Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphological and physiological properties of the A17 amacrine cell of the rat retina

In addition to the well-studied AII amacrine cell, there is another amacrine cell type participating in the rod pathway of the mammalian retina. In cat, this cell is called the A17 amacrine cell, and in rabbits, it is called the indoleamine-accumulating amacrine cell (S1 and S2); however, the presence of the corresponding cell type has not yet been described in detail for the rat retina. To this end, we injected amacrine cells with Neurobiotin in vertical retinal slices. After histological processing, we were able to reconstruct the morphology of a wide-field amacrine cell which showed characteristics of A17 and S1/S2 amacrine cells. The rat wide-field amacrine cells exhibited the same stratification pattern, their dendrites bore varicosities and ramified in sublamina 5 of the inner plexiform layer (IPL), and they were dye-coupled to other amacrine cells. To determine whether those amacrine cells shared electrophysiological characteristics as well, we performed whole-cell patch-clamp recordings and examined their voltage-activated currents and neurotransmitter-induced currents. We never observed voltage-gated Na+ currents and spike-like potentials upon depolarization by current injection in these cells. We identified GABA- and glycine-sensitive Cl− currents that could be blocked by bicuculline and strychnine, respectively. We also observed kainate- and AMPA-activated currents, which could be inhibited by the application of 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX). Finally, a 400-ms full-field light stimulus was used to characterize the light responses of A17 amacrine cells. The light ON-induced inward current could be suppressed by the application of 2,3-Dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulphonamide (NBQX), while the majority of the light OFF-induced current was inhibited by bicuculline and reduced to a smaller extent by NBQX. CPP, an NMDA blocker, had no effect on the light response of rat A17 amacrine cells.
Is the Saudi Stock Market Efficient? A Case of Weak-Form Efficiency

The purpose of the paper is to test the weak-form market efficiency in Saudi Arabia's stock market, Tadawul, which is expected to follow a random walk. All share index and sectoral indices for daily closing prices in Tadawul between October 15, 2006 and November 15, 2012 are collected. The unit root Dickey-Fuller test, Pearson Correlation test, Durbin-Watson test, and Wald-Wolfowitz runs-test are used as basic stochastic tests for a non-stationarity of the daily prices for all the listed companies in the market, both overall and sector-wise. The four tests confirmed the weak-form market efficiency in the Saudi stock market for all share prices and eleven individual sectors. The findings are necessary for all investors in Saudi Arabia and the member states of the Gulf Cooperation Council (GCC). Listed firms could also benefit from the findings by seeing the true picture of their stock price. The finding is used as a basis for testing the market efficiency in the semi-strong form, which has not yet been tested by any researcher. Accordingly, investors in the Saudi market are not expected to generate abnormal returns simply by depending on past information and technical analysis. This paper will add value to the literature of market efficiency in the emerging market and the GCC; since it covers all the listed companies, tests sector-wise, and covers an extended period of time. To confirm the weak-form efficiency in Saudi, the study uses four tests and covers a long period of time during and after the financial crisis.
Pulmonary extraction of [3H]bupivacaine: modification by dose, propranolol and interaction with [14C]5-hydroxytryptamine.

The authors studied the single-pass pulmonary extraction of the potent local anesthetic, bupivacaine, in 21 anesthetized rabbits. Pulmonary extraction of [3H]bupivacaine and [14C]5-hydroxytryptamine (5-HT) was quantified from multiple indicator-dilution outflow curves using indocyanine green as the intravascular reference substance. Pulmonary extraction at control (n = 15; mean +/- S.D.) was 81 +/- 6 and 78 +/- 9% for [3H]bupivacaine and [14C]5-HT, respectively. The apparent volume of distribution of bupivacaine was 38 +/- 9 ml/kg compared with 12 +/- 4 ml/kg for indocyanine green. Simultaneous administration of up to 300 micrograms/kg of bupivacaine did not affect the disposition of either radiolabeled amine; however, injection of 1000 micrograms/kg of bupivacaine significantly (P less than .01) depressed pulmonary extraction of both [3H]bupivacaine and [14C]5-HT. In the presence of 1000 micrograms/kg bupivacaine, the apparent volume of distribution of [3H]bupivacaine decreased to 24 +/- 9 ml/kg (P less than .01). Fifteen minutes after administration of propranolol (100-250 micrograms/kg i.v.), [14C]5-HT removal was unchanged, but the pulmonary extraction of [3H]bupivacaine was significantly decreased to 70 +/- 12% (n = 6; P less than .01). These data suggest that bupivacaine is extensively removed as it enters the lung and that the removal process is a combination of passive diffusion and a small component of saturable specific binding. The interaction of bupivacaine with 5-HT may be part of this specific binding (i.e., endothelial cell uptake) or may have been secondary to direct effects of large concentrations of bupivacaine on membrane function. (ABSTRACT TRUNCATED AT 250 WORDS)
Exchange of genetic information between therian X and Y chromosome gametologs in old evolutionary strata

Abstract Therian X and Y sex chromosomes arose from a pair of autosomes. Y chromosomes consist of a pseudoautosomal region that crosses over with the X chromosome and a male‐specific Y‐chromosomal region that does not. The X chromosome can be structured into “evolutionary strata”. Divergence of X‐chromosomal genes from their gametologs is similar within a stratum, but differs among strata, likely caused by a different onset of suppression of crossing over between gametologs. After stratum formation, exchange of information between gametologs has long been believed absent; however, recent studies have shown limited exchange, likely through gene conversion. Herein we investigate exchange of genetic information between gametologs in old strata that formed before the split of Laurasiatheria (cattle) from Euarchontoglires (primates and rodents) with a new phylogenetic approach. A prerequisite for our test is an overall preradiative topology, that is, all X‐chromosomal gametologs are more similar among themselves than to Y‐chromosomal sequences. Screening multiple sequence alignments of the coding sequences of genes from cattle, mice, and humans identified four genes, DDX3X/Y,RBMX/Y,USP9X/Y, and UTX/Y, exhibiting a preradiation topology. Applying our test, we detected exchange of genetic information between all four X and Y gametologs after stratum formation.
Liver stiffness and portal blood flow modifications induced by a liquid meal consumption: pathogenetic mechanisms and clinical relevance

Abstract Objective. The correlation between liver stiffness (LS) variations and portal blood flow (PBF) modifications induced by a standardized liquid meal consumption and the clinical relevance of this matter are two aspects not yet fully elucidated. Herein, we evaluated the variations of LS and PBF after a standardized liquid meal intake in patients with chronic liver disease. Material and methods. PBF and LS were determined after an overnight fasting period in 54 patients. They were divided in three groups according to baseline LS (absent, moderate, and severe). They consumed 200 ml of water and a standardized liquid meal (300 Kcal/200 ml) after 60 min. PBF and LS were measured at 30 min after water and liquid meal consumption. Results. In all groups, LS and PBF values significantly increased only after meal consumption. A significant correlation between baseline LS values and post-meal increase of LS was observed. Moreover, higher basal stiffness values were associated to a larger increase of LS variation after meal consumption. The effect of the meal on LS remained statistically significant after multiple regression analysis. A significant correlation between increase of LS and PBF was found in patients with absent and moderate baseline LS. Nine patients (17%) switched from a lower to a higher level of LS after meal consumption. Conclusion. A low calories/low-volume meal is capable of significantly increasing LS regardless of the grade of stiffness, determining a reclassification rate of 17%. In presence of minimal or moderate stiffness, the increase of LS is significantly correlated with the augment of PBF.
Optimal bidding strategy for PHEV fleet aggregators - A bilevel model

The shortage of fossil fuels and climate change has urged humans to find new ways of transportation. A solution to this problem could be to start using plug-in hybrid vehicles(PHEV). However, this type of vehicles need to be charged in an organized way to minimize the impact on an already strained electric system. So-called aggregators could have the task to manage vehicle charging centrally, moving it to low load periods. In this thesis a bi-level model is created, which finds the optimal bidding strategy for the PHEV fleet aggregator. The upper level problem is the aggregator’s cost minimization problem, who places bids in a day-ahead market pool for the next 24 hour period. The lower level problem is the market pool, implemented as an Optimal Power Flow, which returns nodal prices for the bids on an hourly basis. By using different mathematical approaches, this problem is turned into a mathematical problem with equality constraints(MPEC). However, the MPEC model was found not to be able to solve large systems. Therefore, the bi-level problem was also implemented as an embedded model. The models were finally tested in case studies with four networks systems of different size and on a full scale model of the swiss power system. It was found that the MPEC was faster at solving the problem and also in some cases it found better solutions than the embedded models. When comparing the minimum charging cost models with a system cost minimization approach, it was found in a specific case that the charging cost was lower with the charging cost models. The reason were the existing congestions in the network. The full scale Swiss model could only be tested with the embedded model, showing results almost identical to the system cost minimization model. However, strategic behavior cannot be ruled out even if the optimization is not able to find it.
Mutagenesis and Beyond! Tools for Understanding Legume Biology1

The family Leguminosae is one of the largest families of flowering plants and includes important crop legumes such as soybean ( Glycine max ) and lentil ( Lens culinaris ) and forage legumes like alfalfa ( Medicago sativa ). Legumes vary in habit from annual to perennial and in their genomes from
On the Reproducibility of Line Integral Convolution for Real-Time Illustration of Molecular Surface Shape and Salient Regions

In this paper, we discuss the reproducibility of our work presented at EuroVis 2014 [LKEP14], which describes an illustrative rendering method tailored to molecular surfaces. We distinguish between the reproducibility of the data sets that were used for figures and performance analysis and the reproducibility in the sense of re-implementing the method. For the latter, we focus on each step of the algorithm and discuss the implementation challenges. We give further details and explain the most difficult parts. Additionally, we discuss how the models that were used can be recreated and the availability of the underlying data. Finally, we discuss the current state of reproducibility of our method and reflect on the problem of offering the source code of a research project in general. The definitive version is available at http://diglib.eg. org/.
Universal behaviour in the mechanical properties of weakly aggregated colloidal particles

We study the evolution of the elastic shear modulus of weakly aggregated colloidal particles during the onset of a delayed collapse under gravity. The early lifetime is characterised by an elastic shear modulus that increases logarithmically in time, following which the gels experience a catastrophic failure and the elastic modulus drops dramatically. As the gel collapses, various complex behaviours are seen, including a temporary stabilisation against collapse, and reformation of a new gel with its own elastic modulus that follows its own trajectory to collapse. Time-lapsed images acquired of identical samples in a transparent cell used to calibrate the measured shear modulus values allow observation of the sample-spanning collective rearrangement involved in the collapse. The loss of propagation of elastic stress in the gel is observed to precede the bulk collapse in all samples, with the two events always well-separated in time. The evolution of the viscoelastic response across a range of colloid volume fractions and polymer concentrations is significantly simplified by scaling the rheology curves for each sample together. From the scaling, we show a critical onset of the elastic modulus as a function of these system parameters. Moreover, our analyses of the time scale for collapse of the elastic shear modulus and of the gel itself over a range of colloid volume fractions and the polymer concentrations support a simple phenomenological model based on the dependence of the microscopic dynamics on the strength and number of sticky interparticle bonds.
The Evolution of an Electronic Trading Community: The Case of the Electrical and Electronics Industry of Southeast Asia

We examine the evolution of an electronic trading community over the Internet on the basis of the case study of two B2B (business-to-business) exchange operators for direct materials in the electrical and electronics industry of Southeast Asia. We identify three distinguishable stages in the transformation of the third party electronic trading community. We also observe that there are two types of online trading community formation at different stages of the third party community evolution: Buyer-driven community formation and supplier-driven community formation. In the end, however, some buyers left the third party community to build their own private electronic trading communities by developing their own in-house systems. In this study, we explain the evolution of the third party community and propose a framework of buyers' community movement. The buyer's decision whether to move to the private community or to remain in the third party community should be made based on what the company expects from the B2B exchange system.
A study of expected and perceived service quality in Croatian and Slovenian hotel industry

The main purpose of present research is the comparison of guests’ expectations and perceptions of service quality in Croatian and Slovenian hotels. In order to measure hotel guests’ expectations and perceptions modified SERVQUAL model was developed. The questionnaire was designed in accordance with researches conducted by Parasuraman et al. (1988), Zeithaml et al. (1990), Snoj and Ogorelc (1998), Pizam and Ellis (1999) and Marković (2003). The questionnaire was divided in three parts: measurement of expected service quality, measurement of perceived service quality and demographic questions. Data were collected in hotel settings in Opatija Riviera (Croatia) and Slovenia’s coastal region. A total of 253 (Croatian sample) and 172 (Slovenian sample) completed and usable questionnaires were gathered. Data were analyzed using descriptive statistics, independent samples t-test, exploratory factor analysis and reliability analysis. The conducted statistical analysis revealed similarities in both surveys. The research results identified high level of guests’ expectations and perceptions regarding the hotel service quality, and importance of intangible aspects of hotel service. A study of expected and perceived service quality in Croatian and Slovenian hotel industry. European Journal of Tourism Research 6(1), 36-52.
LDC Arabic Treebanks and Associated Corpora: Data Divisions Manual

The Linguistic Data Consortium (LDC) has developed hundreds of data corpora for natural language processing (NLP) research. Among these are a number of annotated treebank corpora for Arabic. Typically, these corpora consist of a single collection of annotated documents. NLP research, however, usually requires multiple data sets for the purposes of training models, developing techniques, and final evaluation. Therefore it becomes necessary to divide the corpora used into the required data sets (divisions). This document details a set of rules that have been defined to enable consistent divisions for old and new Arabic treebanks (ATB) and related corpora.
Identification of functionally variant MDR1 alleles among European Americans and African Americans

MDR1 (P‐glycoprotein) is an important factor in the disposition of many drugs, and the involved processes often exhibit considerable interindividual variability that may be genetically determined. Single‐strand conformational polymorphism analysis and direct sequencing of exonic MDR1 deoxyribonucleic acid from 37 healthy European American and 23 healthy African American subjects identified 10 single nucleotide polymorphisms (SNPs), including 6 nonsynonymous variants, occurring in various allelic combinations. Population frequencies of the 15 identified alleles varied according to racial background. Two synonymous SNPs (C1236T in exon 12 and C3435T in exon 26) and a nonsynonymous SNP (G2677T, Ala893Ser) in exon 21 were found to be linked (MDR1ast;2) and occurred in 62% of European Americans and 13% of African Americans. In vitro expression of MDR1 encoding Ala893 (MDR1ast;1) or a site‐directed Ser893 mutation (MDR1ast;2) indicated enhanced efflux of digoxin by cells expressing the MDR1‐Ser893 variant. In vivo functional relevance of this SNP was assessed with the known P‐glycoprotein drug substrate fexofenadine as a probe of the transporter's activity. In humans, MDR1ast;1 and MDR1ast;2 variants were associated with differences in fexofenadine levels, consistent with the in vitro data, with the area under the plasma level–time curve being almost 40% greater in the *1/*1 genotype compared with the *2/*2 and the *1/*2 heterozygotes having an intermediate value, suggesting enhanced in vivo P‐glycoprotein activity among subjects with the MDR1ast;2 allele. Thus allelic variation in MDR1 is more common than previously recognized and involves multiple SNPs whose allelic frequencies vary between populations, and some of these SNPs are associated with altered P‐glycoprotein function.
A Lithium-induced Conformational Change in Serotonin Transporter Alters Cocaine Binding, Ion Conductance, and Reactivity of Cys-109*

Inactivation of serotonin transporter (SERT) expressed in HeLa cells by [2-(trimethylammonium)ethyl]methanethiosulfonate (MTSET) occurred much more readily when Na+ in the reaction medium was replaced with Li+. This did not result from a protective effect of Na+ but rather from a Li+-specific increase in the reactivity of Cys-109 in the first external loop of the transporter. Li+ alone of the alkali cations caused this increase in reactivity. Replacing Na+ withN-methyl-d-glucamine (NMDG+) did not reduce the affinity of cocaine for SERT, as measured by displacement of a high affinity cocaine analog, but replacement of Na+ with Li+ led to a 2-fold increase in theK D for cocaine. The addition of either cocaine or serotonin (5-HT) protected SERT against MTSET inactivation. When SERT was expressed in Xenopus oocytes, inward currents were elicited by superfusing the cell with 5-HT (in the presence of Na+) or by replacing Na+ with Li+but not NMDG+. MTSET treatment of oocytes in Li+ but not in Na+ decreased both 5-HT and Li+ induced currents, although 5-HT-induced currents were inhibited to a greater extent. Na+ antagonized the effects of Li+ on both inactivation and current. These results are consistent with Li+ inducing a conformational change that exposes Cys-109, decreases cocaine affinity, and increases the uncoupled inward current.
Ordering scalar products with applications in financial engineering and actuarial science

Abstract In this paper we build the increasing convex (concave) order for the scalar product of random vectors with an upper (lower) tail permutation decreasing joint density. As applications, we revisit allocations of portfolio risks in financial engineering and of coverage limits and deductibles in insurance. Some related results in the literature are substantially updated.
Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Background: ER-localized mRNAs are anchored to the ER via their functional engagement with translocon-bound ribosomes. Results: Ribosome-engaged mRNAs are ER-bound through distinct and mRNA-selective mechanisms. Conclusion: Multiple ER membrane proteins, including the Sec61 complex, display RNA binding activity and anchor select mRNAs to the ER. Significance: These data reveal new functions for the translocation machinery and advance understanding of RNA localization to the ER. Signal sequence-encoding mRNAs undergo translation-dependent localization to the endoplasmic reticulum (ER) and at the ER are anchored via translation on Sec61-bound ribosomes. Recent investigations into the composition and membrane association characteristics of ER-associated mRNAs have, however, revealed both ribosome-dependent (indirect) and ribosome-independent (direct) modes of mRNA association with the ER. These findings raise important questions regarding our understanding of how mRNAs are selected, localized, and anchored to the ER. Using semi-intact tissue culture cells, we performed a polysome solubilization screen and identified conditions that distinguish polysomes engaged in the translation of distinct cohorts of mRNAs. To gain insight into the molecular basis of direct mRNA anchoring to the ER, we performed RNA-protein UV photocross-linking studies in rough microsomes and demonstrate that numerous ER integral membrane proteins display RNA binding activity. Quantitative proteomic analyses of HeLa cytosolic and ER-bound polysome fractions identified translocon components as selective polysome-interacting proteins. Notably, the Sec61 complex was highly enriched in polysomes engaged in the translation of endomembrane organelle proteins, whereas translocon accessory proteins, such as ribophorin I, were present in all subpopulations of ER-associated polysomes. Analyses of the protein composition of oligo(dT)-selected UV photocross-linked ER protein-RNA adducts identified Sec61α,β and ribophorin I as ER-poly(A) mRNA-binding proteins, suggesting unexpected roles for the protein translocation and modification machinery in mRNA anchoring to the ER. In summary, we propose that multiple mechanisms of mRNA and ribosome association with ER operate to enable an mRNA transcriptome-wide function for the ER in protein synthesis.