Miracle-dz/UniFAR-FTUs huggingface dataset:
A neural network model of contours extraction based on orientation selectivity in the primary visual cortex: applications on real images

The capacity of the primary visual cortex (Vl) to extract salient contours from real black-and-white images is studied using a neural network model of information processing in V1. The model includes the input from the lateral geniculate nucleus, arranged according to the preferred orientation through a Gabor function, a feedforward inhibition from inhibitory interneurons and lateral connections (both excitatory and inhibitory) from the other cortical cells (feedback mechanism). Intracortical excitation is arranged according to experimental data, in order to implement the Gestalt proximity and good continuation criteria. Intracortical inhibition realizes a competitive mechanism among neural groups, to eliminate noise. Simulation results, performed on black-and-white images, demonstrate that the network can easily extract salient contours, by suppressing zones of constant luminance and isolated noise, with an acceptable settling time (30-40 ms). The role of intracortical synapses was also analyzed: too excessive extension of intracortical inhibition can suppress small contours, on the other side too reduced intracortical inhibition can cause the appearance of superimposed noise in the image.
Sialylated Oligosaccharide-specific Plant Lectin from Japanese Elderberry (Sambucus sieboldiana) Bark Tissue Has a Homologous Structure to Type II Ribosome-inactivating Proteins, Ricin and Abrin

Bark lectins from the elderberry species belonging to the genus Sambucus have a unique carbohydrate binding specificity for sialylated glycoconjugates containing NeuAc(α2-6)Gal/GalNAc sequence. To elucidate the structure of the elderberry lectin, a cDNA library was constructed from the mRNA isolated from the bark tissue of Japanese elderberry (Sambucus sieboldiana) with gt11 phage and screened with anti-S. sieboldiana agglutinin (SSA) antibody. The nucleotide sequence of a cDNA clone encoding full-length SSA (LecSSA1) showed the presence of an open reading frame with 1902 base pairs, which corresponded to 570 amino acid residues. This open reading frame encoded a signal peptide and a linker region (19 amino acid residues) between the two subunits of SSA, the hydrophobic (A-chain) and hydrophilic (B-chain) subunits. This indicates that SSA is synthesized as a preproprotein and post-translationally cleaved into two mature subunits. Homology searching as well as molecular modeling studies unexpectedly revealed that each subunit of SSA has a highly homologous structure to the galactose-specific lectin subunit and ribosome-inactivating subunit of plant toxic proteins such as ricin and abrin, indicating a close evolutionary relationship between these carbohydrate-binding proteins.
Prostaglandin Levels in Stimulated Macrophages Are Controlled by Phospholipase A2-activating Protein and by Activation of Phospholipase C and D*

Prostaglandins (PG), which are responsible for a large array of biological functions in eukaryotic cells, are produced from arachidonic acid by phospholipases and cyclooxygenase enzymes COX-1 and COX-2. We demonstrated that PG levels in cells were partly controlled by a regulatory protein, phospholipase A2(PLA2)-activating protein (PLAA). Treatment of murine macrophages with lipopolysaccharide, interleukin-1β, and tumor necrosis factor-α increased PLAA levels at early time points (2–30 min), which correlated with an up-regulation in cytosolic PLA2 and PGE2 levels. Both COX-2 and secretory PLA2 were also increased in lipopolysaccharide-stimulated macrophages, however, at later time points of 4–24 h. The role of PLAA in eicosanoid formation in macrophages was confirmed by the use of an antisense plaa oligonucleotide. Within amino acid residues 503–538, PLAA exhibited homology with melittin, and increased PGE2 production was noted in macrophages stimulated with melittin. In addition to PLA2, we demonstrated that activation of phospholipase C and D significantly controlled PGE2 production. Finally, increased antigen levels of PLAA, COX-2, and phospholipases were demonstrated in biopsy specimens from patients with varying amounts of intestinal mucosal inflammation, which corresponded to increased levels of phospholipase activity. These results could provide a basis for the development of new therapeutic tools to control inflammation.
MATRIX METALLOPROTEINASES CORRELATE WITH ALVEOLAR-CAPILLARY PERMEABILITY ALTERATION IN LUNG ISCHEMIA-REPERFUSION INJURY

Background. Matrix metalloproteinases (MMPs) are able to degrade the endothelial basal lamina and increase vascular permeability. Methods. In a porcine model of isolated-reperfused lung, we studied the alveolar-capillary permeability and the zymographic expression of MMP-9 and MMP-2 in the bronchoalveolar lavage fluid of lungs submitted ex vivo to ischemia in three preservation solutions [modified Euro-Collins (EC), low-potassium-dextran, modified-blood]. Twenty-two pigs were randomly divided into three groups according to the preservation solution used. One lung of each pig was rapidly reperfused and analyzed (control lung) although the other lung was reperfused and analyzed after 8 hr of ischemia (ischemic lung). Results. Alveolar-capillary permeability, evaluated by the transferrin leak index, was increased after 8 hr of ischemia compared with controls in the three groups, but was significantly higher in the modified EC group. In the EC group, after 8 hr of ischemia, both proMMP-9 and MMP-9 increased significantly (8.8- and 22-fold, respectively) compared with controls and this increase correlated with the transferrin leak index. Neither proMMP-9 nor MMP-9 increased with the other two preservation solutions. The MMP-2 increase after ischemia was smaller and was also restricted to the EC group. Conclusion. MMP expression is enhanced during lung ischemia-reperfusion, especially in the presence of EC and this phenomenon correlates with the alteration of alveolar-capillary permeability.
Weighted Essential Non-oscillatory Schemes for Simulations of Shallow Water Equations with Transport of Pollutant on Unstructured Meshes

In this paper we study the third-order finite volume weighted essential non-oscillatory (WENO) schemes to solve the two-dimensional shallow water equations with pollutant propagation on unstructured triangle meshes. Balance of the flux and the source terms make the shallow water equations fit to non-flat bottom problems, in order to maintain genuinely high order accuracy and suit to questions with a rapidly varying bottom topography we use WENO reconstruction not only to the flux but also to the source terms of a algebraic modified shallow water problems. Simulations are performed, as a result, the finite volume WENO schemes can maintain non-oscillatory properties and achieve high resolution.
Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis

Heavy metal exposure is a serious environmental stress in plants. However, plants have evolved several strategies to improve their heavy metal tolerance. Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Here, we identified 46 and 55 HMPs in rice and Arabidopsis, respectively, and named them OsHMP 1–46 and AtHMP 1–55 according to their chromosomal locations. The HMPs from both plants were divided into six clades based on the characteristics of their heavy metal-associated domains (HMA). The HMP gene structures and motifs varied greatly among the different classifications. The HMPs had high collinearity and were segmentally duplicated. A cis-element analysis revealed that the HMPs may be regulated by different transcription factors. An expression profile analysis disclosed that only eight OsHMPs were constitutive in rice tissues. Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. For Arabidopsis, nine AtHMPs presented with very high transcript levels in all organs. Most of the selected OsHMPs were differentially expressed in various tissues under different heavy metal stresses. Only OsHMP09, OsHMP18, and OsHMP22 showed higher expression levels in all tissues under different heavy metal stresses. In contrast, most of the selected AtHMPs had nearly constant expression levels in different tissues under various heavy metal stresses. The AtHMP20, AtHMP23, AtHMP25, AtHMP31, AtHMP35, AtHMP46 expression levels under different heavy metal stresses were higher in the leaves and roots. The foregoing discoveries elucidated HMP evolution in monocotyledonous and dicotyledonous plants and may helpful functionally characterize HMPs in the future.
Effects of Alcohol and Cocaine in a Mutant Mouse Model of Predisposition to Post-Traumatic Stress Disorder

Comorbidity between drug abuse and post-traumatic stress disorder (PTSD), a stress-related dysregulation of fear responses, is very high. While some drugs are known to increase fear and anxiety, there are only few data regarding interactions between voluntary drug consumption and fear memory. The spontaneous chronic consumption of either alcohol or cocaine under a 3-week free-choice progressive paradigm of alcohol (3/6/10%) or cocaine (0.2/0.4/0.6 mg/ml), was assessed in VGV transgenic mice, having full 5-HT2C receptor editing and displaying PTSD-like behaviors. The consequences of these drug consumptions on the potentiated contextual and cued fear conditioning responses of VGV mice were assessed. The effects of drugs on hippocampal brain-derived neurotrophic factor (Bdnf) mRNA were measured as its expression was previously found to be decreased in VGV mice. Chronic alcohol consumption was similar in WT and VGV mice. In the alcohol condition, fear acquisition was not different at the end of the learning session and cue-fear extinction was facilitated. Regarding cocaine, in contrast to WT mice, VGV mice did not increase their drug consumption along with increasing doses, an effect that might be related with enhanced drug stimuli discrimination via increased 5-HT2C receptors. Cocaine-intake VGV mice did not display the contextual fear generalization usually observed in control VGV mice. In addition, Bdnf expression was upregulated after either chronic alcohol or cocaine intake. Altogether, these results suggest that both chronic alcohol and cocaine voluntary oral consumptions can exert some therapeutic-like effects in a mutant model of PTSD predisposition.
The presence of prostate cancer at biopsy is predicted by a number of genetic variants

Several single nucleotide polymorphisms (SNPs) have been associated with an elevated risk of prostate cancer risk. It is not established if they are useful in predicting the presence of prostate cancer at biopsy or if they can be used to define a low‐risk group of men. In this study, 4,548 men underwent a prostate biopsy because of an elevated prostate specific antigen (PSA; ≥4 ng/mL) or an abnormal digital rectal examination (DRE). All men were genotyped for 11 selected SNPs. The effect of each SNP, alone and in combination, on prostate cancer prevalence was studied. Of 4,548 men: 1,834 (40.3%) were found to have cancer. A positive association with prostate cancer was seen for 5 of 11 SNPs studied (rs1800629, rs1859962, rs1447295, rs4430796, rs11228565). The cancer detection rate rose with the number of SNP risk alleles from 29% for men with no variant to 63% for men who carried seven or more risk alleles (OR = 4.2; p = 0.002). The SNP data did not improve the predictive power of clinical factors (age, PSA and DRE) for detecting prostate cancer (AUC: 0.726 vs. 0.735; p = 0.4). We were unable to define a group of men with a sufficiently low prevalence of prostate cancer that a biopsy might have been avoided. In conclusion, our data do not support the routine use of SNP polymorphisms as an adjunct test to be used on the context of prostate biopsy for Polish men with an abnormal screening test.
Enterprise Resource Planning (ERP) Upgrade Decision: Toward A Unified View

To date we are still unclear how ERP client-organizations make their ERP upgrade decision. In this research-in-progress, we (1) review literature on issues surrounding ERP upgrade decision-making, (2) formulate and postulate a conceptual model of ERP upgrade decision based on both the empirical research paper and trade press literature, and (3) empirically validate and modify the proposed conceptual model of ERP upgrade decision. To achieve this, multiple interpretative case studies will be conducted. Participant observations, interviews, documentations and archival records will be used in the data collection. Various qualitative methods including pattern-matching technique are used to analyze the cause-effect between various factors (such as business benefits of a new ERP version, new ERP version’s fit with organization’s way of doing business, organization’s cultural norms and political support from top management) and ERP upgrade decision. In addition, symbolic interactionism is used as a theoretical lens to identify the intrinsic symbols attached to an ERP system. Institutional theory and incentive theory are applied to explain how organizational factors and business benefits factors (which are extrinsic in nature) impact on ERP upgrade decision. The expected main contribution from this study is to propose a unified theory that can comprehensively conceptualize and explain how ERP client-organization made their ERP upgrade decision.
Regulation of Glycogen Synthase Activity in Cultured Skeletal Muscle Cells From Subjects With Type II Diabetes: Role of Chronic Hyperinsulinemia and Hyperglycemia

Human skeletal muscle cultures (HSMCs) from type II diabetic subjects were used to determine whether metabolic abnormalities such as hyperglycemia or hyperinsulinemia contribute to the defective muscle glycogen synthase (GS) activity present in this disorder. Following ∼6 weeks of growth, diabetic cultures were fused for 4 days in normal, hyperglycemia, or hyperinsulinemia medium. Fusion of diabetic HSMCs in hyperglycemia medium (20 mmol/l vs. 5.5 mmol/l) had no effect on GS fractional velocity (FV) or mRNA levels, but impaired acute insulin-stimulation of glycogen synthesis and GS activity at 0.1 mmol/l glucoses-phosphate, and reduced GS protein content by ∼15% (P < 0.05). Fusion of diabetic muscle cultures in hyperinsulinemia medium (30 μmol/l vs. 22 pmol/l) improved basal GS activity, increasing the reduced GS FV by ∼50% (P < 0.05), and decreasing the elevated Km0.1 (half-maximal substrate concentration) by ∼47% (P < 0.05). Hyperinsulinemia also significantly increased (P < 0.05) the reduced GS mRNA and protein levels of diabetic muscle to levels similar to that in nondiabetic subjects. In contrast to the improvements in the basal state, hyperinsulinemia completely abolished acute insulin responsiveness of GS activity and glycogen synthesis in muscle of type II diabetic subjects. The combination of hyperinsulinemia and hyperglycemia produced effects on both basal and insulin-responsive GS FV and mRNA similar to hyperinsulinemia alone, but hyperinsulinemia prevented hyperglycemia's effect of lowering GS protein and glycogen synthesis. We concluded that, in diabetic muscle, hyperinsulinemia may serve to partially compensate for the impaired basal GS activity and for the adverse effects of hyperglycemia on GS protein content, activity, and glycogen formation by both pre- and posttranslational mechanisms. Despite these beneficial effects, hyperinsulinemia also induces severe impairment of insulin-stimulated GS activity and glycogen formation, which may contribute to acquired muscle insulin resistance of type II diabetes.
Attentional Processes in Children With Attentional Problems or Reading Difficulties as Revealed Using Brain Event-Related Potentials and Their Source Localization

Visual attention-related processes include three functional sub-processes: alerting, orienting, and inhibition. We examined these sub-processes using reaction times, event-related potentials (ERPs), and their neuronal source activations during the Attention Network Test (ANT) in control children, attentional problems (AP) children, and reading difficulties (RD) children. During the ANT, electroencephalography was measured using 128 electrodes on three groups of Finnish sixth-graders aged 12–13 years (control = 77; AP = 15; RD = 23). Participants were asked to detect the direction of a middle target fish within a group of five fish. The target stimulus was either preceded by a cue (center, double, or spatial), or without a cue, to manipulate the alerting and orienting sub-processes of attention. The direction of the target fish was either congruent or incongruent in relation to the flanker fish, thereby manipulating the inhibition sub-processes of attention. Reaction time performance showed no differences between groups in alerting, orienting, and inhibition effects. The group differences in ERPs were only found at the source level. Neuronal source analysis in the AP children revealed a larger alerting effect (double-cued vs. non-cued target stimuli) than control and RD children in the left occipital lobe. Control children showed a smaller orienting effect (spatially cued vs. center-cued target stimuli) in the left occipital lobe than AP and RD children. No group differences were found for the neuronal sources related to the inhibition effect. The neuronal activity differences related to sub-processes of attention in the AP and RD groups suggest different underlying mechanisms for attentional and reading problems.
Effect of conceptual and lexical errorless versus trial-and-error learning in amnestic mild cognitive impairment

ABSTRACT Errorless learning (EL), involving presenting the target information during encoding, is generally considered effective for teaching information to memory-impaired populations. However, evidence suggests that trial-and-error learning (TEL) can benefit healthy older adults’ memory when guesses are conceptually related to the target. To determine whether TEL can benefit persons with mild cognitive impairment (aMCI), 24 participants with aMCI were given cues associated with nine target words. Half the sample received Conceptual cues (e.g., “beverage”) and the other half received Lexical cues (e.g., SC_______). All underwent an EL study phase, in which the target was presented immediately after the cue, and a TEL phase, in which they made guesses from the cue before the target was presented. Cued recall was tested immediately and 24 h later. At immediate but not 24-h delayed recall, EL targets were better remembered than TEL targets in both conditions. Verbal memory performance appeared to explain why certain individuals benefited more from EL relative to TEL, while semantic memory performance appeared to explain why some people benefited more from conceptual than lexical errors. Thus, EL-based memory intervention for aMCI is likely to be more effective than TEL, particularly to the extent that semantic or episodic memory is affected.
NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA.

Many cellular processes involve the preferential interaction of an RNA molecule with a specific protein. A detailed analysis of the individual protein and RNA components of these interactions can provide unique insights into the structural features important for protein-RNA recognition. Ribosomal protein S8 of Escherichia coli plays a key role in 30 S ribosomal subunit assembly through its interaction with 16 S rRNA. The binding site for protein S8 comprises a portion of helix 21, nucleotides G588 to G604 and C634 to C651. This region forms a base-paired helix that is interrupted by a non-Watson-Crick segment composed of nine phylogenetically conserved nucleotides. We have investigated the detailed structure of the conserved segment and the interaction of this region with metal ions using NMR spectroscopy. Twenty-four of the 40 calculated structures converged to similar conformations and were grouped into two families. The main difference between the families is the orientation of the base of U641. The rms deviation between the heavy-atoms of the ten lowest-energy structures is 1.24 A. The orientations of the G597.C643 base-pair and A595. (A596.U644) base-triple within the conserved core have been defined and appear to extend the proximal segment of helix 21 into the phylogenetically conserved core. The base of A642 terminates this helix by stacking against C643 and the base of U641 forms hydrogen bonds with core nucleotides. The conserved core also contains a Mg2+-binding site that promotes stabilization of the secondary and tertiary structure elements of the core. A model for the interaction of S8 with its RNA-binding site is proposed.
A Review on Grid Integration : Power Quality Issues and Mitigation Techniques

This paper presents a review on power quality problems associated with the integration of renewable energy systems into micro grid and it gives an overview on different power electronic and FACTS devices in mitigation of power quality problems . issues on integration of wind energy and Photo Voltaic (PV) systems are discussed in this paper. Classification of various different Power Quality problems used by different researchers has been done and put for reference. Various techniques applied to mitigate the different Power Quality problems are also presented for consideration.
Quantum Dot-based Microfluidic Immunocytochemistry Using a Parallel-sequential Multiplexing Method

Immunocytochemistry (ICC) has been widely used for the cell study, such as cell to cell interaction, signal pathway and protein translocation. Particularly, multiplexed protein identification is an important issue on ICC field to explain the complicated cell signaling behavior. Conventional quantum dot (QD)-based ICC has been used to satisfy the need for multiplexing biomarkers. QD multiplexing methods are classified into two methods which are the direct method and the indirect method. Although the indirect method is preferred in QD-ICC due to its brightness and flexibility, it has limitations on multiplexing efficiency and the non-specific binding of QD-secondary antibody. In this thesis, we propose a QD parallel-sequential multiplexing method which provides high multiplexing efficiency to QD indirect method. To demonstrate this novel method, a multichannel-microfluidic device was exploited to investigate the result distortion of QD staining data resulted from the sequence dependency of QD multiplexing. With a precise control of fluid flow in the microfluidic device, we successfully showed reduced non-specific binding of QDs comparing to conventional method. We also demonstrated the feasibility of a QD parallel-sequential method with five different primary antibodies and two kinds of QDs. This parallelsequential method could realize the massive multiplexed protein identification with reducing time, reagents, costs and labors. Reduced non-specific binding of QDs with this approach could offer the realization of massive protein quantification on ICC.