Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of circular RNAs in the silkworm midgut following Bombyx mori cytoplasmic polyhedrosis virus infection

ABSTRACT The pathogenesis of Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection is unclear, although accumulating evidence indicates that circular RNAs (circRNAs), which act as competing endogenous RNAs or positive regulators, play important roles in regulating gene expression in eukaryotes and, thus, may play a role in BmCPV infections. To explore the expression and biological functions of circRNAs in the silkworm midgut following BmCPV infection, silkworm circRNA expression profiles of normal midgut tissue (control) and BmCPV-infected midgut tissue (test) were determined using high-through sequencing. A total of 9,753 and 7,475circRNAs were detected from the control and test samples, respectively. The two samples shared 6,085 circRNAs, while 646 and 737 circRNAs were expressed specifically in the control and test samples, respectively. A total of 3,638 circRNAs were shown to be differentially expressed, and 400 circRNAs were substantially differentially expressed with a fold-change ≥ 2.0 (p< 0.05 and a false discover rate < 0.05), of which 294 were up-regulated and 106 were down-regulated following infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted to determine the principal functions of the substantially differentially regulated genes. circRNA-miRNA interaction networks were constructed based on a correlation analysis between the differentially expressed circRNAs and the nature of their microRNA (miRNA) binding sites. The network inferred that 13 miRNAs interacting with 193 circRNAs were among the 300 most abundant relationships. bmo-miR-3389-5p, bmo-miR-745-3p, and bmo-miR-3262 were related to 30, 34, and 34 circRNAs, respectively. circRNA_8115, circRNA_9444, circRNA_4553, circRNA_0827, and circRNA_6649 contained six, five, four, four, and four miRNA binding sites, respectively. We further found that alternative circularization of circRNAs is a common feature in silkworms and that the junction sites of many silkworm circRNAs are flanked by canonical GT/AG splicing signals. Our study is the first to show the circRNA response to virus infection. Thus, it provides a novel perspective on circRNA-miRNA interactions during BmCPV pathogenesis, and it lays the foundation for future research of the potential roles of circRNAs in BmCPV pathogenesis.
Comparison of Flavivirus Universal Primer Pairs and Development of a Rapid, Highly Sensitive Heminested Reverse Transcription-PCR Assay for Detection of Flaviviruses Targeted to a Conserved Region of the NS5 Gene Sequences

ABSTRACT Arthropod-transmitted flaviviruses are responsible for considerable morbidity and mortality, causing severe encephalitic, hemorrhagic, and febrile illnesses in humans. Because there are no specific clinical symptoms for infection by a determined virus and because different arboviruses could be present in the same area, a genus diagnosis by PCR would be a useful first-line diagnostic method. The six publishedFlavivirus genus primer pairs localized in the NS1, NS3, NS5, and 3′ NC regions were evaluated in terms of specificity and sensitivity with flaviviruses (including the main viruses pathogenic for humans) at a titer of 105 50% tissue culture infectious doses (TCID50s) ml−1 with a common identification step by agarose gel electrophoresis. Only one NS5 primer pair allowed the detection of all tested flaviviruses with the sensitivity limit of 105 TCID50s ml−1. Using a heminested PCR with new primers designed in the same region after an alignment of 30 different flaviviruses, the sensitivity of reverse transcription-PCR was improved and allowed the detection of about 200 infectious doses ml−1 with all of the tick- and mosquito-borne flaviviruses tested. It was confirmed that the sequenced amplified products in the NS5 region allowed predictability of flavivirus species by dendrogram, including the New York 99 West Nile strain. This technique was successfully performed with a cerebrospinal fluid sample from a patient hospitalized with West Nile virus encephalitis.
Iodine‐131 treatment of hyperthyroidism: current issues

None of the three treatments of the hyperthyroidism of Graves’ disease, namely antithyroid drugs, surgery and radioiodine, is entirely satisfactory. The high relapse rate, even after prolonged treatment with antithyroid drugs (Romaldini ef al., 1983), is viewed by many patients and physicians as unacceptable. Despite their added immunosuppressive action (McGregor et al., 1980) the antithyroid drugs do not seem to affect the natural history of the hyperthyroidism of Graves’ disease and the patient who diligently complies with therapy and clinic attendances is no more likely to achieve prolonged remission than those who are less well motivated. The published results of surgical treatment of Graves’ disease usually reflect the figures at the end of the first year and may flatter to deceive as some 30% of patients will have developed hypothyroidism after 20 years (Franklyn et a/., 1991) and 25% of those with recurrence present even later (Kalk et al., 1978). Although in practised hands surgery will result in the longest periods of euthyroidism, neither of the other two treatment choices is associated with a scar or a 1% chance of permanent hypoparathyroidism or vocal cord palsy. Even in the absence of damage to the recurrent laryngeal nerve, significant changes in voice quality may be recorded after submtal thyroidectomy (Kark et al., 1984), making surgeky an inadvisable option for those who depend upon their voice for a living. Iodine-I 31 is almost certainly ultimately thecheapest form of treatment of hyperthyroidism (Spencer et al., 1985). Despite public awareness of the dangers of radioactivity, to some extent heightened in the UK by implementation of the Ionising Radiation Regulations of 1985, it is likely that iodine-131 will be prescribed more liberally in the future as financial considerations inevitably impinge upon therapeutic options in increasingly cost-effective health services. It is therefore timely to review some of the current issues and problems related to this form of treatment of hyperthyroidism.
Cost disease in service sector

ABSTRACT A higher growth rate of the service sector prices, rather than prices in the manufacturing sector, through time is known as cost disease in the service sector. This paper investigates supply and demand-side reasons for cost disease. First, we present an analysis of the supply side of the cost disease, when services and manufacturing play their role both in the intermediate and final demand. Second, we consider a CES utility function for the consumer, which is a function of two commodity services and manufacturing. The results indicate that there are two reasons for cost disease to occur from the supply side in an economy: first, when the growth rate of total factor productivity and technological progress in services is less than that in the manufacturing sector, and second, when the elasticity of substitution between labor and manufacturing input in the services production function is large and elasticity of substitution in manufacturing production function is small. From the demand side, the result shows that the cost disease occurred if the growth rate of the income elasticity of service is more than the manufacturing sector through time.
Nanoparticles of Chitosan Loaded Ciprofloxacin: Fabrication and Antimicrobial Activity

Purpose: Chitosan is a natural mucoadhesive polymer with antibacterial activity. In the present study, chitosan (CS) nanoparticles were investigated as a vehicle for delivery of antibiotic, ciprofloxacin hydrochloride. Methods: Ionotropic gelation method was used for preparation chitosan nanoparticles. The effects of various factors including concentration of CS, concentration of tripolyphosphate (TPP), and homogenization rate on the size of nanoparticles were studied. The effects of various mass ratios of CS to ciprofloxacin hydrochloride on the encapsulation efficiency of nanoparticles were assessed. Results: The particles prepared under optimal condition of 0.45% CS concentration, 0.45% TPP concentration and homogenizer rate at 6000 rpm, had 72 nm diameter. In these particles with 1:0.5 mass ratio of CS to ciprofloxacin hydrochloride, the encapsulation efficiency was 23%. The antibacterial activity of chitosan nanoparticles and ciprofloxacin-loaded nanoparticles against E.coli and S.aureus was evaluated by calculation of minimum inhibitory concentration (MIC). Results showed that MIC of ciprofloxacin loaded chitosan nanoparticles was 50% lower than that of ciprofloxacin hydrochloride alone in both of microorganism species. Nanoparticles without drug exhibited antibacterial activity at higher concentrations and MIC of them against E.coli and S.aureus was 177 and 277 µg/ml, respectively. Conclusion: Therefore chitosan nanoparticles could be applied as carrier for decreasing the dose of antibacterial agents in the infections.
Concise Review: Mesenchymal Stem Cell Tumor‐Homing: Detection Methods in Disease Model Systems

Despite the decline in U.S. cancer incidence and mortality rates, cancer remains the number one cause of death for people under the age of 85 and one in four people in the U.S. will die of cancer, mainly because of metastasis. Recently, interest in mesenchymal stem cell (MSC) tumor‐homing has led to inquires into: (a) why MSCs home to tumors, (b) what the inherent protumor and antitumor consequences are, and (c) how to best capitalize on MSC tumor‐homing for cell‐based diagnostics and therapy. Here, these questions are reviewed and method for addressing them using animal models and tracking methodologies (or, synonymously, detection methodologies) are discussed. First, MSCs in a regenerative and tumor‐homing context are reviewed, followed by MSC delivery and genetic labeling methods for tissue model systems. Finally, the use of the nonoptical methods, magnetic resonance imaging, positron emission tomography, and single photon emission computed tomography, along with optical methods, fluorescence imaging and bioluminescent imaging, are reviewed related to tracking MSCs within disease model settings. The benefits and drawbacks of each detection method in animal models is reviewed along with the utility of each for therapeutic use. STEM CELLS 2011;29:920–927
Cash Flow and Investment: Evidence from Internal Capital Markets

Using data from the 1986 oil price decrease, I examine the capital expenditures of non-oil subsidiaries of oil companies. I test the joint hypothesis that 1) a decrease in cash/collateral decreases investment, holding fixed the profitability of investment, and 2) the finance costs of different parts of the same corporation are interdependent. The results support this joint hypothesis: oil companies significantly reduced their non-oil investment compared to the median industry investment. The 1986 decline in investment was concentrated in non-oil units that were subsidized by the rest of the company in 1985.
Compact stub type microstrip bandpass filter using defected ground plane

Usually a defected ground plane structure (DGS) provides only a band-reject response. However, in this work we introduce a simple band-accept circuit element in the DGS and developed a microstrip stub type compact 3-pole bandpass filter (BPF) at 4.2 GHz. The BPF has bandwidth and insertion loss 38% and 0.6 dB respectively. It has better than 25 dB rejection in the stopband up to 12 GHz.
Serum cystatin C: A useful marker of kidney function in very old people

Abstract Background: Serum creatinine-based estimates of GFR may be inaccurate in the elderly and there is need for improvement. Serum Cystatin C, not being influenced by muscle volume, may be more accurate. Material and methods: GFR was measured with plasma clearance of iohexol in 50 elderly persons aged >70 years. Blood tests were drawn for analysis of creatinine, albumin and urea. Cystatin C was analysed on frozen specimens using the Dade Behring method. GFR estimates based on cystatin C were compared to estimates based on serum creatinine, using earlier published equations. Results: Significant increase with age was found with cystatin C (rs=0.62, p<0.0001) and urea (rs=0.43, p=0.0018) but no correlation with creatinine (rs=0.05, p=0.7502). All equations underestimated GFR with a bias ranging from −2.2 to −31%. The equation with the greatest accuracy was the Hoek equation (Cystatin C based) with 98% of estimates within 30% of mGFR and confidence interval 89–100%. Estimated GFR using the MDRD Study equations (creatinine based) showed accuracy of 94% with 4 or 6 factors used. There was a gender difference with an accuracy higher among males (p<0.002). The Cockcroft Gault equation was not found useful with high bias and a low accuracy. Conclusion: S-cystatin C seems a useful marker for kidney function in the elderly. Two equations based on serum cystatin C as well as the two MDRD equations seem adequate for estimating kidney function.
Molecular Basis for the Dual Mitochondrial and Cytosolic Localization of Alanine:Glyoxylate Aminotransferase in Amphibian Liver Cells*

To gain further insights into the molecular basis of the evolution of alanine:glyoxylate aminotransferase (AGT) intracellular targeting in vertebrates, we have studied the molecular basis of its dual mitochondrial and cytosolic distribution in amphibian liver cells. The AGT gene in Xenopus laevis encodes a polypeptide of 415 amino acids, which includes a 24-residue N-terminal mitochondrial targeting sequence (MTS), at either end of which are located two in-frame potential translation start sites. This MTS is necessary to target Xenopus AGT and sufficient to target a green fluorescent fusion protein to mitochondria in transfected COS cells. The C-terminal tripeptide (KKM), despite being similar to the nonconsensus type 1 peroxisomal targeting sequence in human AGT (KKL), was unable to target Xenopus AGT or human AGT to peroxisomes. The Xenopus AGT gene produces two types of transcript. The longer form encodes a polypeptide that contains the MTS and is targeted to mitochondria. The shorter form encodes a polypeptide that does not contain the MTS and remains in the cytosol. These results are discussed not only in terms of the molecular evolution of AGT targeting but also in terms of the ancillary requirements for the peroxisomal targeting of human AGT.
Predictors of HIV disclosure to secondary partners and sexual risk behavior among a high-risk sample of HIV-positive MSM: results from six epicenters in the US

Abstract This study sought to identify predictors of HIV disclosure and serodiscordant unprotected anal intercourse (SDUAI) among HIV-positive men who have sex with men (MSM). Between January 2005 and April 2006, 675 HIV-positive MSM were recruited into the Positive Connections intervention trial held in six US cities with intentional over-sampling of HIV-positive MSM of Color (74%) and men engaging in unprotected anal intercourse (UAI) in the previous year. Baseline survey data showed 30 and 31%, respectively, of participants disclosed to none or some of their secondary sex partners in the last 90 days. Greater disclosure to secondary partners was associated with having fewer sexual partners, being extremely out as MSM, longer HIV diagnosis, knowledge of CD4 count, detectable viral load and being white. Disclosure to all secondary partners was associated with lower SDUAI. Recommendations for prevention for HIV-positive MSM include the promotion of serodisclosure to all secondary partners and increasing comfort with, and outness about, one's sexuality.
EARLY SENESCENCE1 Encodes a SCAR-LIKE PROTEIN2 That Affects Water Loss in Rice1[OPEN]

An actin nucleation protein affects water loss by regulating stomatal density. The global problem of drought threatens agricultural production and constrains the development of sustainable agricultural practices. In plants, excessive water loss causes drought stress and induces early senescence. In this study, we isolated a rice (Oryza sativa) mutant, designated as early senescence1 (es1), which exhibits early leaf senescence. The es1-1 leaves undergo water loss at the seedling stage (as reflected by whitening of the leaf margin and wilting) and display early senescence at the three-leaf stage. We used map-based cloning to identify ES1, which encodes a SCAR-LIKE PROTEIN2, a component of the suppressor of cAMP receptor/Wiskott-Aldrich syndrome protein family verprolin-homologous complex involved in actin polymerization and function. The es1-1 mutants exhibited significantly higher stomatal density. This resulted in excessive water loss and accelerated water flow in es1-1, also enhancing the water absorption capacity of the roots and the water transport capacity of the stems as well as promoting the in vivo enrichment of metal ions cotransported with water. The expression of ES1 is higher in the leaves and leaf sheaths than in other tissues, consistent with its role in controlling water loss from leaves. GREEN FLUORESCENT PROTEIN-ES1 fusion proteins were ubiquitously distributed in the cytoplasm of plant cells. Collectively, our data suggest that ES1 is important for regulating water loss in rice.
Expression of netrin-1 and its receptors, deleted in colorectal cancer and uncoordinated locomotion-5 homolog B, in rat brain following focal cerebral ischemia reperfusion injury

Netrin-1 is currently one of the most highly studied axon guidance factors. Netrin-1 is widely expressed in the embryonic central nervous system, and together with the deleted in colorectal cancer and uncoordinated locomotion-5 homolog B receptors, netrin-1 plays a guiding role in the construction of neural conduction pathways and the directional migration of neuronal cells. In this study, we established a rat middle cerebral artery ischemia reperfusion model using the intraluminal thread technique. Immunofluorescence microscopy showed that the expression of netrin-1 and deleted in colorectal cancer in the ischemic penumbra was upregulated at 1 day after reperfusion, reached a peak at 14 days, and decreased at 21 days. There was no obvious change in the expression of uncoordinated locomotion-5 homolog B during this time period. Double immunofluorescence labeling revealed that netrin-1 was expressed in neuronal cells and around small vessels, but not in astrocytes and microglia, while deleted in colorectal cancer was localized in the cell membranes and protrusions of neurons and astrocytes. Our experimental findings indicate that netrin-1 may be involved in post-ischemic repair and neuronal protection via deleted in colorectal cancer receptors.
Estimating Return on Initial Public Offering Using Mixtures of Regressions

Financial advisors working in a stock exchange market are often faced with a situation to convince a client of merits of investing in a company that just entered the market. To predict company’s return based on its revenue, a simple linear regression may be used. This thesis finds that a model based on a mixture regressions is superior over a simple linear regression. The error term in each regression component is assumed to follow standard Gaussian distribution. The data is tested on 116 companies that entered the market as Initial Public Offering (IPO). A 2-component mixture regressions is found to provide the best fit for the data. A simulation study is conducted to verify the performance of this model. Optimum number of components is found using Akaike Information Criterion (AIC) and Bayesian Information Criterion (BIC) as well as the parametric bootstrapping of the likelihood ratio test statistics.
Domestic Sources of Transnational Climate Governance

ABSTRACT Transnational climate governance (TCG) is an example of complex governance in which national governments no longer serve as reliable gatekeepers between nonstate and subnational actors and global governance. The articles in this special issue demonstrate that TCG and complex governance do not eliminate the importance of domestic political institutions and actors in explaining national variation in engagement with TCG. Rich democracies provide the most favorable political setting for participation in TCG. National policies that favor climate change mitigation produce greater engagement with TCG on the part of nonstate and subnational actors. The same political ecology that produces favorable national policies supports TCG participation: NGO presence and activism, affluent consumers that encourage corporations to engage with TCG, subnational governments with political incentives and fiscal space to undertake cross-border activism. Although direct effects by TCG on greenhouse gas emissions may be limited, TCG may have longer-run and second-order effects that are larger, particularly if commitments are more precise and binding. Overall, TCG illustrates a complementary rather than competitive relationship between national governments and complex governance, a relationship that should be investigated in other issue areas.
Risk of Spontaneous Preterm Birth is Associated With Common Proinflammatory Cytokine Polymorphisms

Background: Preliminary data suggest that common genetic variation in immune response genes can contribute to the risk for spontaneous preterm birth and possibly small-for-gestational age (SGA). Methods: We investigated the relationship of polymorphisms in 6 cytokine genes associated with inflammation—interleukin (IL)1α, IL1β, IL2, IL6, tumor necrosis factor (TNF), and lymphotoxin α (LTA)—with spontaneous preterm and SGA birth in a nested case–control study drawn from a prospective pregnancy cohort. Women were recruited between 24 and 29 weeks' gestation at the Wake County and University of North Carolina, Chapel Hill obstetric clinics between February 1996 and June 2000. We inferred haplotypes using the EM algorithm and the Bayesian method, PHASE. We then compared haplotype frequency distributions and implemented semi-Bayesian hierarchical logistic regression analyses to obtain odds ratio (OR) estimates and 95% confidence intervals (CIs) for each polymorphism. Results: Two haplotypes spanning the TNF/LTA genes were associated with increased risk for spontaneous preterm birth in white subjects (for the AGG haplotype, OR = 1.5 [95% CI=0.8–2.6]; for the GAC haplotype, 1.6 [0.9–2.9]). Additionally, carriers of the GAG haplotype were found to have decreased risk of spontaneous preterm birth (0.6; 0.3–1.0). The TNF(−488)A and LTA(IVS1−82)C variants, constituents of the AGG and GAC haplotypes respectively, were also strongly associated with increased risk of spontaneous preterm birth. Conclusions: Our results suggest that common genetic variants in proinflammatory cytokine genes could influence the risk for spontaneous preterm birth. Selected TNF/LTA haplotypes were associated with spontaneous preterm birth in both African-American and white subjects. Our data do not support an inflammatory etiology forSGA.