Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples

Summary We consider the problem of identifying differentially expressed genes under different conditions using gene expression microarrays. Because of the many steps involved in the experimental process, from hybridization to image analysis, cDNA microarray data often contain outliers. For example, an outlying data value could occur because of scratches or dust on the surface, imperfections in the glass, or imperfections in the array production. We develop a robust Bayesian hierarchical model for testing for differential expression. Errors are modeled explicitly using a t‐distribution, which accounts for outliers. The model includes an exchangeable prior for the variances, which allows different variances for the genes but still shrinks extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and it can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. The method is illustrated using two publicly available gene expression data sets. We compare our method to six other baseline and commonly used techniques, namely the t‐test, the Bonferroni‐adjusted t‐test, significance analysis of microarrays (SAM), Efron's empirical Bayes, and EBarrays in both its lognormal–normal and gamma–gamma forms. In an experiment with HIV data, our method performed better than these alternatives, on the basis of between‐replicate agreement and disagreement.
Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor

The epidermal growth factor receptor (EGFR) plays a key role in regulating cell proliferation, migration, and differentiation, and aberrant EGFR signaling is implicated in a variety of cancers. EGFR signaling is triggered by extracellular ligand binding, which promotes EGFR dimerization and activation. Ligand-binding measurements are consistent with a negatively cooperative model in which the ligand-binding affinity at either binding site in an EGFR dimer is weaker when the other site is occupied by a ligand. This cooperativity is widely believed to be central to the effects of ligand concentration on EGFR-mediated intracellular signaling. Although the extracellular portion of the human EGFR dimer has been resolved crystallographically, the crystal structures do not reveal the structural origin of this negative cooperativity, which has remained unclear. Here we report the results of molecular dynamics simulations suggesting that asymmetrical interactions of the two binding sites with the membrane may be responsible (perhaps along with other factors) for this negative cooperativity. In particular, in our simulations the extracellular domains of an EGFR dimer spontaneously lay down on the membrane in an orientation in which favorable membrane contacts were made with one of the bound ligands, but could not be made with the other. Similar interactions were observed when EGFR was glycosylated, as it is in vivo.
Implications of China's future bride shortage for the geographical distribution and social protection needs of never-married men

Because sex ratios at birth have risen sharply in China in recent decades, an increasing proportion of men will be unable to find a bride, and will face old age without the support of a wife and children. We project the proportions of never-married men and their geographical distribution in China in the coming decades. Our projections assume that two tendencies in current marriage patterns will persist: that women will continue to migrate to wealthier areas and to prefer men with better prospects. We find that, by 2030, more than 20 per cent of men in China aged 30–39 will never have married, and that the proportion will be especially high among poor men in low-income provinces that are least able to provide social protection programmes. The projected geographic concentration of bachelors could be socially disruptive, and the results suggest a need to expand the coverage and central financing of social protection programmes.
Specific Targeting of a Plasmodesmal Protein Affecting Cell-to-Cell Communication

Plasmodesmata provide the cytoplasmic conduits for cell-to-cell communication throughout plant tissues and participate in a diverse set of non–cell-autonomous functions. Despite their central role in growth and development and defence, resolving their modus operandi remains a major challenge in plant biology. Features of protein sequences and/or structure that determine protein targeting to plasmodesmata were previously unknown. We identify here a novel family of plasmodesmata-located proteins (called PDLP1) whose members have the features of type I membrane receptor-like proteins. We focus our studies on the first identified type member (namely At5g43980, or PDLP1a) and show that, following its altered expression, it is effective in modulating cell-to-cell trafficking. PDLP1a is targeted to plasmodesmata via the secretory pathway in a Brefeldin A–sensitive and COPII-dependent manner, and resides at plasmodesmata with its C-terminus in the cytoplasmic domain and its N-terminus in the apoplast. Using a deletion analysis, we show that the single transmembrane domain (TMD) of PDLP1a contains all the information necessary for intracellular targeting of this type I membrane protein to plasmodesmata, such that the TMD can be used to target heterologous proteins to this location. These studies identify a new family of plasmodesmal proteins that affect cell-to-cell communication. They exhibit a mode of intracellular trafficking and targeting novel for plant biology and provide technological opportunities for targeting different proteins to plasmodesmata to aid in plasmodesmal characterisation.
Experimentation Cooperative Learning Student Team Achievement Division (STAD) Type Viewed From Learning Motivation

Need a way for students to love math, learning models have only focused upon the teacher to make students passive in understanding mathematics. Student Team Achievement Division (STAD) cooperative learning model is expected to provide better learning outcomes. This study is a quasi-experimental study. The study population was all students of class VIII SMP in Surakarta. Sampling was a stratified cluster random sampling. Sample size for this study was 186 students. Data collection method used is the method of documentation, questionnaire method, and the method of testing. There is a preliminary test with the balance test using the t test, and as a prerequisite t test is the test of normality with Lilliefor's test, and the test of homogeneity with Bartlett's test. Techniques of data analysis in this study using two-way Analysis of Variance with unequal cells, a prerequisite analysis using Lilliefor's test for normality test, homogeneity using Bartlett's test, with a significance level (α) = 5%. The result of Student Team Achievement Division (STAD) models provides better learning outcomes than conventional learning models on motivation high, medium or low.
Subacute Inhalation Exposure of Rats to 1,6-Hexamethylene Diisocyanate With Recovery Period

In this subacute inhalation toxicity study of 1,6-hexamethylene diisocyanate (HDI), groups of 10 male and 10 female Sprague-Dawley rats were exposed to 0, 0.005, 0.0175, or 0.150 ppm HDI vapor, 5 h/ /day, 5 days/ /wk for 15 exposure days and included animals sacrificed 2 wk postexposure. The purpose was to characterize the HDI-induced effects and their reversibility, and to determine a no-observed-adverse-effect level (NOAEL). No compound-related effects were found for body weights, clinical chemistry, urinalysis, hematology, and organ weights. Thus, no evidence of systemic toxicity was found in this study. The exposure-related findings were restricted to the portal of entry, the respiratory tract. Transient signs of sensory irritation were observed after the daily exposure periods, but the principal findings were the histopathologic changes of the nasal epithelium. Generally, an anterior to posterior gradient of incidence and severity was found, and the changes were characterized as acanthosis, erosion, hyperkeratosis, epithelial cell hyperplasia, chronic active inflammation, squamous metaplasia, ulceration, transitional epithelial cell degeneration, goblet-cell hyperplasia, and degeneration of the olfactory epithelium. Varying degrees of concordance between exposure concentration and incidence and/or severity of the histopathologic changes were found. During a 2-wk recovery period, a tendency toward recovery was evident for tissue changes in the nasal cavity. A NOAEL of 0.0175 ppm HDI was determined.
Non-linear intramolecular interactions and voltage sensitivity of a KV1 family potassium channel from Polyorchis penicillatus (Eschscholtz 1829)

SUMMARY Voltage sensitivity of voltage-gated potassium channels (VKCs) is a primary factor in shaping action potentials in excitable cells. Variation in the amino acid sequence of the channel proteins is responsible for differences in the voltage range over which the channel opens. Thus, understanding how changes in voltage sensitivity are effected by changes in channel protein sequence illuminates the functional evolution of excitability. The KV1-family channel jShak1, from the jellyfish Polyorchis penicillatus, differs from most other KV1 channels in ways that are useful for studying the problem of how voltage sensitivity is related to channel sequence. We assessed the contributions of changes in sequence of the S4, voltage sensing, helix and changes in one asparagine residue in the S2 helix, to the relative stability of the open and closed states of the channel. Mutation of the neutral S2 residue (Asn227) to glutamate stabilized the open conformation of the channel. Different modifications of charge and length in S4 favoured either the closed conformation or the open conformation. The interactions between pairs of mutations revealed that some of the S4 mutations alter the conformation of the voltage-sensing domain such that the S4 helix is constrained to be closer to the S2 helix than in the wild-type conformation. These results, taken in conjunction with three-dimensional models of the channel, identify intra-molecular interactions that control the balance between open and closed states. These interactions are likely to be relevant to understanding the functional characteristics of members of this channel family from other organisms.
Color stability of glazed and polished dental porcelains.

PURPOSE The purpose of this study was to compare the visual and colorimetric color stability of two ultra low-fusing and three conventional low-fusing porcelains on both glazed and polished surfaces. MATERIALS AND METHODS Twelve disks, 10 mm in diameter and 3 mm in thickness, were fabricated for each porcelain. Specimens were glazed using their specific glaze materials. For each type of porcelain, the specimens were divided into two groups: one group was immersed in methylene blue and the other group in distilled water as a control. The surfaces were visually examined for staining without magnification. Objective color measurement was performed for each sample using a Tristimulus colorimeter. After examining the color of the glazed specimens, glazed layers were removed from the surface of the specimens to simulate an intraoral environment. Then, porcelain polishing points and diamond polishing paste were applied. The samples were immersed again in methylene blue and distilled water, and after removing from the staining solution and distilled water, visual and objective measurements were performed again. RESULTS Visually discernible stain was present on the polished groups of all five porcelains immersed in methylene blue, whereas the glazed group immersed in methylene blue showed no staining. No staining was observed with glazed and polished samples immersed in distilled water. The objective evaluation showed that the polished porcelain surface of all five porcelain products had statistically significant color deviation than the glazed surface in the same group after immersion in methylene blue. The results of this study show a statistically significant difference in color stability between the polished and glazed specimens. CONCLUSION It may be concluded that the glazed specimens showed a better color stability, although the staining observed in the polished specimens was not clinically noticeable.
Mutational Analysis of the Disulfide Catalysts DsbA and DsbB

ABSTRACT In prokaryotes, disulfides are generated by the DsbA-DsbB system. DsbB functions to generate disulfides by quinone reduction. These disulfides are passed to the DsbA protein and then to folding proteins. To investigate the DsbA-DsbB catalytic system, we performed an in vivo selection for chromosomal dsbA and dsbB mutants. We rediscovered many residues previously shown to be important for the activity of these proteins. In addition, we obtained one novel DsbA mutant (M153R) and four novel DsbB mutants (L43P, H91Y, R133C, and L146R). We also mutated residues that are highly conserved within the DsbB family in an effort to identify residues important for DsbB function. We found classes of mutants that specifically affect the apparent Km of DsbB for either DsbA or quinones, suggesting that quinone and DsbA may interact with different regions of the DsbB protein. Our results are consistent with the interpretation that the residues Q33 and Y46 of DsbB interact with DsbA, Q95 and R48 interact with quinones, and that residue M153 of DsbA interacts with DsbB. All of these interactions could be due to direct amino acid interactions or could be indirect through, for instance, their effect on protein structure. In addition, we find that the DsbB H91Y mutant severely affects the kcat of the reaction between DsbA and DsbB and that the DsbB L43P mutant is inactive, suggesting that both L43 and H91 are important for the activity of DsbB. These experiments help to better define the residues important for the function of these two protein-folding catalysts.
A comparative evaluation of 3D keypoint detectors in a RGB-D Object Dataset

When processing 3D point cloud data, features must be extracted from a small set of points, usually called keypoints. This is done to avoid the computational complexity required to extract features from all points in a point cloud. There are many keypoint detectors and this suggests the need of a comparative evaluation. When the keypoint detectors are applied to 3D objects, the aim is to detect a few salient structures which can be used, instead of the whole object, for applications like object registration, retrieval and data simplification. In this paper, we propose to do a description and evaluation of existing keypoint detectors in a public available point cloud library with real objects and perform a comparative evaluation on 3D point clouds. We evaluate the invariance of the 3D keypoint detectors according to rotations, scale changes and translations. The evaluation criteria used are the absolute and the relative repeatability rate. Using these criteria, we evaluate the robustness of the detectors with respect to changes of point-of-view. In our experiments, the method that achieved better repeatability rate was the ISS3D method.
User Acceptance of Information Technology: Theories and Models

Cet article traite de l'acceptation des utilisateurs des technologies de l'information mais aussi de la resistance de certains utilisateurs pour la conception et l'implementation des technologies de l'information. Apres une definition de la notion de l'acceptation par l'utilisateur, plusieurs approches theoriques sont examinees : la theorie de la diffusion innovation, la comprehension de la psychologie de l'acceptation de l'utilisateur, la conception de la technologie acceptable et les interactions homme-machine
Recombination in IS26 and Tn2 in the Evolution of Multiresistance Regions Carrying blaCTX-M-15 on Conjugative IncF Plasmids from Escherichia coli

ABSTRACT CTX-M-15 now appears to be the dominant extended-spectrum β-lactamase worldwide, and a number of different factors may contribute to this success. These include associations between blaCTX-M-15 and particular plasmids (IncF) and/or strains, such as Escherichia coli ST131, as well as the genetic contexts in which this gene is found. We previously identified blaCTX-M-15 as the dominant ESBL gene in the western Sydney area, Australia, and found that it was carried mainly on IncF or IncI1 plasmids. Here, we have mapped the multiresistance regions of the 11 conjugative plasmids with one or more IncF replicons obtained from that survey and conducted a limited comparison of plasmid backbones. Two plasmids with only an IncFII replicon appear to be very similar to the published plasmids pC15-1a and pEK516. The remaining nine plasmids, with multiple IncF replicons, have multiresistance regions related to those of pC15-1a and pEK516, but eight contain additional modules previously found in resistance plasmids from different geographic locations that carry a variety of different resistance genes. Differences between the multiresistance regions are largely due to IS26-mediated deletions, insertions, and/or rearrangements, which can explain the observed variable associations between blaCTX-M-15 and certain other resistance genes. We found no evidence of independent movement of blaCTX-M-15 or of a large multiresistance region between different plasmid backbones. Instead, homologous recombination between common components, such as IS26 and Tn2, appeared to be more important in creating new multiresistance regions, and this may be coupled with recombination in plasmid backbones to reassort multiple IncF replicons as well as components of multiresistance regions.
High-Affinity Interaction of Sartans with H+/Peptide Transporters

Sartans are very effective drugs for treatment of hypertension, heart failure, and other cardiovascular disorders. They antagonize the effects of angiotensin II at the AT1 receptor and display p.o. bioavailability rates of 13 to 80%. Because some sartans sterically resemble dipeptide derivatives, we investigated whether they are transported by peptide transporters. We first assessed the effects of sartans on [14C]glycylsarcosine uptake into Caco-2 cells expressing H+/peptide transporter (PEPT) 1 and into SKPT cells expressing PEPT2. Losartan, irbesartan, valsartan, and eprosartan inhibited [glycine-1-14C]glycylsarcosine ([14C]Gly-Sar) uptake into Caco-2 cells in a competitive manner with Ki values of 24, 230, 390, and >1000 μM. Losartan and valsartan also strongly inhibited the total transepithelial flux of [14C]Gly-Sar across Caco-2 cell monolayers. In SKPT cells, [14C]Gly-Sar uptake was inhibited with Ki values of 2.2 μM (losartan), 65 μM (irbesartan), 260 μM (valsartan), and 490 μM (eprosartan). We determined by the two-electrode voltage-clamp technique whether the compounds elicited transport currents by PEPT1 or PEPT2 when expressed in Xenopus laevis oocytes. No currents were observed for any of the sartans, but the compounds strongly and reversibly inhibited peptide-induced currents. Uptake of valsartan, losartan, and cefadroxil was quantified in HeLa cells after heterologous expression of human PEPT1 (hPEPT1). In contrast to cefadroxil, no PEPT1-specific uptake of valsartan and losartan was found. We conclude that the sartans tested in this study display high-affinity interaction with PEPTs but are not transported themselves. However, they strongly inhibit hPEPT1-mediated uptake of dipeptides and cefadroxil.
The large tumor antigen of simian virus 40 encodes at least two distinct transforming functions

The large tumor antigen (T antigen) of simian virus 40 is necessary and sufficient for the neoplastic transformation of a number of established cell lines. Mutational analysis has revealed that a biochemical activity residing within the amino-terminal 121 amino acids of T antigen is sufficient to induce the transformation of some cell lines, such as C3H10T1/2. The same domain of the molecule also encodes the transactivation function of T antigen and the ability to complex with the retinoblastoma susceptibility gene product. However, the transformation of other lines, such as REF52, requires an additional activity that is affected by mutations in other portions of the molecule.
Administrative law

This review of developments in New Zealand administrative law covers the period from mid 2016 to mid 2019. The developments I have selected for discussion concern Bill of Rights methodology; heightened scrutiny reasonableness review; substantive legitimate expectations; a duty of consistency; privative clauses; and justiciability. A few further developments are noted in brief at the end.
The dopamine D4 receptor.

The observation that receptors which mediate their signals through heterotrimeric guanosine triphosphate (GTP)-binding proteins (Gproteins) share a considerable amount of sequence similarity has resulted in the rapid molecular characterization of this receptor superfamily. Moreover, it became clear that several receptor families consisted of more receptor subtypes than originally anticipated from pharmacological studies. The dopamine (DA) receptor family, which was originally thought to comprise two receptor types (D1 and D2), includes to date five different DA receptor genes (Bunzow et al. 1988; Dearry et al. 1990; Sokoloff et al. 1990; Sunahara et al. 1990, 1991; Tiberi et al. 1991; Van Tol et al. 1991; Zhou et al. 1990). The major difference between the D1-like receptors D1 and D5/D1B lies in their distribution, but pharmacologically and functionally these two receptors are almost indistinguishable (Sunahara et al. 1991; Tiberi et al. 1991). The D2-like receptor family includes two alternatively spliced forms of the D2 receptor (Dal Toso et al. 1989; Giros et al. 1989; Grandy et al. 1989; Monsma et al. 1989), and the D3 (Sokoloff et al. 1990) and D4 (Van Tol et al. 1991) receptors. Apart from clear differences in distribution profiles, the D2-like receptors also display pharmacological differences. The cloned D2 receptor is able to inhibit adenylyl cyclase (Albert et al. 1990), and is also able to activate several other signal transduction pathways (Elsholtz et al. 1991; Kanterman et al. 1991; Vallar et al. 1990). Moreover, the two alternatively spliced forms of the D2 receptor are not identical in their functional activity (Hayes et al. 1992; Montmayeur et al. 1993).
Experimental and theoretical studies of a coupled chemical oscillator: phase death, multistability, and in-phase and out-of-phase entrainment

The oscillatory Belousov-Zhabotinskii reaction with acetylacetone as substrate has been studied in a pair of stirred tank reactors coupled by mass flow. The inputs to the two cells, and hence the uncoupled oscillation frequencies, are slightly different. Depending upon the coupling strength, three types of behavior are observed: in-phase entrainment, out-of-phase entrainment, or phase death (cessation of oscillations and transition to a steady state). For some values of the coupling, more than one of these three states may be stable. The origins of this behavior are discussed in term of the Field-Korijs-Noyes mechanism for the chemistry and the role of the intercell transport. Simulations using two coupled three-variable Oregonator models and a phase plane analysis of those results give good agreement with the experiments and support our mechanistic interpretation of the dynamical behavior.