Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmid-mediated susceptibility to intestinal microbial antagonisms in Escherichia coli

Self-transferable plasmid pIP1100 confers to Escherichia coli an unusually high level of resistance (1 to 2 mg/ml) to erythromycin by production of an erythromycin esterase. The effect of pIP1100 on the destiny of E. coli strains in the intestines of gnotobiotic mice was studied. In germfree mice, pIP1100 was efficiently transferred to a plasmid-free E. coli recipient. Intestinal counts of the donor, the recipient, and the transconjugants were greater than 8.5 log CFU/g of feces. When erythromycin was added to the diet of the mice, counts of the plasmid-bearing strains were only slightly lowered and partial inactivation of erythromycin was observed in the feces. Transfer of pIP1100 also occurred in human-flora-associated mice. In this model all the E. coli strains were subject to microbial antagonisms caused by the anaerobic components of the flora. However, strains harboring pIP1100 were strongly inhibited (less than 2.5 log CFU/g of feces), whereas their plasmid-free counterparts persisted at much higher population levels (greater than 5.2 log CFU/g of feces). The ecological disadvantage conferred by pIP1100 to E. coli when a complex human flora was concomitantly present in the intestine of the mice persisted during erythromycin administration. These results provide an explanation for the low incidence of isolation of highly erythromycin-resistant E. coli strains despite the extensive use of the antibiotic.
Efficient density estimation via piecewise polynomial approximation

We give a computationally efficient semi-agnostic algorithm for learning univariate probability distributions that are well approximated by piecewise polynomial density functions. Let p be an arbitrary distribution over an interval I, and suppose that p is τ-close (in total variation distance) to an unknown probability distribution q that is defined by an unknown partition of I into t intervals and t unknown degree d polynomials specifying q over each of the intervals. We give an algorithm that draws Õ(t(d + 1)/ε2) samples from p, runs in time poly(t, d + 1, 1/ε), and with high probability outputs a piecewise polynomial hypothesis distribution h that is (14τ + ε)-close to p in total variation distance. Our algorithm combines tools from real approximation theory, uniform convergence, linear programming, and dynamic programming. Its sample complexity is simultaneously near optimal in all three parameters t, d and ε; we show that even for τ = 0, any algorithm that learns an unknown t-piecewise degree-d probability distribution over I to accuracy ε must use [EQUATION] samples from the distribution, regardless of its running time. We apply this general algorithm to obtain a wide range of results for many natural density estimation problems over both continuous and discrete domains. These include state-of-the-art results for learning mixtures of log-concave distributions; mixtures of t-modal distributions; mixtures of Monotone Hazard Rate distributions; mixtures of Poisson Binomial Distributions; mixtures of Gaussians; and mixtures of k-monotone densities. Our general technique gives improved results, with provably optimal sample complexities (up to logarithmic factors) in all parameters in most cases, for all these problems via a single unified algorithm.
Structural Requirements for O-Glycosylation of the Mouse Hepatitis Virus Membrane Protein*

The mouse hepatitis virus (MHV) membrane (M) protein contains only O-linked oligosaccharides. We have used this protein as a model to study the structural requirements forO-glycosylation. We show that MHV M is modified by the addition of a single oligosaccharide side chain at the cluster of 4 hydroxylamino acids present at its extreme amino terminus and identified Thr at position 5 as the functional acceptor site. The hydroxylamino acid cluster, which is quite conserved amongO-glycosylated coronavirus M proteins, is not in itself sufficient for O-glycosylation. Downstream amino acids are required to introduce a functional O-glycosylation site into a foreign protein. In a mutagenic analysisO-glycosylation was found to be sensitive to some particular changes but no unique sequence motif forO-glycosylation could be identified. Expression of mutant M proteins in cells revealed that substitution of any 1 residue was tolerated, conceivably due to the occurrence of multiple UDP-N-acetylgalactosamine:polypeptideN-acetylgalactosaminyltransferases (GalNAc transferases). Indeed, MHV M served as a substrate for GalNac-T1, -T2, and -T3, as was demonstrated using an in situ glycosylation assay based on the co-expression of endoplasmic reticulum-retained forms of the GalNAc transferases with endoplasmic reticulum-resident MHV M mutants. The GalNAc transferases were found to have largely overlapping, but distinct substrate specificities. The requirement for a threonine as acceptor rather than a serine residue and the requirement for a proline residue three positions downstream of the acceptor site were found to be distinctive features.
Modulation of the Lexical–Semantic Network by Auditory Semantic Priming: An Event-Related Functional MRI Study

The current event-related fMRI study specifies the neuroanatomical correlates of semantic priming and differences in semantic relation types using an auditory primed lexical decision task (LDT). Word pairs consisted of different relation types, associations (key-chain), pure categorical relations (cow-dog), and unrelated words (table-window), as well as word-pseudoword (way-tinne) and pseudoword-pseudoword (ahurn-döva) pairs. The factor lexical status, i.e., the processing of words compared to pseudowords, was associated with activation in the middle temporal gyri and the left striatum. The factor relatedness, i.e., the contrast between unrelated and related target words, was associated with increased activation of the left inferior frontal gyrus, the deep frontal operculum bilaterally, and the middle frontal gyri. A direct contrast between the two semantic relation types indicated that the processing of purely categorical compared to associative information recruits the right precuneus, the isthmus gyrus cinguli, and the cuneus, suggesting more effortful processing of the former information type. The present data show that the factors lexical status, semantic relatedness, and type of semantic relation in a primed LDT modulate the hemodynamic response in cerebral areas that subserve auditory word recognition and subsequent lexical-semantic processing.
Rule Formats for Nominal Process Calculi

The nominal transition systems (NTSs) of Parrow et al. describe the operational semantics of nominal process calculi. We study NTSs in terms of the nominal residual transition systems (NRTSs) that we introduce. We provide rule formats for the specifications of NRTSs that ensure that the associated NRTS is an NTS and apply them to the operational specifications of the early and late pi-calculus. We also explore alternative specifications of the NTSs in which we allow residuals of abstraction sort, and introduce translations between the systems with and without residuals of abstraction sort. Our study stems from the Nominal SOS of Cimini et al. and from earlier works in nominal sets and nominal logic by Gabbay, Pitts and their collaborators.
Apolipoprotein E, Statins, and Risk of Intracerebral Hemorrhage

Background and Purpose— Apolipoprotein E (ApoE) genotypes have been associated with lobar intracerebral hemorrhage (ICH). Although statins have been associated with an increased risk of ICH, meta-analyses have not consistently shown a statin-induced risk of ICH. Here, we test whether hypercholesterolemia (HC) and ApoE polymorphisms affect the risk of ICH by statin use. Methods— The Genetic and Environmental Risk Factors for Hemorrhagic Stroke (GERFHS) study is a prospective, demographically matched case–control study of ICH. A similar study of ICH, Genetic Risks for Medication-Related Hemorrhagic Stroke (GOCHA), was used as a replication cohort. Subjects were classified as normocholesterolemia, HC without statin use, and HC with statin use. Statistical comparisons were performed using Fisher exact test, &khgr;2 tests, and the Breslow–Day test. Results— The discovery cohort consisted of 558 ICH cases and 1444 controls, and the replication cohort consisted of 1020 ICH cases and 382 controls. The association of lower risk for HC was not attenuated by statin use. Statin use was observed to confer a higher risk for lobar ICH in those carrying ApoE4/E4 and ApoE2/E4 genotypes in both discovery and replication cohorts, and a test for interaction showed a trend towards significance (P=0.11 for statin and ApoE4/E4). Conclusions— Statin use does not seem to attenuate the association of HC with decreased risk for nonlobar ICH. Our data support a gene-by-drug effect for lobar ICH, but larger sample sizes are needed to confirm the association before any clinical change is warranted. Clinical Trial Registration— URL: http://clinicaltrials.gov. Unique identifier: NCT00930280.
Hey Arent your Shoes the Ones in the 50 Cent Video? Examining the Context of Music Videos on Brand Evaluations

This paper explores the impact of product placement in music videos on young adults’ attitudes and behaviours. We find that images (the context in which brands appear) in music videos influence brand image, and that the process that influences consumers' attitudes toward the placed brand is likely nonconscious. We discuss these findings in terms of public policy, managerial and theoretical implications.
Evolutionary unit testing of object-oriented software using strongly-typed genetic programming

Evolutionary algorithms have successfully been applied to software testing. Not only approaches that search for numeric test data for procedural test objects have been investigated, but also techniques for automatically generating test programs that represent object-oriented unit test cases. Compared to numeric test data, test programs optimized for object-oriented unit testing are more complex. Method call sequences that realize interesting test scenarios must be evolved. An arbitrary method call sequence is not necessarily feasible due to call dependences which exist among the methods that potentially appear in a method call sequence. The approach presented in this paper relies on a tree-based representation of method call sequences by which sequence feasibility is preserved throughout the entire search process. In contrast to other approaches in this area, neither repair of individuals nor penalty mechanisms are required. Strongly-typed genetic programming is employed to generate method call trees. In order to deal with runtime exceptions, we use an extended distance-based fitness function. We performed experiments with four test objects. The initial results are promising: high code coverages were achieved completely automatically for all of the test objects.
Layer-by-layer nanoparticles co-loading gemcitabine and platinum (IV) prodrugs for synergistic combination therapy of lung cancer

Purpose Cisplatin plus gemcitabine (GEM) is a standard regimen for the first-line treatment of advanced non-small cell lung cancer. The aim of this study was to prepare biocompatible and biodegradable polymeric prodrugs and construct nanoparticles (NPs) with layer-by-layer (LbL) technique. Methods Platinum (Pt) (IV) complex with a carboxyl group was conjugated to the amino group of chitosan (CH), resulting in a CH-Pt conjugation with positive charge. GEM with amino group was conjugated to the carboxyl group of hyaluronic acid (HA), resulting in a HA-GEM conjugation with negative charge. Novel LbL NPs consisting of the CH-Pt core and the HA-GEM layer, named as HA-GEM/CH-Pt NPs, were constructed. The physicochemical properties of the HA-GEM/CH-Pt NPs were investigated. In vitro cytotoxicity against human non-small lung cancer cells (NCl-H460 cells) was investigated, and in vivo antitumor efficiency was evaluated on mice bearing NCl-H460 cells xenografts. Results HA-GEM/CH-Pt NPs have a size of about 187 nm, a zeta potential value of −21 mV and high drug encapsulation efficiency of 90%. The drug release of HA-GEM/CH-Pt NPs exhibited a sustained behavior. HA-GEM/CH-Pt NPs could significantly enhance in vitro cytotoxicity and in vivo antitumor effect against lung cancer animal model compared to the single-drug-loaded NPs and free drug solutions. Conclusion The results demonstrated that the HA-GEM/CH-Pt NPs might be a promising system for the synergetic treatment of lung carcinoma.
DBLSTM based multilingual articulatory feature extraction for language documentation

With more than 7,000 living languages in the world and many of them facing extinction, the need for language documentation is now more pressing than ever. This process is time-consuming, requiring linguists as each language features peculiarities that need to be addressed. While automating the whole process is difficult, we aim at providing methods to support linguists during documentation. One important step in the workflow is the discovery of the phonetic inventory. In the past, we proposed a first approach of first automatically segmenting recordings into phone-line units and second clustering these segments based on acoustic similarity, determined by articulatory features (AFs). We now propose a refined method using Deep Bi-directional LSTMs (DBLSTMs) over DNNs. Additionally, we use Language Feature Vectors (LFVs) which encode language specific peculiarities in a low dimensional representation. In contrast to adding LFVs to the acoustic input features, we modulated the output of the last hidden LSTM layer, forcing groups of LSTM cells to adapt to language related features. We evaluated our approach multilingually, using data from multiple languages. Results show an improvement in recognition accuracy across AF types: While LFVs improved the performance of DNNs, the gain is even bigger when using DBLSTMs.
Intracranial Blood Flow Velocities in Acute Ischemic Stroke

Background and Purpose Transcranial Doppler sonography (TCD) can evaluate noninvasively the blood flow velocities and patency of the main trunk of the middle cerebral artery (MCA). Using TCD we evaluated MCA patency and patterns of flow through the circle of Willis in patients with acute stroke. Methods Patients with symptoms of hemispheric stroke were evaluated with serial TCD tests during admission. The Canadian Neurological Scale was used to assess neurological deficits. In all cases computed tomographic scan, 99mTc hexamethylpropyleneamine oxime single‐photon emission computed tomography, and carotid duplex were performed, and in some cases cerebral angiography. Results Seventy‐five consecutive patients with symptoms of acute ischemic stroke (mean time, 8±4 hours) were studied. Four circle of Willis perfusion patterns were observed: normal, collateral, stenotic, and occlusive. MCA occlusion or stenosis was seen in 70% of initial TCD studies in the stroke group (n=50) but not in patients with transient ischemic attacks (n=25). Eighty‐six percent of the initial MCA occlusions had recanalized by 2 weeks after onset. Four patients, evaluated within the first 4 hours after onset, illustrated different patterns of MCA flow. TCD findings were compared with cerebral angiography, computed tomography, and single‐photon emission computed tomography. Conclusions TCD allows early differentiation of patency and natural history of MCA thromboembolic events. This may have important implications in the decision for thrombolytic therapy. (Stroke. 1994;25:1378‐1383.)
Itk and Fyn Make Independent Contributions to T Cell Activation

Itk is a member of the Btk/Tec/Itk family of nonreceptor protein tyrosine kinases (PTKs), and has been implicated in T cell antigen receptor (TCR) signal transduction. Lck and Fyn are the Src-family nonreceptor PTKs that are involved in TCR signaling. To address the question of how these members of different families of PTKs functionally contribute to T cell development and to T cell activation, mice deficient for both Itk and either Lck or Fyn were generated. The Itk/Lck doubly deficient mice exhibited a phenotype similar to that of Lck-deficient mice. The phenotype of the Itk/Fyn doubly deficient mice was similar to that of Itk deficient mice. However the Itk/Fyn doubly deficient mice exhibited a more severe defect in TCR-induced proliferation of thymocytes and peripheral T cells than did mice deficient in either kinase alone. These data support the notion that Itk and Fyn both make independent contributions to TCR-induced T cell activation.
INTERPROVINCIAL MIGRATION OF CANADIAN IMMIGRANTS

This paper is for presentation at the 27th International Population of the International Union for the Scientific Study of Population, Busan, Republic of Korea, 26 to 31 August 2013. The research was partly supported by a research grant from the Research Grants Program, Canadian Embassy, Washington, D.C. Our thanks to the Research on Immigration and Integration in the Metropolis (RIIM) program, Simon Fraser University and the Department of Sociology, University of Toronto for providing research support. Our appreciation to colleagues at Simon Fraser University, University of Toronto, and University of Victoria who provided comments and suggestions on earlier presentations of this work.
Low-complexity frequency-domain turbo equalization for single-carrier transmissions over doubly-selective channels

Single-carrier transmissions with frequency-domain equalization have gained much interest due to their comparable complexity and performance to OFDM, which conversely suffers from a high peak-to-average power ratio. In this paper, we develop a new frequency-domain block turbo equalizer for single-carrier (SC) transmissions over doubly-selective channels. The main feature of the proposed equalizer is its low complexity, which is only linear in the block length. A comparison between SC and OFDM systems with channel coding in doubly-selective channels is also given.
Neuroanatomical dissociation for taxonomic and thematic knowledge in the human brain

It is thought that semantic memory represents taxonomic information differently from thematic information. This study investigated the neural basis for the taxonomic-thematic distinction in a unique way. We gathered picture-naming errors from 86 individuals with poststroke language impairment (aphasia). Error rates were determined separately for taxonomic errors (“pear” in response to apple) and thematic errors (“worm” in response to apple), and their shared variance was regressed out of each measure. With the segmented lesions normalized to a common template, we carried out voxel-based lesion-symptom mapping on each error type separately. We found that taxonomic errors localized to the left anterior temporal lobe and thematic errors localized to the left temporoparietal junction. This is an indication that the contribution of these regions to semantic memory cleaves along taxonomic-thematic lines. Our findings show that a distinction long recognized in the psychological sciences is grounded in the structure and function of the human brain.
Patient INformation about Options for Treatment (PINOT): a prospective national study of information given to incident CKD Stage 5 patients.

BACKGROUND Informed decision-making requires the presentation of all possible courses of action; however, it is unclear what proportion of Stage 5 chronic kidney disease (CKD) patients are routinely informed of all their treatment options. The aim of this study was to determine the effect of patient and unit characteristics on the type and timing of information provided. METHODS A prospective national multi-centre study of information was given to incident pre-emptive transplant, dialysis and conservatively managed patients in Australian renal units, over a 3-month period. RESULTS Sixty-six of 73 renal units participated in the study. Seven hundred and twenty-one incident CKD Stage 5 patients including 102 who chose not to dialyse were identified. Of these, 603 (84%) were presented with information about their options prior to commencing treatment. Three quarters (n = 543) were presented with home dialysis, one-third (n = 230) pre-emptive transplantation and 65% (n = 470) were informed about conservative care as an option. Patients were more likely to receive information prior to commencing treatment if they were known to a nephrologist for more than 3 months (OR 7.29, 95% CI 3.86-13.79) or were treated in small units with < 100 dialysis patients (OR 2.40, 95% CI 1.26-4.60). The mean estimated glomerular filtration rate at the time information was first presented was 13.3 mL/min/1.73 m(2) (95% CI 12.7-13.8) and mean serum creatinine was 449 μmol/L (95% CI 431-467). CONCLUSIONS Most Australian patients were informed of their treatment options prior to starting treatment, albeit in late stage CKD. Earlier education and support for informed decision-making may help optimize the uptake of pre-emptive transplantation and home dialysis therapies.
Drug Therapy for Behavioral and Psychological Symptoms of Dementia

Dementia, which can be induced by diverse factors, is a clinical syndrome characterized by the decline of cognitive function. Behavioral and psychological symptoms of dementia (BPSD) include depression, agitation, and aggression. Dementia causes a heavy burden on patients and their caregivers. Patients with BPSD should be assessed comprehensively by practitioners and offered appropriate non-pharmacologic and pharmacologic therapy. Non-pharmacologic therapy has been recommended as the basal treatment for BPSD; however, pharmacologic therapy is required under many situations. Medications, including antipsychotic agents, antidepressants, sedative and hypnotic agents, mood stabilizers, cholinesterase inhibitors, and amantadine, are extensively used in clinical practice. We have reviewed the progression of pharmacologic therapy for BPSD.
Is Combining Contextual and Behavioral Targeting Strategies Effective in Online Advertising?

Online targeting has been increasingly used to deliver ads to consumers. But discovering how to target the most valuable web visitors and generate a high response rate is still a challenge for advertising intermediaries and advertisers. The purpose of this study is to examine how behavioral targeting (BT) impacts users’ responses to online ads and particularly whether BT works better in combination with contextual targeting (CT). Using a large, individual-level clickstream data set of an automobile advertising campaign from an Internet advertising intermediary, this study examines the impact of BT and CT strategies on users’ click behavior. The results show that (1) targeting a user with behavioral characteristics that are closely related to ads does not necessarily increase the click through rates (CTRs); whereas, targeting a user with behavioral characteristics that are loosely related to ads leads to a higher CTR, and (2) BT and CT work better in combination. Our study contributes to online advertising design literature and provides important managerial implications for advertising intermediaries and advertisers on targeting individual users.
Horizontal differentiation and price competition with sequential entry

We study a class of differentiation games a la Hotelling. Two firms choose a price and a location in the consumers’ space. The leader first chooses both variables, and the follower observes them before playing. It is shown that in such games, any equilibrium has the property that the follower always gets a greater profit (in the absence of entry barrier). An equilibrium is shown to always exist with linear costs and we qualify the equilibria with respect to the willingness to pay for the family of products. Some extensions are looked at. In particular, we investigate the effect of entry barriers on the strategies of the leader.