Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification, Genomic Organization, and Analysis of the Group III Capsular Polysaccharide Genes kpsD, kpsM,kpsT, and kpsE from an Extraintestinal Isolate of Escherichia coli (CP9, O4/K54/H5)

ABSTRACT Group III capsular polysaccharides (e.g., K54) of extraintestinal isolates of Escherichia coli, similar to group II capsules (e.g., K1), are important virulence traits that confer resistance to selected host defense components in vitro and potentiate systemic infection in vivo. The genomic organization of group II capsule gene clusters has been established as a serotype-specific region 2 flanked by regions 1 and 3, which contain transport genes that are highly homologous between serotypes. In contrast, the organization of group III capsule gene clusters is not well understood. However, they are defined in part by an absence of genes with significant nucleotide homology to group II capsule transport genes in regions 1 and 3. Evaluation of isogenic, TnphoA-generated, group III capsule-minus derivatives of a clinical blood isolate (CP9, O4/K54/H5) has led to the identification of homologs of the group II capsule transport genes kpsDMTE. These genes and their surrounding regions were sequenced and analyzed. The genomic organization of these genes is distinctly different from that of their group II counterparts. Although kpsK54DMTE are significantly divergent from their group II homologs at both the DNA and protein levels phoA fusions and computer-assisted analyses suggest that their structures and functions are similar. The putative proteins KpsK54M and KpsK54T appear to be the integral membrane component and the peripheral ATP-binding component of the ABC-2 transporter family, respectively. The putative KpsK54E possesses features similar to those of the membrane fusion protein family that facilitates the passage of large molecules across the periplasm. At one boundary of the capsule gene cluster, a truncated kpsM (kpsMtruncated) and its 5′ noncoding regulatory sequence were identified. In contrast to the complete kpsK54M, this region was highly homologous to the group II kpsM. Fifty-three base pairs 3′ from the end of kpsMtruncated was a sequence 75% homologous to the 39-bp inverted repeat in the IS110 insertion element from Streptomyces coelicolor. Southern analysis established that two copies of this element are present in CP9. These findings are consistent with the hypothesis that CP9 previously possessed group II capsule genes and acquired group III capsule genes via IS110-mediated horizontal transfer.
Gene induction pathways mediated by distinct IRFs during viral infection.

During viral infection, interferon-alpha/beta (IFN-alpha/beta) and many IFN-inducible genes are induced to elicit antiviral responses of the host. Using cells with a gene disruption(s) for the IRF family of transcription factors, we provide evidence that these genes, containing similar IRF-binding cis-elements, are classified into distinct groups, based on the gene induction pathway(s). The IFN-beta gene induction is dependent on either IRF-3 or IRF-7, whereas induction of the IFN-alpha gene family is IRF-7-dependent. On the other hand, ISG15, ISG54 and IP-10 are induced by either IRF-3 or IFN stimulated gene factor 3 (ISGF3). We also show that another group of genes is totally dependent on ISGF3. Thus, during viral infection, a given gene responds either directly to a virus or virus-induced IFN-alpha/beta or both through distinct pathways. The differential utilization of these induction pathways for these genes during viral infection may reflect their distinct functional roles in the efficient antiviral response.
Prognostic and clinicopathological features of E-cadherin, alpha-catenin, beta-catenin, gamma-catenin and cyclin D1 expression in human esophageal squamous cell carcinoma.

AIM To investigate the expression of E-cadherin, alpha-catenin, beta-catenin, gamma-catenin and cyclin D(1) in patients with esophageal squamous cell carcinoma (ESCC), and analyze their interrelationship with clinicopathological variables and their effects on prognosis. METHODS Expression of E-cadherin, alpha-catenin, beta-catenin, gamma-catenin and cyclin D(1) was determined by EnVision or SABC immunohistochemical technique in patients with ESCC consecutively, their correlation with clinical characteristics was evaluated and analyzed by univariate analysis. RESULTS The reduced expression rate of E-cadherin, alpha-catenin, beta-catenin and gamma-catenin was 88.7%, 69.4%, 35.5% and 53.2%, respectively. Cyclin D1 positive expression rate was 56.5%. Expression of gamma-catenin was inversely correlated with the degree of tumor differentiation and lymph node metastasis (chi(2) = 4.183 and chi(2) = 5.035, respectively, P<0.05), whereas the expression of E-cadherin was correlated only with the degree of differentiation (chi(2) = 5.769, P<0.05). Reduced expression of E-cadherin and gamma-catenin was associated with poor differentiation of tumor, reduced expression of gamma-catenin was also associated with lymph node metastasis. There obviously existed an inverse correlation between level of E-cadherin and gamma-catenin protein and survival. The 3-year survival rates were 100% and 56% in E-cadherin preserved expression group and in reduced expression one and were 78% and 48% in gamma-catenin preserved expression group and in reduced expression one, respectively. The differences were both statistically significant. Correlation analysis showed the expression level of alpha-catenin correlated with that of E-cadherin and beta-catenin (P<0.05). CONCLUSION The reduced expression of E-cadherin and gamma-catenin, but not alpha-catenin, beta-catenin and cyclin D1, implies more aggressive malignant behaviors of esophageal carcinoma cells and predicts the poor prognosis of patients.
Determining Lectin Specificity from Glycan Array Data Using Motif Segregation and GlycoSearch Software

The glycan array is a powerful tool for investigating the specificities of glycan‐binding proteins. By incubating a glycan‐binding protein on a glycan array, the relative binding to hundreds of different oligosaccharides can be quantified in parallel. Based on these data, much information can be obtained about the preference of a glycan‐binding protein for specific subcomponents of oligosaccharides, or motifs. In many cases, the analysis and interpretation of glycan array data can be time consuming and imprecise if done manually. Recently, GlycoSearch software was developed to facilitate the analysis and interpretation of glycan array data based on two previously developed methods, Motif Segregation and Outlier Motif Analysis. Here, the principles behind this method and the use of this new tool for mining glycan array data are described. The automated, objective, and precise analysis of glycan array data should enhance the value of these data for a broad range of research applications. Curr. Protoc. Chem. Biol. 5:157‐169 © 2013 by John Wiley & Sons, Inc.
innovative methodology Cluster analysis of muscle functional MRI data

Damon, Bruce M. , Danielle M. Wigmore, Zhaohua Ding, John C. Gore, and Jane A. Kent-Braun. Cluster analysis of muscle functional MRI data. J Appl Physiol 95: 1287–1296, 2003. First published May 23, 2003; 10.1152/ japplphysiol.00178. 2003. —Muscle functional magnetic resonance imaging (mfMRI) is frequently used to determine spatial patterns of muscle involvement in exercising humans. A frequent finding in mfMRI is that, even within synergistic muscle groups, signal intensity (SI) data from individual voxels can be quite heterogeneous. The purpose of this study was to develop a novel method for organizing heterogeneous mfMRI data into clusters whose members behave similarly to each other but distinctly from members of other clusters and apply it in studies of functional compartmentalization in the anterior compartment of the leg. An algorithm was developed that compared the SI time courses of adjacent voxels and grouped together voxels that were sufficiently similar. The algorithm’s performance was verified by using simulated data sets with known regional differences in SI time courses that were then applied to experimental mfMRI data acquired from six male subjects (age 22.6 0.9 yr, mean SE) who sustained isometric contractions of the dorsiflexors at 40% of maximum voluntary contraction. The experimental data were also characterized by using a traditional analysis (userspecified regions of interest from a single image), in which the relative change in SI and the contrast-to-noise ratio [CNR; 100% (SIRESTING SIACTIVE)/(noise standard deviation)] were measured. In general, clusters were found in areas in which the CNR exceeded 5. Cluster analysis made functional distinctions between regions of muscle that were not seen with traditional analysis. In conclusion, cluster analysis’s use of the full SI time course provides more sensitivity to muscle functional compartmentation than traditional analysis.
Genotype-Phenotype Associations of IL6 and PRG4 With Conjunctival Fibrosis After Glaucoma Surgery

Importance Postsurgical fibrosis is a critical determinant of the long-term success of glaucoma surgery, but no reliable biomarkers are currently available to stratify the risk of scarring. Objective To compare the clinical phenotype of patients with conjunctival fibrosis after glaucoma surgery with candidate gene expression tissue biomarkers of fibrosis. Design, Setting, and Participants In this cross-sectional study, 42 patients were recruited at the time of glaucoma surgery at the Moorfields Eye Hospital from September 1, 2014, to September 1, 2016. The participants were divided into those with fibrosis and those without fibrosis. Main Outcomes and Measures Genotype-phenotype correlations of the IL6 or PRG4 gene and detailed clinical phenotype. The IL6 and PRG4 protein expression in conjunctival tissues was also assessed using in situ immunohistochemical analysis. Central bleb area, maximal bleb area, and bleb height were graded on a scale of 1 to 5 (1 indicating 0%; 2, 25%; 3, 50%; 4, 75%; and 5, 100%). Bleb vascularity was graded on a scale of 1 to 5 (1 indicating avascularity; 2, normal; 3, mild; 4, moderate; and 5, severe hyperemia). Results A total of 42 patients were recruited during the study period; 28 participants (67%) had previously undergone glaucoma surgery (fibrotic group) (mean [SD] age, 43.8 [3.6 years]; 16 [57%] female; 22 [79%] white), and 14 participants (33%) had not previously undergone glaucoma surgery (nonfibrotic group) (mean [SD] age, 47.7 [6.9] years; 4 [29%] female; 9 [64%] white). The fibrotic group had marked bleb scarring and vascularization and worse logMAR visual acuity. The mean (SD) grades were 1.4 (0.1) for central bleb area, 1.4 (0.1) for bleb height, and 3.4 (0.2) for bleb vascularity. The IL6 gene was upregulated in fibrotic cell lines (mean, 0.040) compared with nonfibrotic cell lines (mean, 0.011) (difference, 0.029; 95% CI, 0.015-0.043; P = .003). The PRG4 gene was also downregulated in fibrotic cell lines (0.002) compared with nonfibrotic cell lines (mean, 0.109; difference, 0.107; 95% CI, 0.104-0.110; P = .03). The study found a strong correlation between the IL6 gene and the number of glaucoma operations (r = 0.94, P < .001) and logMAR visual acuity (r = 0.64, P = .03). A moderate correlation was found between the PRG4 gene and the number of glaucoma operations (r = −0.72, P = .005) and logMAR visual acuity (r = −0.62, P = .03). Conclusions and Relevance IL6 and PRG4 represent potential novel tissue biomarkers of disease severity and prognosis in conjunctival fibrosis after glaucoma surgery. Future longitudinal studies with multiple postoperative measures are needed to validate the effect of these potential biomarkers of fibrosis.
An Admission Control Mechanism for 5G LWA

To alleviate the spectrum scarcity problem in fifth-generation (5G) networks, traditional mobile data offloading schemes from long term evolution (LTE) to wireless local area networks (WLANs) have been revised by the third-generation partnership project (3GPP) in release 13, which is known as LTE-WLAN aggregation (LWA). With LWA, user equipment units (UEs) supporting both LTE and WLAN can utilize both LTE and WLAN links simultaneously. Thus, UEs under the coverage of an LWA network will be surrounded by multiple standards, such as LTE, WLAN, and LWA, along with cells of different sizes and coverage. Providing the LWA service to all UEs unconditionally may lead to serious intra-cell unfairness, degradation of system-level quality of service (QoS), and a reduction in system resource utilization. Hence, to resolve this issue, two important challenges need to be addressed: Which LTE UEs should be transferred, and how many LTE UEs need to be transferred. In this paper, we propose a user-offloading algorithm for evolved node B (eNB) hardware that smartly allocates the deprived LTE UEs and assigns the LWA service to an optimal number of UEs without degrading the QoS for existing WLAN UEs. With this proposed scheme, all LWA-preferred UEs with poor LTE performance and a good WLAN condition have the opportunity to access LWA service to improve performance. We show that the proposed scheme maximizes the throughput performance of the whole network.
Impacts of Trump tax reforms on growth, inequality and debt

Reforming the tax system of the US has become a major policy agenda of the Trump administration. After months of negotiations the “Big Six”, including the Treasury Secretary, National Economic Director, Republicans in the House and the Senate are gradually converging on the degree and scale of tax reforms. What will be the impacts of such reforms on growth, efficiency and redistribution of income among households is an issue of immense interest among the American people. We provide summary of findings of study conducted by a team of economists in the University of Hull in England and Suffolk University in Boston for the National Centre for Policy Analysis that have also been published in refereed journals.
Nitric Oxide Can Differentially Modulate Striatal Neurotransmitter Concentrations via Soluble Guanylate Cyclase and Peroxynitrite Formation

Abstract: in vivo microdialysis was used to investigate whether nitric oxide (NO) modulates striatal neurotransmitter release in the rat through inducing cyclic GMP formation via soluble guanylate cyclase or formation of peroxynitrite (ONOO‐). When NO donors, S‐nitroso‐N‐acetyl‐DL‐penicillamine (SNAP; 1 mM) or (Z)‐1‐[2‐(2‐aminoethyl)‐N‐(2‐ammonioethyl)amino]diazen‐1‐ium‐1,2‐diolate (NOC‐18; 1 mM), were retrodialysed for 15 min, acetylcholine (ACh), serotonin (5‐HT), glutamate (Glu), γ‐aminobutyric acid (GABA), and taurine levels were significantly increased, whereas those of dopamine (DA), dihydroxyphenylacetic acid (DOPAC), and 5‐hydroxyindoleacetic acid (5‐HIAA) were decreased. Only effects on ACh, 5‐HT, and GABA showed calcium dependency. Inhibition of soluble guanylate cyclase by 1H‐[1,2,4]oxadiazolo[4,3‐α]quinoxalin‐1‐one (ODQ; 100 and 200 μM) dose‐dependently reduced NO donor‐evoked increases in ACh, 5‐HT, Glu, and GABA levels. Coperfusion of SNAP or NOC‐18 with an ONOO‐ scavenger, L‐cysteine (10 mM) resulted in enhanced concentrations of Glu and GABA. On the other hand, DA concentrations increased rather than decreased, and no reductions in DOPAC and 5‐HIAA occurred. This increase in DA and the potentiation of Glu and GABA were calcium‐dependent and prevented by ODQ. Similar to NO, infusions of ONOO‐ (10 or 100 μM) decreased DA, DOPAC, and 5‐HIAA. Overall, these results demonstrate that NO increases ACh, 5‐HT, Glu, and GABA levels primarily through a cyclic GMP‐dependent mechanism. For DA, DOPAC, and 5‐HIAA, effects are determined by levels of ONOO‐ stimulated by NO donors. When these are high, they effectively reduce extracellular concentrations through oxidation. When they are low, DA concentrations are increased in a cyclic GMP‐dependent manner and may act to facilitate Glu and GABA release further. Thus, changes in brain levels of antioxidants, and the altered ability of NO to stimulate cyclic GMP formation during ageing, or neurodegenerative pathologies, may particularly impact on the functional consequences of NO on striatal dopaminergic and glutamatergic function.
Urban (Un)Sustainability: Cases of Vilnius’s Informal and Illegal Settings

The current analysis addresses cases of both informal and illegal settlements in Vilnius, Lithuania. By using semiotic means (specifically, semiotic squares), the author presents the Romani district (tabors), as well the Šnipiškės district, describing the circumstances of their emerging and comparing these cases. In addition to that, the philosophical questions about the dichotomies ‘formal/informal’, ‘temporal/eternal’, ‘order/chaos’, ‘legal/illegal’, ‘sustainable/unsustainable’ are discussed. On the one hand, illegal buildings serve as a signal about too high a barrier of bureaucracy, about a surfeit of law and even about the violation of certain rights. On the other hand, some urban districts can become illegal because of a changed urban vision reflected in a new General Plan. The paper also analyzes the issue of public interest. Additionally, the tendency of democratic society to turn into bureaucratic society is analyzed. The paper addresses sensitive issues related to sustainable development of cities, intercultural dialogue and equal opportunities.
Motivation, preference and willingness to pay for selected credence food attributes

The thesis examines consumer choices, in terms of motives, preferences and willingness to pay for credence labelled food products. The results show that consumers are willing to pay premiums for different credence claims. Thereby, the choice seems to be primarily driven by egoistic motivation, aiming for health and food safety. This, in turn, is believed to be achieved through a contaminant free production process, e.g. through organic production or no use of antibiotics in animal husbandry.
Interobserver variability in the CT assessment of honeycombing in the lungs.

PURPOSE To quantify observer agreement and analyze causes of disagreement in identifying honeycombing at chest computed tomography (CT). MATERIALS AND METHODS The institutional review board approved this multiinstitutional HIPAA-compliant retrospective study, and informed patient consent was not required. Five core study members scored 80 CT images with a five-point scale (5 = definitely yes to 1 = definitely no) to establish a reference standard for the identification of honeycombing. Forty-three observers from various subspecialties and geographic regions scored the CT images by using the same scoring system. Weighted κ values of honeycombing scores compared with the reference standard were analyzed to investigate intergroup differences. Images were divided into four groups to allow analysis of imaging features of cases in which there was disagreement: agreement on the presence of honeycombing, agreement on the absence of honeycombing, disagreement on the presence of honeycombing, and other (none of the preceding three groups applied). RESULTS Agreement of scores of honeycombing presence by 43 observers with the reference standard was moderate (Cohen weighted κ values: 0.40-0.58). There were no significant differences in κ values among groups defined by either subspecialty or geographic region (Tukey-Kramer test, P = .38 to >.99). In 29% of cases, there was disagreement on identification of honeycombing. These cases included honeycombing mixed with traction bronchiectasis, large cysts, and superimposed pulmonary emphysema. CONCLUSION Identification of honeycombing at CT is subjective, and disagreement is largely caused by conditions that mimic honeycombing.
Development and validation of the Biphasic Alcohol Effects Scale.

Alcohol produces stimulant and sedative effects, and both types of effect are thought to influence drinking practices. This article describes the development and preliminary validation of the Biphasic Alcohol Effects Scale (BAES), a self-report, unipolar adjective rating scale designed to measure both stimulant and sedative effects of alcohol. An initial pool of 12 stimulant and 12 sedative items was derived from previous alcohol effect measures, and from descriptors of intoxication generated by subjects during interviews conducted on both the ascending and descending limbs of the blood alcohol curve. This item pool was administered to a sample of sober college students twice, with a 2-week inter-test interval. Items that were difficult to comprehend, or that had high ratings or low test-retest reliability, were eliminated, resulting in a seven-item stimulant subscale and a seven-item sedative subscale. These subscales showed high internal consistency in a sober state, which was not improved by additional item deletion. The data from this study also provided a basis for revising the instructions for the BAES. The new 14-item instrument was then given to 30 male and 12 female nonalcoholics on the ascending and descending limbs of the blood alcohol curve, after the administration of either 0.75 ml/kg alcohol (males) or 0.65 ml/kg alcohol (females). Internal consistency was high for both BAES subscales on both limbs of the blood alcohol curve (Cronbach's alpha = 0.85 to 0.94), and was not improved by additional item deletion. Factor analyses conducted on both limbs of the blood alcohol curve supported the proposed factor structure of the BAES. (ABSTRACT TRUNCATED AT 250 WORDS)
Identification and Inference in First-Price Auctions with Risk-Averse Bidders and Selective Entry

We study identification and estimation in first-price auctions with risk averse bidders and selective entry, building on a flexible entry and bidding framework we call the Affiliated Signal with Risk Aversion (AS-RA) model. This framework extends the AS model of Gentry and Li (2014) to accommodate arbitrary bidder risk aversion, thereby nesting a variety of standard models as special cases. It poses, however, a unique methodological challenge – existing results on identification with risk aversion fail in the presence of selection, while the selection-robust bounds of Gentry and Li (2014) fail in the presence of risk aversion. Motivated by this problem, we translate excludable variation in potential competition into identified sets for AS-RA primitives under various classes of restrictions on the model. We show that a single parametric restriction – on the copula governing selection into entry – is typically sufficient to restore point identification of all primitives. In contrast, a parametric form for utility yields point identification of the utility function but only partial identification of remaining primitives. Finally, we outline a simple semiparametric estimator combining Constant Relative Risk Aversion utility with a parametric signal-value copula. Simulation evidence suggests that this estimator performs very well even in small samples, underscoring the practical value of our identification results.