Miracle-dz/UniFAR-FTUs huggingface dataset:
Disrupted Bile Acid Homeostasis Reveals an Unexpected Interaction among Nuclear Hormone Receptors, Transporters, and Cytochrome P450*

Sister of P-glycoprotein (SPGP) is the major hepatic bile salt export pump (BSEP). BSEP/SPGP expression varies dramatically among human livers. The potency and hierarchy of bile acids as ligands for the farnesyl/bile acid receptor (FXR/BAR) paralleled their ability to induce BSEP in human hepatocyte cultures. FXR:RXR heterodimers bound to IR1 elements and enhanced bile acid transcriptional activation of the mouse and human BSEP/SPGP promoters. In FXR/BAR nullizygous mice, which have dramatically reduced BSEP/SPGP levels, hepatic CYP3A11 and CYP2B10 were strongly but unexpectedly induced. Notably, the rank order of bile acids as CYP3A4 inducers and activators of pregnane X receptor/steroid and xenobiotic receptor (PXR/SXR) closely paralleled each other but was markedly different from their hierarchy and potency as inducers of BSEP in human hepatocytes. Moreover, the hepatoprotective bile acid ursodeoxycholic acid, which reverses hydrophobic bile acid hepatotoxicity, activates PXR and efficaciously induces CYP3A4 (a bile-metabolizing enzyme) in primary human hepatocytes thus providing one mechanism for its hepatoprotection. Because serum and urinary bile acids increased in FXR/BAR −/− mice, we evaluated hepatic transporters for compensatory changes that might circumvent the profound decrease in BSEP/SPGP. We found weak MRP3 up-regulation. In contrast, MRP4 was substantially increased in the FXR/BAR nullizygous mice and was further elevated by cholic acid. Thus, enhanced hepatocellular concentrations of bile acids, due to the down-regulation of BSEP/SPGP-mediated efflux in FXR nullizygous mice, result in an alternate but apparent compensatory up-regulation of CYP3A, CYP2B, and some ABC transporters that is consistent with activation of PXR/SXR by bile acids.
Proliferation, neurogenesis and regeneration in the non-mammalian vertebrate brain

Post-embryonic neurogenesis is a fundamental feature of the vertebrate brain. However, the level of adult neurogenesis decreases significantly with phylogeny. In the first part of this review, a comparative analysis of adult neurogenesis and its putative roles in vertebrates are discussed. Adult neurogenesis in mammals is restricted to two telencephalic constitutively active zones. On the contrary, non-mammalian vertebrates display a considerable amount of adult neurogenesis in many brain regions. The phylogenetic differences in adult neurogenesis are poorly understood. However, a common feature of vertebrates (fish, amphibians and reptiles) that display a widespread adult neurogenesis is the substantial post-embryonic brain growth in contrast to birds and mammals. It is probable that the adult neurogenesis in fish, frogs and reptiles is related to the coordinated growth of sensory systems and corresponding sensory brain regions. Likewise, neurons are substantially added to the olfactory bulb in smell-oriented mammals in contrast to more visually oriented primates and songbirds, where much fewer neurons are added to the olfactory bulb. The second part of this review focuses on the differences in brain plasticity and regeneration in vertebrates. Interestingly, several recent studies show that neurogenesis is suppressed in the adult mammalian brain. In mammals, neurogenesis can be induced in the constitutively neurogenic brain regions as well as ectopically in response to injury, disease or experimental manipulations. Furthermore, multipotent progenitor cells can be isolated and differentiated in vitro from several otherwise silent regions of the mammalian brain. This indicates that the potential to recruit or generate neurons in non-neurogenic brain areas is not completely lost in mammals. The level of adult neurogenesis in vertebrates correlates with the capacity to regenerate injury, for example fish and amphibians exhibit the most widespread adult neurogenesis and also the greatest capacity to regenerate central nervous system injuries. Studying these phenomena in non-mammalian vertebrates may greatly increase our understanding of the mechanisms underlying regeneration and adult neurogenesis. Understanding mechanisms that regulate endogenous proliferation and neurogenic permissiveness in the adult brain is of great significance in therapeutical approaches for brain injury and disease.
Analysis of the Korean Emergency Department Syndromic Surveillance System: Mass Type Acute Diarrheal Syndrome

OBJECTIVES This study was designed to compare the data from the emergency department syndromic surveillance system of Korea in detection and reporting of acute diarrheal syndrome (mass type) with the data from the Korea Food and Drug Administration. And to offer fundamental materials for making improvements in current surveillance system was our purpose. METHODS A study was conducted by reviewing the number of cases reported as acute diarrheal syndrome (mass type) from the Korean Center for Disease Control and Prevention between June, 2002 and July, 2008. And the data were compared with the number of mass food poisoning cases during the same period, reported from the Korea Food and Drug Administration. The difference between two groups was measured and their transitions were compared. RESULTS The emergency department syndromic surveillance system's reports of the numbers of acute diarrheal syndrome (mass type) cases were different from the transition of mass food poisonings, reported by the Korea Food and Drug Administration. Their reports were not accurate and they could not follow the trends of increase in mass food poisonings since 2002. CONCLUSIONS Current problems in the emergency department syndromic surveillance system in Korea are mostly related to inaccuracies of daily data reporting system. Manual data input by the reporters could play a big role in such inaccuracies. There need to be improvements in the ways of reporting data, such as automated information transport system linking electronic medical record.
How Concentrated Are The Haloes Of Low Surface Brightness Galaxies In The Cold Dark Matter Model

We investigate whether a correlation exists between the concentration (2¸00) and spin (λ) parameters of dark matter haloes forming inCDM N-body simulations. In partic- ular, we focus on haloes with virial masses in the range 10 11 6 Mvir/h −1 M⊙ 6 2×10 12 , characteristic of the hosts of Low Surface Brightness (LSB) and High Surface Bright- ness (HSB) galaxies. Our analysis demonstrates that 2¸00 and λ are anti-correlated. If we assume that a galaxy disk forms in one of these haloes from baryons that approx- imately conserved angular momentum during their dissipation into the rotationally supported disk, then it is possible to estimate the disk's central surface density. For an appropriate choice of mass-to-light ratio, we can place constraints on the central surface brightness of the disk and hence identify the analogues of the host haloes of LSB and HSB galaxies. We find that our LSB galaxy analogues occupy haloes that have lower concentrations than might be expected based on consideration of the Mvir-cvir relation for theCDM cosmology. The distribution of concentrations peaks at 2� 6, in good agreement with observational data, although there are important differences between the shapes of the simulated and observationally inferred distributions. This suggests that LSB galaxies inhabit a biased subsample of the halo population, and that this bias may be an important ingredient for resolving the current debate regarding the structure of LSB galaxy dark matter haloes.
Asymmetric hybridization in Rhododendron agastum: a hybrid taxon comprising mainly F1s in Yunnan, China.

BACKGROUND AND AIMS Rhododendron (Ericaceae) is a large woody genus in which hybridization is thought to play an important role in evolution and speciation, particularly in the Sino-Himalaya region where many interfertile species often occur sympatrically. Rhododendron agastum, a putative hybrid species, occurs in China, western Yunnan Province, in mixed populations with R. irroratum and R. delavayi. METHODS Material of these taxa from two sites 400 km apart (ZhuJianYuan, ZJY and HuaDianBa, HDB) was examined using cpDNA and internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) loci, to test the possibility that R. agastum was in fact a hybrid between two of the other species. Chloroplast trnL-F and trnS-trnG sequences together distinguished R. irroratum, R. delavayi and some material of R. decorum, which is also considered a putative parent of R. agastum. KEY RESULTS All 14 R. agastum plants from the HDB site had the delavayi cpDNA haplotype, whereas at the ZJY site 17 R. agastum plants had this haplotype and four had the R. irroratum haplotype. R. irroratum and R. delavayi are distinguished by five unequivocal point mutations in their ITS sequences; every R. agastum accession had an additive pattern (double peaks) at each of these sites. Data from AFLP loci were acquired for between ten and 21 plants of each taxon from each site, and were analysed using a Bayesian approach implemented by the program NewHybrids. The program confirmed the identity of all accessions of R. delavayi, and all R. irroratum except one, which was probably a backcross. All R. agastum from HDB and 19 of 21 from ZJY were classified as F1 hybrids; the other two could not be assigned a class. CONCLUSIONS Rhododendron agastum represents populations of hybrids between R. irroratum and R. delavayi, which comprise mostly or only F1s, at the two sites examined. The sites differ in that at HDB there was no detected variation in cpDNA type or hybrid class, whereas at ZJY there was variation in both.
Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology.

Like their host cells, many viruses express noncoding RNAs. Despite the technical challenge of ascribing function to noncoding RNAs (ncRNAs), diverse biological roles for virally expressed ncRNAs have been described, including regulation of viral replication, modulation of host gene expression, host immune evasion, cellular survival, and cellular transformation. Insights into conserved interactions between viral ncRNAs and host cell machinery frequently lead to novel findings concerning host cell biology. In this review, we discuss the functions and biogenesis of ncRNAs produced by animal viruses. Specifically, we describe noncanonical pathways of microRNA (miRNA) biogenesis and novel mechanisms used by viruses to manipulate miRNA and messenger RNA stability. We also highlight recent advances in understanding the function of viral long ncRNAs and circular RNAs. Expected final online publication date for the Annual Review of Virology Volume 6 is September 30, 2019. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Functional redundancy among Nanos proteins and a distinct role of Nanos2 during male germ cell development

The mouse Nanos proteins, Nanos2 and Nanos3, are required for germ cell development and share a highly conserved zinc-finger domain. The expression patterns of these factors during development, however, differ from each other. Nanos3 expression in the mouse embryo commences in the primordial germ cells (PGCs) just after their formation, and a loss of this protein results in the germ cell-less phenotype in both sexes. By contrast, Nanos2 expression begins only in male PGCs after their entry into the genital ridge and a loss of this protein results in a male germ cell deficiency, irrespective of the co-expression of Nanos3 in these cells. These results indicate that these two Nanos proteins have distinct functions, which depend on the time and place of their expression. To further elucidate this, we have generated transgenic mouse lines that express Nanos2 under the control of the Oct4ΔPE promoter and examined Nanos2 function in a Nanos3-null genetic background. We find that ectopically produced Nanos2 protein rescues the Nanos3-null defects, because the germ cells fully develop in both sexes in the transgenic mice. This result indicates that Nanos2 can substitute for Nanos3 during early PGC development. By contrast, our current data show that Nanos3 does not rescue the defects in Nanos2-null mice. Our present findings thus indicate that there are redundant functions of the Nanos proteins in early PGC development, but that Nanos2 has a distinct function during male germ cell development in the mouse.
Combining digital watermarks and collusion secure fingerprints for digital images

Digital watermarking is the enabling technology to prove ownership on copyrighted material, detect originators of illegally made copies, monitor the usage of the copyrighted multimedia data, and analyze the spread spectrum of the data over networks and servers. Embedding of unique customer identification as a watermark into data is called fingerprinting to identify illegal copies of documents. Basically, watermarks embedded into multimedia data for enforcing copyrights must uniquely identify the data and must be difficult to remove, even after various media transformation processes. Digital fingerprinting raises the additional problem that we produce different copies for each customer. Attackers can compare several fingerprinted copies to find and destroy the embedded identification string by altering the data in those places where a difference was detected. In our paper we present a technology for combining a collusion-secure fingerprinting scheme based on finite geometries and a watermarking mechanism with special marking points for digital images. The only marking positions the pirates cannot detect are those positions which contain the same letter in all the compared documents, called intersection of different fingerprints. The proposed technology for a maximal number d of pirates, puts enough information in the intersection of up to d fingerprints to uniquely identify all the pirates.
Inhibiting Cell Division in Escherichia coli Has Little If Any Effect on Gene Expression

ABSTRACT DNA microarrays were used to compare gene expression in dividing and nondividing (filamentous) cultures of Escherichia coli. Although cells from these cultures differed profoundly in morphology, their gene expression profiles were nearly identical. These results extend previous evidence that there is no division checkpoint in E. coli, and progression through the cell cycle is not regulated by the transcription of different genes during different parts of the cell cycle.
Concurrent Direct Network Access for Virtual Machine Monitors

This paper presents hardware and software mechanisms to enable concurrent direct network access (CDNA) by operating systems running within a virtual machine monitor. In a conventional virtual machine monitor, each operating system running within a virtual machine must access the network through a software-virtualized network interface. These virtual network interfaces are multiplexed in software onto a physical network interface, incurring significant performance overheads. The CDNA architecture improves networking efficiency and performance by dividing the tasks of traffic multiplexing, interrupt delivery, and memory protection between hardware and software in a novel way. The virtual machine monitor delivers interrupts and provides protection between virtual machines, while the network interface performs multiplexing of the network data. In effect, the CDNA architecture provides the abstraction that each virtual machine is connected directly to its own network interface. Through the use of CDNA, many of the bottlenecks imposed by software multiplexing can be eliminated without sacrificing protection, producing substantial efficiency improvements
RELIABILITY OF THE CROATIAN LONG VERSION OF THE INTERNATIONAL PHYSICAL ACTIVITY QUESTIONNAIRE

Studies have shown satisfactory reliability of different language versions of the International Physical Activity Questionnaire (IPAQ). However, to the best of our knowledge, no previous study reported data on reliability of the Croatian version of IPAQ. Therefore, the aim of this study was to determine test-retest reliability of IPAQ in Croatia. We assessed physical activity levels using the Croatian long version of IPAQ in a random stratified sample of 122 Croatian adults (60.1% female) aged 15 to 65 years and in a random stratified sample of 133 university students (61.1% female) living in student dormitories in Zagreb. IPAQ was administered on two occasions, 3-4 and 1-2 weeks apart, in the general population and university students, respectively. Spearman’s rank correlation coefficients between test and retest data for domain-specific and intensity-specific physical activity levels ranged between . 45 and . 77 in the general population, and between . 49 and . 59 in university students. To conclude, the Croatian long version of IPAQ showed satisfactory reliability for measuring domain-specific and intensity-specific physical activity levels. Nevertheless, a significant amount of unsystematic error in the IPAQ results should always be considered when interpreting the results in relational studies.
Induction of a Mitosis Delay and Cell Lysis by High-Level Secretion of Mouse α-Amylase from Saccharomyces cerevisiae

ABSTRACT Some foreign proteins are produced in yeast in a cell cycle-dependent manner, but the cause of the cell cycle dependency is unknown. In this study, we found that Saccharomyces cerevisiae cells secreting high levels of mouse α-amylase have elongated buds and are delayed in cell cycle completion in mitosis. The delayed cell mitosis suggests that critical events during exit from mitosis might be disturbed. We found that the activities of PP2A (protein phosphatase 2A) and MPF (maturation-promoting factor) were reduced in α-amylase-oversecreting cells and that these cells showed a reduced level of assembly checkpoint protein Cdc55, compared to the accumulation in wild-type cells. MPF inactivation is due to inhibitory phosphorylation on Cdc28, as a cdc28mutant which lacks an inhibitory phosphorylation site on Cdc28 prevents MPF inactivation and prevents the defective bud morphology induced by overproduction of α-amylase. Our data also suggest that high levels of α-amylase may downregulate PPH22,leading to cell lysis. In conclusion, overproduction of heterologous α-amylase in S. cerevisiaeresults in a negative regulation of PP2A, which causes mitotic delay and leads to cell lysis.
Positional information, in bits

Significance In a developing embryo, individual cells need to “know” where they are to do the right thing. How much do they know, and where is this knowledge written down? Here, we show that these questions can be made mathematically precise. In the fruit fly embryo, information about position is thought to be encoded by the concentration of particular protein molecules, and we measure this information, in bits. Just four different kinds of molecules are almost enough to specify the identity of every cell along the long axis of the embryo, and we argue that the way in which this information is distributed reflects an optimization principle, maximizing the information available from a limited number of molecules. Cells in a developing embryo have no direct way of “measuring” their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for “positional information. ” We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as would be expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell’s location with an error bar of along the anterior/posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.
UNIVERSITY OF SOUTHERN CALIFORNIA Center for Applied Financial Economics (CAFE) Can Oil Prices Forecast Exchange Rates?

This paper investigates whether oil prices have a reliable and stable out-of-sample relationship with the Canadian/U.S dollar nominal exchange rate. Despite state-of-theart methodologies, we nd little systematic relation between oil prices and the exchange rate at the monthly and quarterly frequencies. In contrast, the main contribution is to show the existence of a very short-term relationship at the daily frequency, which is rather robust and holds no matter whether we use contemporaneous (realized) or lagged oil prices in our regression. However, in the latter case the predictive ability is ephemeral, mostly appearing after instabilities have been appropriately taken into account. J.E. L. Codes: F31, F37, C22, C53. Acknowledgments: We would like to thank K. Sheppard and D. Wang for providing data related to this project, as well as R. Alquist, H. Guay, A. Herrera, M. Chinn, L. Kilian, M. Obstfeld, J. Wright and participants at the 2011 Bank of Canada-ECB conference on "Exchange Rates and Macroeconomic Adjustment", the 2012 American Economic Association Meetings and the Paris School of Economics for comments.
Reducing PMD impairments

We review the optical and electrical PMD compensation schemes that can be found in the literature. Because of the statistical nature of PMD, most of them are composed of an adaptive counteractive element, a feedback signal and a tracking algorithm. We also mention the importance of PMD statistics emulation and of the long-term field experiments related to PMD.
Compact kernel classifiers trained with minimum classification error criterion

Unlike Support Vector Machine (SVM), Kernel Minimum Classification Error (KMCE) training frees kernels from training samples and jointly optimizes weights and kernel locations. Focusing on this feature of KMCE training, we propose a new method for developing compact (small scale but highly accurate) kernel classifiers by applying KMCE training to support vectors (SVs) that are selected (based on the weight vector norm) from the original SVs produced by the Multi-class SVM (MSVM). We evaluate our proposed method in four classification tasks and clearly demonstrate its effectiveness: only a 3% drop in classification accuracy (from 99.1 to 89.1%) with just 10% of the original SVs. In addition, we mathematically reveal that the value of MSVM's kernel weight indicates the geometric relation between a training sample and margin boundaries.
Joint DOA and fundamental frequency estimation based on relaxed iterative adaptive approach and optimal filtering

In this work, the problem of joint direction-of-arrival and fundamental frequency estimation for multi-channel harmonic sinusoidal signals is addressed. Different from the conventional optimal filtering method, we estimate the covariance matrix with the 2-D iterative adaptive approach, which is based on a single snapshot. In addition, to improve the estimation accuracy for the off-grid sources, a relaxation technique is utilized. Then, joint estimation is conducted on this covariance matrix estimate with the optimal filtering method. As a result, the relaxed iterative adaptive approach - optimal filtering method is devised. Statistical evaluation with synthetic signals shows the accurate performance of the proposed method compared with the Cramér-Rao lower bound.
Efficient robust private set intersection

Computing Set Intersection privately and efficiently between two mutually mistrusting parties is an important basic procedure in the area of private data mining. Assuring robustness, namely, coping with potentially arbitrarily misbehaving (i.e., malicious) parties, while retaining protocol efficiency (rather than employing costly generic techniques) is an open problem. In this work the first solution to this problem is presented.