Miracle-dz/UniFAR-FTUs huggingface dataset:
Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins

The widely conserved protein CsrA (carbon storage regulator A) globally regulates bacterial gene expression at the post-transcriptional level. In many species, CsrA activity is governed by untranslated sRNAs, CsrB and CsrC in Escherichia coli, which bind to multiple CsrA dimers, sequestering them from lower affinity mRNA targets. Both the synthesis and turnover of CsrB/C are regulated. Their turnover requires the housekeeping endonuclease RNase E and is activated by the presence of a preferred carbon source via the binding of EIIAGlc of the glucose transport system to the GGDEF-EAL domain protein CsrD. We demonstrate that the CsrB 3′ segment contains the features necessary for CsrD-mediated decay. RNase E cleavage in an unstructured segment located immediately upstream from the intrinsic terminator is necessary for subsequent degradation to occur. CsrA stabilizes CsrB against RNase E cleavage by binding to two canonical sites adjacent to the necessary cleavage site, while CsrD acts by overcoming CsrA-mediated protection. Our genetic, biochemical and structural studies establish a molecular framework for sRNA turnover by the CsrD-RNase E pathway. We propose that CsrD evolution was driven by the selective advantage of decoupling Csr sRNA decay from CsrA binding, connecting it instead to the availability of a preferred carbon source.
Recombinant retroviruses that transduce middle T antigen cDNAs derived from polyomavirus mutants: separation of focus formation and soft-agar growth in transformation assays and correlations with kinase activities in vitro

To study correlations between cellular transformation and the biochemical properties of polyomavirus middle T antigen, middle T cDNAs have been derived from the polyomavirus mutants dl1015, dl23, and NG59b and have been introduced into rodent fibroblast cell lines by using a retrovirus vector. It was found that all three mutants are completely defective in inducing growth in soft agar but possess a range of activities in assays of focus formation on cell monolayers. Furthermore, when assays of middle T antigen-associated kinase activities were performed in vitro, a correlation between the level of associated phosphatidylinositol kinase activity and the ability of mutant middle T antigens to induce focus formation was observed. However, the association of this activity with middle T antigen does not appear to be sufficient to bring about full transformation, since the middle T antigen derived from dl1015 is completely defective for soft-agar growth but is associated with a level of phosphatidylinositol kinase activity which is comparable to that of the wild type. Therefore, some other unidentified middle T antigen function may also be required for full transformation.
Latissimus Dorsi Stimulation in Dynamic Cardiomyoplasty : How Should We Proceed ?

Improved understanding of the mechanisms of action in dynamic cardiomyoplasty (DCMP) and continued research in the stimulation of the latissimus dorsi muscle (LDM) contribute to the development of new stimulation strategies aimed at improving DCMP outcomes. Cautious initiation of LDM stimulation sooner after surgery than currently practiced may provide the patient earlier hemodynamic assistance. During training and chronic stimulation, adjustment of stimulation amplitude, number of pulses in a burst, the interval between pulses, the synchronization ratio and the synchronization delay will all have important effects on the acute and chronic contractile properties of the LDM, thus impacting its capacity to improve cardiac function. Allowing the LDM periods of rest each day can be extremely beneficial to the muscle and may ultimately improve clinical outcome. Non-invasive monitoring of LDM contraction is essential to implementing and testing new stimulation regimes. Recent development of such monitoring techniques allows safe clinical evaluation of experimentally validated concepts. This review considers each LDM stimulation parameter in terms of improving LDM function and optimizing DCMP benefit during both training and chronic stimulation phases. Post-operative stimulation techniques currently possible with today's technology are discussed in light of recent research and clinical findings.
Multi-Networks Joint Learning for Large-Scale Cross-Modal Retrieval

This paper proposes a novel deep framework of multi-networks joint learning for large-scale cross-modal retrieval. For most existing cross-modal methods, the processes of training and testing don't care about the problem of memory requirement. Hence, they are generally implemented on small-scale data. Moreover, they take feature learning and latent space embedding as two separate steps which cannot generate specific features to accord with the cross-modal task. To alleviate the problems, we first disintegrate the multiplication and inverse of some big matrices, usually involved in existing methods, into that of many sub-matrices. Each sub-matrix is targeted to dispose one pair of image-sentence, for which we further design a novel sampling strategy to select the most representative samples to construct the cross-modal ranking loss and within-modal discriminant loss functions. By this way, the proposed model consumes less memory each time such that it can scale to large-scale data. Furthermore, we apply the proposed discriminative ranking loss to effectively unify two heterogenous networks, deep residual network for images and long short-term memory for sentences, into an end-to-end deep learning architecture. Finally, we can simultaneously achieve specific features adapting to cross-modal task and learn a shared latent space for images and sentences. Extensive evaluations on two large-scale cross-modal datasets show that the proposed method brings substantial improvements over other state-of-the-art ranking methods.
Enforcement, Socioeconomic Diversity, and Tax Filing Compliance in the United States

In this paper we examine the determinants of tax filing compliance in the United States. We use county-level data on non-filing rates for the tax year 2000, obtained directly from the Internal Revenue Service. We include explanatory variables identified in the "rational compliance" framework, including an enforcement index against identified non-filers, the audit rate of filers, and the average penalty rate for both filers and non-filers. We also examine the role of socio-economic diversity on tax compliance, testing whether within-county heterogeneity in household income, language, race, and religion can help explain variation in non-filing rates. We find that non-filing is increasing with heterogeneity by race, though not by income or language, and that non-filing is decreasing with heterogeneity by religious membership. As for enforcement variables, we find that non-filing rates tend to fall with the enforcement index. Other variables have somewhat mixed results.
Cerebral venous thrombosis in adult patients with acute lymphoblastic leukemia or lymphoblastic lymphoma during induction chemotherapy with l‐asparaginase: The GRAALL experience

Central nervous system (CNS) thrombotic events are a well‐known complication of acute lymphoblastic leukemia (ALL) induction therapy, especially with treatments including l‐asparaginase (l‐ASP). Data on risk factors and clinical evolution is still lacking in adult patients. We report on the clinical evolution of 22 CNS venous thrombosis cases occurring in 708 adults treated for ALL or lymphoblastic lymphoma (LL) with the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)‐induction protocol, which included eight L‐ASP (6,000 IU/m2) infusions. The prevalence of CNS thrombosis was 3.1%. CNS thrombosis occurred after a median of 18 days (range: 11–31) when patients had received a median of three l‐ASP injections (range: 2–7). Patients with CNS thrombosis exhibited a median antithrombin (AT) nadir of 47.5% (range: 36–67%) at Day 17 (range: D3–D28), and 95% of them exhibited AT levels lower than 60%. There were no evident increase in hereditary thrombotic risk factors prevalence, and thrombosis occurred despite heparin prophylaxis which was performed in 90% of patients. Acquired AT deficiency was frequently detected in patients with l‐ASP‐based therapy, and patients with CNS thrombosis received AT prophylaxis (45%) less frequently than patients without CNS thrombosis (83%), P = 0.0002). CNS thrombosis was lethal in 5% of patients, while 20% had persistent sequelae. One patient received all planned l‐ASP infusions without recurrence of CNS thrombotic whereas l‐ASP injections were discontinued in 20 patients during the management of thrombosis without a significant impact on overall survival (P = 0.4). Am. J. Hematol. 90:986–991, 2015. © 2015 Wiley Periodicals, Inc.
Empirical tests of asset pricing models

The Capital Asset Pricing Model (CAPM) developed by Sharpe (1964) and Lintner (1965) is widely viewed as one of the most important contributions to our understanding of nance over the last 50 years. The CAPM predicts that non-diversi able risk ( ) is the only risk that matters for the pricing of assets, and that an assets expected return is a positive linear function of its non-diversi able risk. However, the empirical performance of the CAPM has been poor. This poor performance may reect theoretical failings. Alternatively, it may be due to di¢ culties in implementing valid tests of the model. This dissertation focuses on the second possibility. In the rst essay I develop a Bayesian approach to test the cross-sectional predictions of the CAPM at the rm level. Using a broad cross-section of NYSE, AMEX, and NASDAQ listed stocks over the period July 1927 June 2005, I nd evidence of a robust positive relation between and average returns. Fama and French (1993) propose two additional risk factors related to rm size and book-to-market equity. I nd no evidence that these additional risk factors help to explain the cross-sectional variation in average returns. These results are consistent with the empirical predictions of the CAPM. The use of portfolios as test assets in cross-sectional tests of asset pricing models is widespread, principally to help mitigate statistical problems. However, there is a considerable theoretical literature showing that the use of portfolios can make bad
The epidemiology of major depressive episodes: results from the International Consortium of Psychiatric Epidemiology (ICPE) surveys

Absence of a common diagnostic interview has hampered cross‐national syntheses of epidemiological evidence on major depressive episodes (MDE). Community epidemiological surveys using the World Health Organization Composite International Diagnostic Interview administered face‐to‐face were carried out in 10 countries in North America (Canada and the US), Latin America (Brazil, Chile, and Mexico), Europe (Czech Republic, Germany, the Netherlands, and Turkey), and Asia (Japan). The total sample size was more than 37,000.
Efficacy of Ronidazole for Treatment of Cats Experimentally Infected with a Korean Isolate of Tritrichomonas foetus

To evaluate the efficacy of ronidazole for treatment of Tritrichomonas foetus infection, 6 Tritrichomonas-free kittens were experimentally infected with a Korean isolate of T. foetus. The experimental infection was confirmed by direct microscopy, culture, and single-tube nested PCR, and all cats demonstrated trophozoites of T. foetus by day 20 post-infection in the feces. From day 30 after the experimentally induced infection, 3 cats were treated with ronidazole (50 mg/kg twice a day for 14 days) and 3 other cats received placebo. Feces from each cat were tested for the presence of T. foetus by direct smear and culture of rectal swab samples using modified Diamond's medium once a week for 4 weeks. To confirm the culture results, the presence of T. foetus rRNA gene was determined by single-tube nested PCR assay. All 3 cats in the treatment group receiving ronidazole showed negative results for T. foetus infection during 2 weeks of treatment and 4 weeks follow-up by all detection methods used in this study. In contrast, rectal swab samples from cats in the control group were positive for T. foetus continuously throughout the study. The present study indicates that ronidazole is also effective to treat cats infected experimentally with a Korean isolate of T. foetus at a dose of 50 mg/kg twice a day for 14 days.
Secondary Conformations and Temperature Effect on Structural Transformation of Amyloid β(1–28),(1–40) and (1–42) Peptides

Abstract Secondary structure of three amyloid β-peptides [Aβ(1–28), Aβ(1–40) and Aβ(1–42)] in the solid state was respectively determined by Fourier transform infrared (FT-IR) microspec- troscopy. Their thermal-dependent structural transformation were also investigated by FT- IR microspectroscopy equipped with a thermal analyzer. The present result demonstrates that the solid-state Aβ(1–28), Aβ(1–40) and Aβ(1–42) peptides showed a significant IR spectral difference in the amide I and II bands. The secondary conformation of Aβ(1–28) peptide was the combination of major β-sheet and minor α-helix with little random coil structures, but Aβ(1–40) peptide showed the co-existence of major β-sheet and minor random coil with little α-helix structures. Aβ(1–42) peptide mainly consisted of the predominant β-sheet structure. Although the intact Aβ(1–28), Aβ(1–40) or Aβ(1–42) peptide exhibits a different secondary structure, a similar β-conformation may form after thermal treatment. A thermal- dependent transition was found for solid Aβ(1–28) and Aβ(1–40) peptides near 40° C and 45° C, respectively. There was no transition temperature for solid Aβ(1–42) peptide, however, due to only a very little level of α-helix and random coil structure containing in the solid Aβ(1–42) peptide. The thermal denaturation plays an important role in the structural transformation from α-helix/random coil to β-sheet.
An Axiomatic Analysis of Diversity Evaluation Metrics: Introducing the Rank-Biased Utility Metric

Many evaluation metrics have been defined to evaluate the effectiveness ad-hoc retrieval and search result diversification systems. However, it is often unclear which evaluation metric should be used to analyze the performance of retrieval systems given a specific task. Axiomatic analysis is an informative mechanism to understand the fundamentals of metrics and their suitability for particular scenarios. In this paper, we define a constraint-based axiomatic framework to study the suitability of existing metrics in search result diversification scenarios. The analysis informed the definition of Rank-Biased Utility (RBU) -- an adaptation of the well-known Rank-Biased Precision metric -- that takes into account redundancy and the user effort associated to the inspection of documents in the ranking. Our experiments over standard diversity evaluation campaigns show that the proposed metric captures quality criteria reflected by different metrics, being suitable in the absence of knowledge about particular features of the scenario under study.
What Can Instructors Focus on when Improving Undergraduate Science Experiments? Supporting a Cross-Disciplinary Approach

For nearly two decades, the Australian national project Advancing Science and Engineering through Laboratory Learning (ASELL), has been using an evidence based approach to improve undergraduate experiments. This paper presents the ASELL Students Laboratory Experience (ASLE) survey, administered to 2691 students in five disciplines: biochemistry, biology, chemistry, physics, and pharmacology. The 14 item survey probes students’ perceptions of an experiment, practical or fieldwork. An exploratory factor analysis extracted two factors, ‘experiment-based motivators’ and ‘course-level resources’, and both factors correlate well with ‘overall’ learning experiences. Each survey item was also compared to the ‘overall’ learning experiences of the experiment, revealing the most critical elements of each experiment. The implications of this analysis, for practitioners is that the survey items in the ‘course-level resources’ taper off indicating that after an optimum value, further investment in these aspects do not necessarily influence student perceptions of their learning experiences. On the other hand, the survey items in the ‘experiment-based motivators’ behave differently in that they do not taper off indicating that further investment can influence experiences. How these factors relate to the overall experience suggest they correspond to the well-known two-factor theory of motivation.
Revisiting the factor structure of the strengths and difficulties questionnaire: United States, 2001.

OBJECTIVE The Strengths and Difficulties Questionnaire is a 25-item instrument developed to assess emotional and behavioral problems. The current study attempted to replicate previous European structural analyses and to describe the latent dimensions that underlie responses to the parent-reported version of the Strengths and Difficulties Questionnaire for a representative sample of U.S. children and adolescents. METHOD Parents/guardians of a national probability sample of 9,574 children and adolescents 4 to 17 years of age were administered the Strengths and Difficulties Questionnaire to assess emotional and behavioral problems within the past 1 month. A principal components analysis was performed for replication purposes, and exploratory and confirmatory factor analyses were performed to extract the underlying factors. RESULTS The predicted five-component structure (emotional, hyperactivity, prosocial, peer, conduct) was not entirely confirmed. Some items intended to assess conduct problems were more closely related to hyperactivity, and some items intended to assess peer problems were more strongly correlated with emotional or prosocial problems. Factor analyses revealed a stable three-factor model consisting of externalization problems, internalization problems, and a positive construal factor. CONCLUSIONS The current analyses suggest that U.S. parents may construe conduct problems and peer problems differently than do European parents. These cultural differences may affect the assessment of psychopathology for children.
Taking cues on multidimensional issues: the case of attitudes toward immigration

Abstract What determines popular attitudes toward immigration? Recent work emphasises the importance of education rather than economic or labour market factors. Missing from this work, however, is a consideration of elite positions. This study extends education-based accounts in two key ways: by acknowledging the multidimensional nature of the immigration issue and by incorporating cues from party elites. Cues from trusted elites inform popular attitudes on immigration. But rather than serving as a heuristic for the less sophisticated, elite cues on immigration are disproportionately employed by those more educated individuals who rely on elite positions to form opinions on multidimensional issues, like immigration, on which they are cross-pressured. Theoretical expectations are supported by evidence from cross-national analyses of party positions and public opinion and from a longitudinal examination of mass and party positions in Denmark. The results call attention to the importance of dimensionality in the formation of issue opinions.
Species–environment interactions changed by introduced herbivores in an oceanic high-mountain ecosystem

We studied the fitness of an endemic and vulnerable violet species along its altitudinal range (2,400 m - 3,500 m), and we found it to be mainly affected by inter-annual and microhabitat variability along the gradient, especially at the lowest edge. Despite the increasingly adverse environmental conditions, the plant showed no pollen limitation with elevation, which is attributed to the increase in selfing and decrease in competition for pollinators at higher elevations. Plant fitness was extremely reduced owing to the presence of non-native rabbits, which changed plant trait-environment interactions along the gradient, threatening the survival of this violet.
Sparse FIR Filter Design Based on Cascaded Compensation Structure

In this paper, a sparse FIR filter design method based on cascaded compensation structure is proposed. The proposed method is a two-stage filter design approach with novel attenuation and transition controls of the subfllters. The model filter is elaborately designed with decreasing stopband attenuation to improve the sparsity of the filter. A compensating filter with careful transition band and stopband design is cascaded with the model filter to compensate the decreasing stopband attenuation of the model filter so as to synthesize the desired uniform attenuation. Simulation results show that the proposed cascaded compensation design of sparse FIR filters leads to a significant improvement of sparsity than the exiting conventional direct form or transposed direct form filter designs.
Correlation between angiogenic/inflammatory mediators in Wister rat model of liver dysplasia

ABSTRACT Angiogenesis plays a critical role in tumor development and progression. It is regulated through the elaboration of many inflammatory/angiogenic mediators. In this study, we followed angiogenesis in hepatocarcinogenesis process from cancer initiation to sever dysplasia by measuring several inflammatory/angiogenic mediators. Wister rat model of liver cancer was set up using diethylnitrosamine (DEN). One hundred twenty rats were divided into 7 groups: normal untreated and 1- to 6-month DEN-treated animals. Every month, group of DEN-treated animals were sacrificed. Histopathological examination of livers was done. Plasma levels of vascular endothelial and platelet derived growth factors (VEGF and PDGF), interleukin-8 (IL-8), IL-4, tumor necrosis factor (TNF-α), and cyclooxygenase-2 (COX-2) were quantified by enzyme-linked immunosorbent assay (ELISA). Histopathological findings were confirmatory to the gradual formation of liver cancer with time (from mild to moderate to irreversible severe dysplasia). Increase in angiogenic (VEGF and IL-8) (P < 0.001) and inflammatory (IL-4 and COX-2) (P < 0.001) mediators were observed. Elevation in TNF-α and PDGF secretion levels was recorded after 3 months of DEN injection (P < 0.001). Our data stressed on the importance of inflammation/angiogenesis processes in dysplasia. The exact regulatory mechanisms of liver cancer remain to be clarified.