Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine

Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.
COI barcoding of true bugs (Insecta, Heteroptera)

Several recent studies have proposed that partial DNA sequences of the cytochrome c oxidase I (COI) mitochondrial gene might serve as DNA barcodes for identifying and differentiating between animal species, such as birds, fish and insects. In this study, we tested the effectiveness of a COI barcode to identify true bugs from 139 species collected from Korea and adjacent regions (Japan, Northeastern China and Fareast Russia). All the species had a unique COI barcode sequence except for the genus Apolygus (Miridae), and the average interspecific genetic distance between closely related species was about 16 times higher than the average intraspecific genetic distance. DNA barcoding identified one probable new species of true bug and revealed identical or very recently divergent species that were clearly distinguished by morphological characteristics. Therefore, our results suggest that COI barcodes can reveal new cryptic true bug species and are able to contribute for the exact identification of the true bugs.
Design of performance evaluation index system of public security financial expenditure based on analytic hierarchy process

Public security financial expenditure is a fundamental factor to affect the development and construction of public security management work. The performance evaluation of public security financial expenditure is an effective way to make the management system of public security financial fund more scientific and meticulous. It has great practical significance. Based on the analytic hierarchy process (AHP), this paper establishes a performance evaluation index system which suits to financial expenditure of public security organs with the comprehensive performance evaluation of public financial expenditure as an example, and selects logical evaluation indexes and defines weight of each evaluation index. We hope it can be a reference for the future performance evaluation of public security financial expenditure.
Computational Generation of Referring Expressions: A Survey

This article offers a survey of computational research on referring expression generation (REG). It introduces the REG problem and describes early work in this area, discussing what basic assumptions lie behind it, and showing how its remit has widened in recent years. We discuss computational frameworks underlying REG, and demonstrate a recent trend that seeks to link REG algorithms with well-established Knowledge Representation techniques. Considerable attention is given to recent efforts at evaluating REG algorithms and the lessons that they allow us to learn. The article concludes with a discussion of the way forward in REG, focusing on references in larger and more realistic settings.
Doppler synthetic aperture hitchhiker imaging

In this paper we consider passive airborne receivers that use backscattered signals from sources of opportunity transmitting single-frequency or ultra-narrowband waveforms. Because of its combined passive synthetic aperture and the single-frequency nature of the transmitted waveforms, we refer to the system under consideration as Doppler synthetic aperture hitchhiker (DSAH). We present a novel image formation method for DSAH. Our method first correlates the windowed signal obtained from one receiver with the windowed, filtered, scaled and translated version of the received signal from another receiver. This processing removes the transmitter-related variables from the phase of the Fourier integral operator that maps the radiance of the scene to the correlated signal. Next, we use microlocal analysis to reconstruct the scene radiance by the weighted backprojection of the correlated signal. The image reconstruction method is applicable to both cooperative and non-cooperative sources of opportunity using one or more airborne receivers. It has the desirable property of preserving the visible edges of the scene radiance. Additionally, it is an analytic reconstruction technique that can be made computationally efficient. We present numerical simulations to demonstrate the performance of the image reconstruction method and to verify the theoretical results.
Thermal Study of High-Power Nitride-Based Flip-Chip Light-Emitting Diodes

This paper presents a chip-level thermal study of high-power nitride-based flip-chip (FC) light-emitting diodes (LEDs). In order to understand the thermal performance of the high-power FC LEDs thoroughly, a quantitative parametric analysis of the thermal dependence on the chip contact area, bump configuration, and bump defects was performed by finite-element model (FEM) numerical simulation and thermal infrared (IR) microscopy testing, respectively. FEM numerical simulation results proved that the optimized bump configuration design was essential to get a uniform temperature distribution in the active layer and improve the thermal performance of the FC LED. IR microscopy testing results recognized that bump defects formed in the LED chip solder processing would lead to surface hot spots around the vicinity of these bump defects, particularly under high-current working conditions. In addition, a light-emitting dark zone was also observed in the optical field for FC LEDs with bump defects. In summary, optimized LED FC bump configuration design and good bonding quality in the chip bonding process are proved to be critical for improving the thermal performance and extending the operating longevity of high-power FC LEDs.
Haar-like wavelets defined over tetrahedrical grids

We systematically define Haar-like wavelets over a tetrahedral grid which is generated by a regular subdivision method. These wavelets form an unconditional basis for L/sup P/(T,/spl Sigma/,/spl mu/), 1<p</spl infin/, /spl mu/ being the Lebesgue measure and /spl Sigma/ the /spl sigma/-algebra of all tetrahedra generated from a tetrahedron T by the chosen subdivision method.
The Distorted Effect of Financial Development on International Trade Flows

This paper investigates the effects of financial development on the intensive and extensive margins of countries exports, at different stages of economic development. The paper develops a partial equilibrium model with monopolistic competition. In this model, firms are heterogeneous in terms of productivity and have access to external liquidity. The effect of financial development on the intensive and extensive margins of countries exports is predicted to be positive, especially in sectors with a higher demand for external finance. In countries with poor financial institutions though, only the most productive firms benefit from an increased access to financial resources and start exporting, with little effect on aggregate exports. The effect of financial development on exports is therefore higher for a better initial development of financial institutions. The empirical analysis confirms that financial development promotes both the intensive and extensive margins of countries’ exports. This is more the case in industries with a higher demand for external finance. Though, more than 60% of the effect of financial development channels through the intensive margin. In industries where the demand for external finance is high, the effect of financial development is the highest in economies characterized by an intermediate development of financial institutions, and the lowest in countries with poor or advanced financial institutions. This contradicts the traditional expectation that financial development benefits more in terms of exports to countries where financial constraints are the most binding.
Anti-Brucella Antibodies in Moose (Alces alces gigas), Muskoxen (Ovibos moschatus), and Plains Bison (Bison bison bison) in Alaska, USA

Abstract We used an indirect enzyme-linked immunosorbent assay (iELISA) and the rose bengal test (RBT) to test for anti-Brucella antibodies in moose (Alces alces gigas), muskoxen (Ovibos moschatus), and plains bison (Bison bison bison) from various game management units (GMUs) in Alaska, US, sampled from 1982 to 2010. A portion of the sera had previously been tested with the standard plate test (SPT), the buffered Brucella antigen (BBA) card test, and the card test (CARD). No antibody-positive plains bison were identified. Anti-Brucella antibodies were detected in moose (iELISA, n=4/87; RBT, n=4/87; SPT, n=4/5; BBA, n=4/4) from GMU 23 captured in 1992, 1993, and 1995 and in muskoxen (iELISA, n=4/52; RBT, n=4/52; CARD, n=4/35) from GMUs 26A and 26B captured in 2004, 2006, and 2007. A negative effect of infection on the health of individuals of these species is probable. The presence of antibody-positive animals from 1992 to 2007 suggests presence of brucellae over time. The antibody-positive animals were found in northern Alaska, an area with a historically higher prevalence of Brucella-positive caribou, and a spillover of Brucella suis biovar 4 from caribou may have occurred. Brucella suis biovar 4 causes human brucellosis, and transmission from consumption of moose and muskoxen is possible.
Tissue Distribution and Metabolism of the Tyrosine Kinase Inhibitor ZD6474 (Zactima) in Tumor-Bearing Nude Mice following Oral Dosing

ZD6474 [N-(4-bromo-2-fluorophenyl)-6-methoxy-7-[(1-methylpiperidin-4-yl)methoxy]-quinazolin-4-amine; Zactima] is a tyrosine kinase inhibitor with antiangiogenic and antitumor activity currently undergoing human trials for cancer treatment. Pharmacokinetic studies in animal models are an important component in the clinical development of this agent to relate preclinical studies to patient treatment. In the studies presented here, the pharmacokinetics of ZD6474 was determined in plasma and tissues of MCF-7 tumor-bearing nude mice following single p.o. doses at 10, 25, and 50 mg/kg. Plasma area under the curve and Cmax were linear, increasing proportionally with dose. Tissue analysis showed that ZD6474 is extensively distributed to tissues, with liver and lung accumulating concentrations of 212 μg/g (∼450 μM) and 161 μg/g (∼340 μM), respectively. Tumor levels ranged from 27 to 71 μg/g at Cmax levels across the three dose ranges, and ZD6474 was distributed to all of the tissues in a dose-dependent manner. Analysis of putative ZD6474 metabolites in feces found four, with the N-demethyl-piperidinyl-ZD6474 metabolite being the most prominent but still accounting for less than 2% of the total amount of ZD6474 present. The lack of significant metabolism of ZD6474 is consistent with the relatively long half-life in mice (∼30 h), as well as that seen in humans (∼120 h), and the primary method of drug elimination appears to be unchanged in the feces (∼25%). The incorporation of an empirical approach to dosing in mouse models of cancer in preclinical studies may allow for better prediction of clinical efficacy for ZD6474 alone and in combination with other therapeutic modalities based on equivalent drug exposure.
Genomic deletion of GIT2 induces a premature age-related thymic dysfunction and systemic immune system disruption

Recent research has proposed that GIT2 (G protein-coupled receptor kinase interacting protein 2) acts as an integrator of the aging process through regulation of ‘neurometabolic’ integrity. One of the commonly accepted hallmarks of the aging process is thymic involution. At a relatively young age, 12 months old, GIT2−/− mice present a prematurely distorted thymic structure and dysfunction compared to age-matched 12 month-old wild-type control (C57BL/6) mice. Disruption of thymic structure in GIT2−/− (GIT2KO) mice was associated with a significant reduction in the expression of the cortical thymic marker, Troma-I (cytokeratin 8). Double positive (CD4+CD8+) and single positive CD4+ T cells were also markedly reduced in 12 month-old GIT2KO mice compared to age-matched control wild-type mice. Coincident with this premature thymic disruption in GIT2KO mice was the unique generation of a novel cervical ‘organ’, i.e. ‘parathymic lobes’. These novel organs did not exhibit classical peripheral lymph node-like characteristics but expressed high levels of T cell progenitors that were reflexively reduced in GIT2KO thymi. Using signaling pathway analysis of GIT2KO thymus and parathymic lobe transcriptomic data we found that the molecular signaling functions lost in the dysfunctional GIT2KO thymus were selectively reinstated in the novel parathymic lobe – suggestive of a compensatory effect for the premature thymic disruption. Broader inspection of high-dimensionality transcriptomic data from GIT2KO lymph nodes, spleen, thymus and parathymic lobes revealed a systemic alteration of multiple proteins (Dbp, Tef, Per1, Per2, Fbxl3, Ddit4, Sin3a) involved in the multidimensional control of cell cycle clock regulation, cell senescence, cellular metabolism and DNA damage. Altered cell clock regulation across both immune and non-immune tissues therefore may be responsible for the premature ‘aging’ phenotype of GIT2KO mice.
Selected physiologic compatibilities and incompatibilities between human and porcine organ systems

Abstract: The shortage of donor organs is a major barrier to clinical organ transplantation. Although xenotransplantation is considered one of the alternatives to human organ transplantation, there are immunologic and physiologic incompatibilities between humans and pigs. With the exception of coagulation, the major potential physiologic incompatibilities relating to function of the kidney, heart, liver, lungs, pancreatic islets, and hormones are reviewed. Some of these physiologic differences can be overcome by producing genetically altered pigs to improve compatibility with humans. The possibility of producing such pigs for organ transplantation is considered.
An Evaluation of Sepsis Web Sites for Patient and Family Education

More and more consumers are using the Internet to find answers to questions about healthcare. Unfortunately, information at health Web sites may be incorrect, biased, and outdated. The purpose of our project was to identify Web sites on sepsis that could be used for patient and family education. We evaluated 30 sites on the basis of the Health on the Net criteria for medical and health Web sites, key content areas that patients and families should know in relation to sepsis, and readability. This article shares the process we used to evaluate the Web sites and identify the top sites for patient education.
Iterative methods for nonlinear ill-posed problems in Banach spaces: convergence and applications to parameter identification problems

In this paper, we study convergence of two different iterative regularization methods for nonlinear ill-posed problems in Banach spaces. One of them is a Landweber type iteration, the other one the iteratively regularized Gauss–Newton method with an a posteriori chosen regularization parameter in each step. We show that a discrepancy principle as a stopping rule renders these iteration schemes regularization methods, i.e., we prove their convergence as the noise level tends to zero. The theoretical findings are illustrated by two parameter identification problems for elliptic PDEs.
Comparison of Polar Decoders with Existing Low-Density Parity-Check and Turbo Decoders

Polar codes are a recently proposed family of provably capacity-achieving error-correction codes that received a lot of attention. While their theoretical properties render them interesting, their practicality compared to other types of codes has not been thoroughly studied. Towards this end, in this paper, we perform a comparison of polar decoders against LDPC and Turbo decoders that are used in existing communications standards. More specifically, we compare both the error-correction performance and the hardware efficiency of the corresponding hardware implementations. This comparison enables us to identify applications where polar codes are superior to existing error-correction coding solutions as well as to determine the most promising research direction in terms of the hardware implementation of polar decoders.
Protective effect of picolinic acid on mice intracerebrally infected with lethal doses of Candida albicans

We have studied the effects of picolinic acid (PLA), a product of tryptophan degradation, on mouse susceptibility to intracerebral infection with Candida albicans. We show that intraperitoneal administration of PLA significantly enhances the median survival time of mice inoculated with the lethal challenge. Furthermore, intracerebral administration of this agent induces a protective state against the local lethal infection, the phenomenon depending upon the administration schedule and doses of PLA employed. According to survival data, yeast growth in the brain as well as yeast colonization of the kidneys are drastically reduced in PLA-treated mice compared with those for untreated controls. Northern (RNA) blot analysis of brain tissues demonstrates that mRNA levels specific for tumor necrosis factor and interleukin 1 are augmented and induced, respectively, after inoculation of PLA. These results indicate that PLA has a protective effect likely involving elicitation of a cytokine response in vivo against fungal infections.
A Theoretical Study of the Signal Contribution of Regions of the Adult Head to Near-Infrared Spectroscopy Studies of Visual Evoked Responses

Near-infrared (NIR) spectroscopy has been used in studies of the cerebral hemodynamic response to visual processing. In this paper, we present theoretical results from finite element and Monte Carlo modeling in order to help understand the contribution to the NIR signal from different parts of the head. The results from the models show that at the typical optode spacings used in these studies, an infrared spectroscopy measurement of intensity is sensitive to the outer 1-2 mm of the cortical gray matter and the partial optical path length in the gray matter is approximately 10 mm, compared with a total optical path length of 400 mm. When the NIR measurement is of change in mean photon arrival time (or phase shift), the signal comes from the upper 2-4 mm of the cortical surface and there is an increased lateral spread of the contributing tissue. We predict that for a 4-cm separation of input and detection optodes at 800 nm, a 1 microM change in hemoglobin concentration in the cortex corresponds to an attenuation change of approximately 0.001 OD (optical density) or 1 ps mean time change. Movement of the brain caused by this increase in volume will cause an absorption change of approximately half this magnitude, but does not affect the photon arrival time at 4-cm spacing. A discrepancy between the predicted and the experimentally measured intensities may support the supposition that the NIR signal is actually very sensitive to changes occurring in the pial cerebral vessels lying on the brain surface.
Estimation of Forward-Looking Relationships in Closed Form: An Application to the New Keynesian Phillips Curve

We illustrate the importance of placing model-consistent restrictions on expectations in the estimation of forward-looking Euler equations. In two-stage limited-information settings where first-stage estimates are used to proxy for expectations, parameter estimates can differ substantially, depending on whether these restrictions are imposed or not. This is shown in an application to the New Keynesian Phillips Curve (NKPC), first in a Monte Carlo exercise, and then on actual data. The closed-form (CF) estimates require by construction that expectations of inflation be model-consistent at all points in time, while the difference-equation (DE) estimates impose no model discipline on expectations. Between those two polar extremes there is a wide range of alternative DE specifications based on the same dynamic relationship that explicitly imposes model restrictions on expectations for a finite number of periods. In our application, these last estimates quickly converge to the CF estimates and illustrate that the DE estimates in Cogley and Sbordone (2008) are not robust to imposing modest model requirements on expectations. In particular, our estimates show that the NKPC is not purely forward-looking, and thus that time-varying trend inflation is insufficient to explain inflation persistence.
The Coordinated Evolution of Yeast Proteins Is Constrained by Functional Modularity

Material and methods Evolutionary rates estimation We used the data set of the evolutionary rates of yeast proteins from a recent study by Hirsh et al. [1] The evolutionary rate di of a protein i is defined as the ratio of non-synonymous (dN) substitution per site to synonymous substitution (dS) per site of this protein [2]. The evolutionary rates of 3036 open reading frames were calculated by Hirsh et al. [1], based on four complete genomes of Saccharomyces species (Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces mikatae and Saccharomyces bayanus) [3], with corrections for non-neutral dS [1]. Measure of co-evolution strength of expression level We used codon adaptation index (CAI) [4] of each gene as a proxy for its expression level [2,5–8], kindly provided by Aaron. E. Hirsh [1]. The CAI value is defined as following: L 1 k k) w (CAI ∏ = = 1 L , where L is the total number of codons in a given gene and wk is the ratio of the frequency of the k th codon over the frequency of the optimal codon for the same amino acid. Both frequencies are calculated from a set of highly expressed genes in the organism being studied [4]. For a given pair of orthologous gene sets, we use the Pearson correlation coefficient between the CAI values in the corresponding sets (four CAI values in each set) as a measure of the co-evolution strength of expression level between this pair [5]. We calculated all pairwise CAI correlation coefficients within and between modules. The formation of functional modules by proteins is achieved by physical or functional interactions between proteins. Here, we define interactions that result in proteins association as physical interactions and those between two proteins having no direct physical interactions as functional interactions. For example, a repressor protein has a functional interaction with a protein that is encoded in the gene it is repressing. Various functional genomics techniques such as microarray [9], yeast two-hybrid [10,11], synthetic lethal screens [12] and affinity purification coupled with mass spectrometry [13,14] are available for characterizing either physical or functional interactions between proteins. The interactions characterized in these experiments feature functional associations between proteins. However, each of these techniques captures different aspects of functional associations. Methods that rely solely on the experimental data obtained from one technique can give rise to systematic errors in the characterization of functional modules. For example, some modules formed …