Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Activation of ydeA, Which Encodes a Member of the Major Facilitator Superfamily, Interferes with Arabinose Accumulation and Induction of the Escherichia coli Arabinose PBADPromoter

ABSTRACT Induction of genes expressed from the arabinose PBADpromoter is very rapid and maximal at low arabinose concentrations. We describe here two mutations that interfere with the expression of genes cloned under arabinose control. Both mutations map to theydeA promoter and stimulate ydeA transcription; overexpression of YdeA from a multicopy plasmid confers the same phenotype. One mutation is a large deletion that creates a more efficient −35 region (ATCACA changed to TTCACA), whereas the other affects the initiation site (TTTT changed to TGTT). TheydeA gene is expressed at extremely low levels in exponentially growing wild-type cells and is not induced by arabinose. Disruption of ydeA has no detectable effect on cell growth. Thus, ydeA appears to be nonessential under usual laboratory growth conditions. The ydeA gene encodes a membrane protein with 12 putative transmembrane segments. YdeA belongs to the largest family of bacterial secondary active transporters, the major facilitator superfamily, which includes antibiotic resistance exporters, Lac permease, and the nonessential AraJ protein. Intracellular accumulation of arabinose is strongly decreased in mutant strains overexpressing YdeA, suggesting that YdeA facilitates arabinose export. Consistent with this interpretation, very high arabinose concentrations can compensate for the negative effect ofydeA transcriptional activation. Our studies (i) indicate that YdeA, when transcriptionally activated, contributes to the control of the arabinose regulon and (ii) demonstrate a new way to modulate the kinetics of induction of cloned genes.
Discrete Dopant Fluctuation in Limited-Width FinFETs for VLSI Circuit Application: A Theoretical Study

The random dopant fluctuation (RDF) in double-gate (DG) devices is investigated via physical analyses and numerical simulations. Our results show that extremely scaled devices, especially FinFETs with narrow device width (fin height) in each individual fin, are susceptible to RDF effects. Even in an undoped silicon channel, the existence of unwanted impurity dopant will still have a significant impact on device characteristics. Design implication from RDF is also discussed
On Algebraic Solutions to Painleve VI

We announce some results which might bring a new insight into the classification of algebraic solutions to the sixth Painlevé equation. They consist of the rationality of parameters, trigonometric Diophantine conditions, and what the author calls the Tetrahedral Theorem regarding the absence of algebraic solutions in certain situations. The method is based on fruitful interactions between the moduli theoretical formulation of Painlevé VI and dynamics on character varieties via the Riemann-Hilbert correspondence.
Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans

To gain a better understanding of the genetic variants associated with carboplatin-induced cytotoxicity in individuals of African descent, we present a step-wise approach integrating genotypes, gene expression, and sensitivity of HapMap cell lines to carboplatin. Cell lines derived from 30 trios of African descent (YRI) were used to develop a preclinical model to identify genetic variants and gene expression that contribute to carboplatin-induced cytotoxicity. Cytotoxicity was determined as cell growth inhibition at increasing concentrations of carboplatin for 72 h. Gene expression of 89 HapMap YRI cell lines was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. Single nucleotide polymorphism genotype and the percent survival at different treatment concentrations along with carboplatin IC50 were linked through whole genome association. A second association test was done between single nucleotide polymorphism genotype and gene expression, and linear regression was then used to capture those genes whose expression correlated to drug sensitivity phenotypes. This approach allows us to identify genetic variants that significantly associate with sensitivity to the cytotoxic effects of carboplatin through their effect on gene expression. We found a gene (GPC5) whose expression is important in all carboplatin treatment concentrations as well as many genes unique to either low (e.g., MAPK1) or high (e.g., BRAF, MYC, and BCL2L1) concentrations of drug. Our whole genome approach enables us to evaluate the contribution of genetic and gene expression variation to a wide range of cellular phenotypes. The identification of concentration specific genetic signatures allows for potential integration of pharmacokinetics, pharmacodynamics, and pharmacogenetics in tailoring chemotherapy. [Mol Cancer Ther 2008;7(9):3038–46]
Receptor, FcRn Salvage by the MHC Class I-Related Visualizing the Site and Dynamics of IgG

The MHC class I-related receptor, FcRn, plays a central role in regulating the serum levels of IgG. FcRn is expressed in endothelial cells, suggesting that these cells may be involved in maintaining IgG levels. We have used live cell imaging of FcRn-green ﬂuorescent protein transfected human endothelial cells to analyze the intracellular events that control IgG homeostasis. We show that segregation of FcRn-IgG complexes from unbound IgG occurs in the sorting endosome. FcRn or FcRn-IgG complexes are gradually depleted from sorting endosomes to ultimately generate multivesicular bodies whose contents are destined for lysosomal degradation. In addition, the pathways taken by FcRn and the transferrin receptor overlap, despite distinct mechanisms of ligand uptake. The studies provide a dynamic view of the trafﬁcking of FcRn and its ligand and have relevance to understanding how FcRn functions to maintain IgG homeostasis. The Journal of Immunology, 2004, 172: 2021–2029. ecent data indicate that in addition to its earlier known role in transferring maternal IgG from mother to young (1–4), the MHC class I-related receptor, FcRn, regulates the serum levels of IgG Analyses in mice indicate that endothelial cells lining the (micro) vasculature are a possible site at which IgG homeostasis is Knowledge about how FcRn carries out its function in these cells is therefore of relevance to understanding how IgG levels are regulated and also to the effective delivery of therapeutic Abs. In this study we have used live cell ﬂuorescence imaging of FcRn-green ﬂuorescent protein (GFP) 3 -transfected endothelial cells to analyze in real time the trafﬁcking of this receptor and its ligand. A custom-built, multiwavelength laser excitation microscope imaging system has been used in conjunction with an intensiﬁed camera to analyze the processes that regulate IgG homeostasis on a rapid time scale and for a larger number of acquisitions than could be achieved with a more standard imaging conﬁguration. Our studies provide a dynamic view of the events that are involved in sorting FcRn-IgG complexes from uncomplexed IgG and identify the intracellular site at which these processes occur. They also show that the pathways taken by the transferrin receptor and FcRn within cells in-tersect, despite fundamentally different mechanisms of ligand uptake. These studies therefore provide novel insight into the pathways involved in IgG homeostasis.
Effects of glycemic load on metabolic risk markers in subjects at increased risk of developing metabolic syndrome.

BACKGROUND Epidemiologic studies suggest that diets with a low glycemic index (GI) or glycemic load (GL) are associated with a decreased risk of developing metabolic syndrome. Intervention studies are inconsistent, however, possibly due to differences in macronutrient and fiber compositions of the experimental diets. OBJECTIVE We tested side-by-side test foods with similar macronutrient and fiber compositions but with different sucrose-flour ratios or carbohydrate source to determine the effects of different GIs and GLs on metabolic risk markers in overweight subjects. DESIGN Overweight men (n = 9) and women (n = 6) received in random order for 11 wk 4 test foods with an increased GI or a decreased GI (69 compared with 40, 86 compared with 48, 63 compared with 37, and 51 compared with 20, respectively). There was a GL difference of 32 units between the 2 interventions. RESULTS At the end of the 11-wk intervention periods, the decreased GL test foods did not change fasting plasma glucose (mean +/- SD: 5.83 +/- 0.6 compared with 5.94 +/- 0.6 mmol/L) or insulin (8.3 +/- 2.8 compared with 9.8 +/- 5.1 mU/L) concentrations compared with increased GL test foods. Serum total cholesterol (5.56 +/- 0.90 compared with 5.76 +/- 1.04 mmol/L), LDL-cholesterol (3.57 +/- 0.72 compared with 3.68 +/- 0.80 mmol/L), HDL-cholesterol (1.21 +/- 0.38 compared with 1.24 +/- 0.37 mmol/L), and triacylglycerol (1.61 +/- 0.77 compared with 1.78 +/- 1.04 mmol/L) concentrations were also not significantly different for decreased and increased GL test foods, respectively. Finally, proinflammatory (high-sensitivity C-reactive protein, interleukin-6, tumor necrosis factor-alpha, monocyte chemoattractant protein 1) and prothrombotic (plasminogen activator inhibitor 1) markers were not affected. Glucose and lipids were also analyzed after 1 and 5 wk of intervention and were not affected by the intervention. CONCLUSION When incorporated into a habitual diet, consumption of test foods with a decreased GL does not ameliorate metabolic risk markers in overweight subjects.
A novel regulatory element (E77) isolated from CHO‐K1 genomic DNA enhances stable gene expression in Chinese hamster ovary cells

Abstract Vectors flanked by regulatory DNA elements have been used to generate stable cell lines with high productivity and transgene stability; however, regulatory elements in Chinese hamster ovary (CHO) cells, which are the most widely used mammalian cells in biopharmaceutical production, are still poorly understood. We isolated a novel gene regulatory element from CHO‐K1 cells, designated E77, which was found to enhance the stable expression of a transgene. A genomic library was constructed by combining CHO‐K1 genomic DNA fragments with a CMV promoter‐driven GFP expression vector, and the E77 element was isolated by screening. The incorporation of the E77 regulatory element resulted in the generation of an increased number of clones with high expression, thereby enhancing the expression level of the transgene in the stable transfectant cell pool. Interestingly, the E77 element was found to consist of two distinct fragments derived from different locations in the CHO genome shotgun sequence. High and stable transgene expression was obtained in transfected CHO cells by combining these fragments. Additionally, the function of E77 was found to be dependent on its site of insertion and specific orientation in the vector construct. Our findings demonstrate that stable gene expression mediated by the CMV promoter in CHO cells may be improved by the isolated novel gene regulatory element E77 identified in the present study.
A report of undergraduates' bonding misconceptions

The types of misconceptions related to electronegativity, bonding, geometry, and microscopic representations that undergraduate chemistry majors hold is described. Fifty-six students from six different courses, representing freshmen through senior level chemistry majors were interviewed. The qualitative coding scheme of the interview transcripts revealed a number of misconceptions not previously documented. In addition, the stability of the misconceptions was investigated as a function of educational level, indicating that some students' misconceptions relating to bonding are resistant to change despite increased chemistry education.
Exploring NoC jitter effect on simulation of spiking neural networks

The major bottleneck in simulation of large-scale neural networks is the communication problem due to one-to-many neuron connectivity. Network-on-Chip concept has been proposed to address the problem. This work explores the drawback that is introduced by interconnection networks - a delay jitter. The preliminary experiment is held in the spiking neural network simulator introducing variable communicational delay to the simulation. The performance degradation is reported.
Sucrose-Specific Induction of Anthocyanin Biosynthesis in Arabidopsis Requires the MYB75/PAP1 Gene1

Sugar-induced anthocyanin accumulation has been observed in many plant species. We observed that sucrose (Suc) is the most effective inducer of anthocyanin biosynthesis in Arabidopsis (Arabidopsis thaliana) seedlings. Other sugars and osmotic controls are either less effective or ineffective. Analysis of Suc-induced anthocyanin accumulation in 43 Arabidopsis accessions shows that considerable natural variation exists for this trait. The Cape Verde Islands (Cvi) accession essentially does not respond to Suc, whereas Landsberg erecta is an intermediate responder. The existing Landsberg erecta/Cvi recombinant inbred line population was used in a quantitative trait loci analysis for Suc-induced anthocyanin accumulation (SIAA). A total of four quantitative trait loci for SIAA were identified in this way. The locus with the largest contribution to the trait, SIAA1, was fine mapped and using a candidate gene approach, it was shown that the MYB75/PAP1 gene encodes SIAA1. Genetic complementation studies and analysis of a laboratory-generated knockout mutation in this gene confirmed this conclusion. Suc, in a concentration-dependent way, induces MYB75/PAP1 mRNA accumulation. Moreover, MYB75/PAP1 is essential for the Suc-mediated expression of the dihydroflavonol reductase gene. The SIAA1 locus in Cvi probably is a weak or loss-of-function MYB75/PAP1 allele. The C24 accession similarly shows a very weak response to Suc-induced anthocyanin accumulation encoded by the same locus. Sequence analysis showed that the Cvi and C24 accessions harbor mutations both inside and downstream of the DNA-binding domain of the MYB75/PAP1 protein, which most likely result in loss of activity.
The Incomplete Perfect Phylogeny Haplotype Problem

The problem of resolving genotypes into haplotypes, under the perfect phylogeny model, has been under intensive study recently. All studies so far handled missing data entries in a heuristic manner. We prove that the perfect phylogeny haplotype problem is NP-complete when some of the data entries are missing, even when the phylogeny is rooted. We define a biologically motivated probabilistic model for genotype generation and for the way missing data occur. Under this model, we provide an algorithm, which takes an expected polynomial time. In tests on simulated data, our algorithm quickly resolves the genotypes under high rates of missing entries.
The identification, cloning and functional expression of the gene encoding orotidine 5'-monophosphate (OMP) decarboxylase from Plasmodium falciparum

Abstract The coding region of a putative orotidine 5'-monophosphate decarboxylase gene from Plasmodium falciparum was identified in genomic data from the Malarial Genome Sequencing Project. The gene encodes a protein of 323 amino acids with a predicted molecular weight of 37.8 kDa. The gene was cloned into a bacterial expression vector and over-expressed in Escherichia coli. The recombinant protein was purified and shown to have orotidine 5'-monophosphate decarboxylase activity, confirming the identity of the gene.
Heuristic M ethod for A utomatic I mage A nnotation in HTML D ocuments

An automatic heuristic method for embedded image annotation in HTML documents is exposed. This method exploits the tree structure present in HTML documents trying to identify nodes that contain relevant information about the embedded image, and then using the text in these nearest nodes to expand the information collected about the image, increasing the recall of a Web Search Engine. The proposed heuristic was evaluated using the Agreement Index: the text contained in the identified nodes and the corresponding image was assessed and assigned a category of how well the text was related (i.e. described) with the image. In our test cases the calculated Agreement Index was over 85%, validating the proposed method. Keywords— image annotation, HTML, information retrieval, search engine, web Digital Object Identifier (DOI): http://dx.doi. org/10.18687/LACCEI2015.1. 1.057 ISBN: 13 978-0-9822896-8-6
On the limits of treating interference as noise for two-user symmetric Gaussian interference channels

The limits of treating interference as noise are studied for the canonical two-user symmetric Gaussian interference channel. A two-step approach is proposed for finding approximately optimal input distributions in the high signal-to-noise ratio (SNR) regime. First, approximately and precisely optimal input distributions are found for the Avestimehr-Diggavi-Tse (ADT) linear deterministic model. These distributions are then translated, systematically, into Gaussian models, which we show can achieve the sum capacity to within O(log log(SNR)).
Staging of Lewy-related pathology in dementia.

OBJECTIVE Lewy-related pathology is the characteristic feature of Parkinson's disease with and without dementia and dementia with Lewy bodies (DLB). There are two neuropathological staging systems for Lewy-related pathology commonly employed today: the staging system for Parkinson-related pathology by Braak et al., and the staging system by the Consortium on DLB. There are also several modified systems based on these two scales. METHODS We applied a total of eight different staging systems for Lewy-related pathology to 36 consecutive demented patients with various dementia disorders. RESULTS The staging systems varied considerably in number of unclassifiable cases (range 0 – 16 out of 36 cases), while the diagnostic agreement between the systems that were able to classify all or the very majority of cases varied only slightly (weighted κ 0.86 – 0.92 and Spearman's σ 0.80 – 1.0). CONCLUSION The different staging systems for Lewy-related pathology that exist today vary in staging procedure and proportion of unclassifiable cases. The choice of system may affect the stage of Lewy-related pathology and ultimately final diagnosis.
Incarcerated Fathers and Their Children

High incarceration rates have led to more interest in the effects of incarceration on families, especially children. Most research has focused on the relationship between incarcerated mothers and their children. This study centered on father–child relationships and potential barriers to maintaining and developing them. A sample of 185 incarcerated fathers was interviewed within a maximum security state prison in the southern United States. Multiple regression analyses indicated two family barriers (children’s mother’s attitude and children’s attitude) made a statistically significant contribution to explaining inmates’ self-reports concerning relationships with their children. Measures of institutional barriers were not found to statistically contribute to the models. Fathers’ responses to an open-ended question about relationships with their children support the quantitative findings. The research suggests that strategies for improving parent–child relationships for the male incarcerated population should focus not only on institutional barriers but also on family barriers.
Sinica-IASL Chinese spelling check system at Sighan-7

We developed a Chinese spelling check system for error detection and error correction subtasks in the 2013 SIGHAN-7 Chinese Spelling Check Bake-off. By using the resources of Chinese phonology and orthographic components, our system contains four parts: high confidence pattern matcher, the detection module, the correction module, and the merger. We submitted 2 official runs for both subtasks. The evaluation result show that our system achieved 0.6016 in error detection F-score of subtask 1, and 0.448 in correction accuracy of subtask 2. 1
In Advances in Neural Information Processing Systems ( NIPS-12 ) pages 1036-1042 , Denver , Colorado , December 1999 Reinforcement Learning Using Approximate Belief States

The problem of developing good policies for partially observable Markov decision problems (POMDPs) remains one of the most challenging areas of research in stochastic planning. One line of research in this area involves the use of reinforcement learning with belief states, probability distributions over the underlying model states. This is a promising method for small problems, but its application is limited by the intractability of computing or representing a full belief state for large problems. Recent work shows that, in many settings, we can maintain an approximate belief state, which is fairly close to the true belief state. In particular, great success has been shown with approximate belief states that marginalize out correlations between state variables. In this paper, we investigate two methods of full belief state reinforcement learning and one novel method for reinforcement learning using factored approximate belief states. We compare the performance of these algorithms on several well-known problem from the literature. Our results demonstrate the importance of approximate belief state representations for large problems.
CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and the Circadian Control of Stomatal Aperture1[OPEN]

Stomatal guard cells are controlled by a modified circadian oscillator to ensure correct daylength-dependent regulation of stomatal aperture. The endogenous circadian (∼24 h) system allows plants to anticipate and adapt to daily environmental changes. Stomatal aperture is one of the many processes under circadian control; stomatal opening and closing occurs under constant conditions, even in the absence of environmental cues. To understand the significance of circadian-mediated anticipation in stomatal opening, we have generated SGC (specifically guard cell) Arabidopsis (Arabidopsis thaliana) plants in which the oscillator gene CIRCADIAN CLOCK ASSOCIATED1 (CCA1) was overexpressed under the control of the guard-cell-specific promoter, GC1. The SGC plants showed a loss of ability to open stomata in anticipation of daily dark-to-light changes and of circadian-mediated stomatal opening in constant light. We observed that under fully watered and mild drought conditions, SGC plants outperform wild type with larger leaf area and biomass. To investigate the molecular basis for circadian control of guard cell aperture, we used large-scale qRT-PCR to compare circadian oscillator gene expression in guard cells compared with the “average” whole-leaf oscillator and examined gene expression and stomatal aperture in several lines of plants with misexpressed CCA1. Our results show that the guard cell oscillator is different from the average plant oscillator. Moreover, the differences in guard cell oscillator function may be important for the correct regulation of photoperiod pathway genes that have previously been reported to control stomatal aperture. We conclude by showing that CONSTANS and FLOWERING LOCUS T, components of the photoperiod pathway that regulate flowering time, also control stomatal aperture in a daylength-dependent manner.
De novo identification of repeat families in large genomes

MOTIVATION De novo repeat family identification is a challenging algorithmic problem of great practical importance. As the number of genome sequencing projects increases, there is a pressing need to identify the repeat families present in large, newly sequenced genomes. We develop a new method for de novo identification of repeat families via extension of consensus seeds; our method enables a rigorous definition of repeat boundaries, a key issue in repeat analysis. RESULTS Our RepeatScout algorithm is more sensitive and is orders of magnitude faster than RECON, the dominant tool for de novo repeat family identification in newly sequenced genomes. Using RepeatScout, we estimate that approximately 2% of the human genome and 4% of mouse and rat genomes consist of previously unannotated repetitive sequence. AVAILABILITY Source code is available for download at http://www-cse.ucsd. edu/groups/bioinformatics/software.html