM- 1 (or of its Fab fragment) with arterial SM actin increased polymerization in physiological salt conditions; the antibody binding did not hinder the incorporation of the actin antibody complex into the filaments. This action was not exerted on skeletal muscle actin. After microinjection of the alpha-SM actin NH2-terminal decapeptide or of the epitopic peptide into cultured aortic smooth muscle cells, double immunofluorescence for alpha-SM actin and total actin showed a selective disappearance of alpha-SM actin staining, detectable at approximately 30 min. When a control peptide (e.g. alpha-skeletal [SK] actin NH2-terminal peptide) was microinjected, this was not seen. This effect is compatible with the possibility that the epitopic peptide traps a protein involved in alpha-SM actin polymerization during the dynamic filament turnover in stress fibers. Whatever the mechanism, this is the first evidence that the NH2 terminus of an actin isoform plays a role in the regulation of polymerization in vitro and in vivo.
Simultaneous prevention of glutamine synthesis and high-affinity transport attenuates Salmonella typhimurium virulence

In Salmonella typhimurium, transcription of the glnA gene (encoding glutamine synthetase) is under the control of the nitrogen-regulatory (ntr) system comprising the alternate sigma factor sigma54 (NtrA) and the two-component sensor-transcriptional activator pair NtrB and NtrC. The glnA, ntrB, and ntrC genes form an operon. We measured the virulence of S. typhimurium strains with nitrogen-regulatory mutations after intraperitoneal (i.p.) or oral inoculations of BALB/c mice. Strains with single mutations in glnA, ntrA, ntrB, or ntrC had i.p. 50% lethal doses (LD50s) of <10 bacteria, similar to the wild-type strain. However, a strain with a delta(glnA-ntrC) operon deletion had an i.p. LD50 of >10(5) bacteria, as did delta glnA ntrA and delta glnA ntrC strains, suggesting that glnA strains require an ntr-transcribed gene for full virulence. High-level transcription of the glutamine transport operon (glnHPQ) is dependent upon both ntrA and ntrC, as determined by glnHp-lacZ fusion measurements. Moreover, delta glnA glnH and delta glnA glnQ strains are attenuated, similar to delta glnA ntrA and delta glnA ntrC strains. These results reveal that access of S. typhimurium to host glutamine depends on the ntr system, which apparently is required for the transcription of the glutamine transport genes. The delta(glnA-ntrC) strain exhibited a reduced ability to survive within the macrophage cell line J774, identifying a potential host environment with low levels of glutamine. Finally, the delta(glnA-ntrC) strain, when inoculated at doses as low as 10 organisms, provided mice with protective immunity against challenge by the wild-type strain, demonstrating its potential use as a live vaccine.
Saving Growth from Unequal Influence

The dominant view of how inequality and poverty are positively correlated relies not on the first causing the second, but on a common causal factor, poor political and economic institutions inherited from the past, that is responsible for both. I will argue that a simpler explanation is more compelling that when endowments and opportunities are unequally distributed in a poor society, disagreements over the most appropriate reform path are harder to resolve (see Rajan (2006) for a more technical version of this paper). The desire of each subgroup to preserve its economic rents against all others – what I term competitive rent preservation – tends to ensure that it is very hard to move away from the status quo.
Behavioral history as a determinant of the effects of d-amphetamine on punished behavior

Food-maintained responding by four squirrel monkeys (Saimiri sciureus) was suppressed by the presentation of electric shock (punishment). Two of these monkeys were experimentally naive and two had a history of responding maintained by both shock-postponement and shock-presentation schedules. In accord with earlier studies, d-amphetamine did not increase punished responding by naive monkeys. However, it did increase punished responding in the others. Subsequently, d-amphetamine also increased punished responding by the initially naive monkeys after they were trained under a shock-postponement schedule. Even though not evident in current behavior, an organism's prior experience can influence the behavioral effects of drugs.
Direct ex vivo analysis reveals distinct phenotypic patterns of HIV‐specific CD8+ T lymphocyte activation in response to therapeutic manipulation of virus load

Therapeutic intervention with antiretroviral therapy (ART) enables the modulation of HIV virus load and hence provides a unique opportunity to study the consequences of varying antigen load onthe phenotype of virus‐specific CD8+ T lymphocytes in a persistent human viral infection. The recent advent of tetrameric peptide / HLA class I complexes has enabled the direct phenotypic characterization of antigen‐specific T cell populations ex vivo. Here, we use this technology to examine directly ex vivo the consequences of therapeutic manipulation of HIV virus load on the phenotype of HIV‐specific CTL. Our observations show that: (1) distinct sequential activation patterns of CD8+ T cells are associated with increasing virus load; (2) T cell receptor (TCR) down‐regulation without apoptosis represents an early event during the generation of a T cell response in a natural infection and precedes the emergence of two distinct antigen‐specific CD8+ T cell populations which differ in TCR and CD8 expression levels. Clear differences in surface Annexin V staining were observed between these populations. The observation that CTL activation, demonstrated by TCR and CD8 down‐regulation, in response to rising levels of virus load, co‐segregates with apoptosis only during later stages of the response indicates that antigen‐associated cell death is restricted to distinct subpopulations of CTL.
Set Utilization Based Dynamic Shared Cache Partitioning

As the number of processors sharing a cache increases, conflict misses due to interference amongst competing processes have an increasing impact on the individual performance of processes. Cache partitioning is a method of allocating a cache between concurrently executing processes in order to counteract the effects of inter-process conflicts. However, cache partitioning methods commonly divide a shared cache into private partitions dedicated to a single processor, which can lead to underutilized portions of the cache when set accesses are non-uniform. Our proposed method compliments these cache partitioning algorithms by creating an additional shared partition able to be shared amongst all processors. Underutilized areas of the cache are identified by a monitoring circuit and used for the shared partition. Detection of underutilization is based on the number of unique set accesses for a given allocated way. For a 16-way set associative cache, the implementation of our method requires 64 bytes of storage overhead per core in addition to that needed for the method that determines the sizes of the private partitions. For the tested system, our method is able to improve performance over the traditional LRU policy for a number of selected benchmark sets by an average of 1.4% and up to 13.3% for a two core system and an average of 1.4% and up to 7.8% for a four core system, and is able to improve the performance of a conventional cache partitioning method (Utility-Based Cache Partitioning) by an average of 0.1% and up to 0.5% for both a two and four core systems.
Use of Rich Linguistic Information to Translate Prepositions and Grammar Cases to Basque

This paper presents three successful techniques to translate prepositions heading verbal complements by means of rich linguistic information, in the context of a rule-based Machine Translation system for an agglutinative language with scarce resources. This information comes in the form of lexicalized syntactic dependency triples, verb subcategorization and manually coded selection rules based on lexical, syntactic and semantic information. The first two resources have been automatically extracted from monolingual corpora. The results obtained using a new evaluation methodology show that all proposed techniques improve precision over the baselines, including a translation dictionary compiled from an aligned corpus, and a state-of-the-art statistical Machine Translation system. The results also show that linguistic information in all three techniques are complementary, and that a combination of them obtains the best F-score results overall.
Halloysite Nanotubes and Applications: A Review

Various successful results of nanotechnology like carbon nanotubes, nanofluids, nanoparticles, nano emulsions, nano capsules, etc are not considered to be safe for humans as well as for environment because of their toxicology potencies. Halloysite nanotubes are naturally occurring eco-friendly nanotubes with low cost that are harmless to human. Halloysite Nanotubes (HNTs) are unique and versatile nanomaterials composed of double layered aluminosilicate minerals with a predominantly hollow tubular structure in submicron range. They are nontoxic in nature, have tuneable release rates and fast adsorption rates. These nanotubes have got wide range of applications in anticancer therapy, sustained delivery for certain agents, act as template or nanoreactor for biocatalyst, have found use in personal care and cosmetics and even used as environment protective.
Analysis of wave energy reduction and sediment stabilization by mangroves in Gazi Bay, Kenya

Ndirangu MD, Chira RM, Wang’ondu V, Kairo JG. 2018. Wave energy reduction and sediment stabilization by mangroves in Gazi Bay, Kenya. Biodiversitas 19: 83-94. Mangrove forests provide natural protection to the coast by attenuating wave energy and stabilizing sediments. The efficiency of coastal protection is likely to decline with increased degradation and losses of mangrove forests. Nevertheless, there are few empirical studies to test these hypotheses. The objective of the study was to investigate how wave energy and sediment stabilization vary with tree density in a monospecies stand of mangroves (Sonneratia alba) at Gazi Bay, Kenya. Seven belt transects were randomly selected along 900 m stretches of shoreline with homogenous emergent wave energy. Structural parameters, including; tree density, pneumatophores density, and basal areas were quantified using two quadrat measuring 25 m by 20 m along each transect. Three intertidal stations, each with five sampling points were sampled for wave energy using uniform plaster of Paris clod cards. Sediment stability was measured using improvised sinking metal disks made from bicycle spokes, and sediment accretion was monitored by Surface Elevation Tables (SETs). All transects showed significant difference in pneumatophores density (F (2.39) =25.15), tree density (F (2.33) =24.79), and basal area (F (2.39) = 29.66). The wave energy sampled by tree stems between stations and the correlation of wave energy reduction against tree density/ha, pneumatophores density, and basal areas per m2 also showed a significant difference. Regression analysis showed a significant difference in the sediment stability against tree density (R2 = 61%) and basal areas (R2 = 72.8%) while there was no significant difference between sediment stability and pneumatophores density (R2= 47%). Regression analysis between mean sediment accretion rates against all parameters were not significant. This study will help the managers and the government on the merit of using mangroves as bio-shields in protecting coastlines against erosion and stabilizing sediment in the wake of much anticipated global changing climate and sea-level rise.