Miracle-dz/UniFAR-FTUs huggingface dataset:
The level of c-fgr RNA is increased by EBNA-2, an Epstein-Barr virus gene required for B-cell immortalization

The efficient immortalization of primary resting human B lymphocytes by Epstein-Barr virus (EBV) requires several viral genes and presumably the altered expression of an unknown number of cellular genes as well. In this paper, I show that infection of primary human B cells with EBV increased the transcript level of the proto-oncogene, c-fgr, 10-fold. This effect on the level of c-fgr transcripts in B cells was not secondary to blast formation, because levels of c-fgr RNA were also increased 10-fold in two proliferating EBV-negative Burkitt's lymphoma-derived cell lines, Ramos and BJAB, 2 days after infection with EBV. Two lines of evidence indicated that EBV nuclear antigen 2 (EBNA-2) mediates this increase in c-fgr RNA levels: acute infection of BJAB and Ramos cells by a mutant strain of EBV that lacked the EBNA-2 open reading frame, P3HR1, did not affect c-fgr RNA levels; and cell lines constitutively expressing only the EBNA-2 gene of EBV had increased levels of c-fgr RNA relative to those in the parental cell lines. Since P3HR1, a nonimmortalizing strain of EBV, failed to affect c-fgr RNA levels and since a viral gene required for B-cell immortalization was responsible for the induction of c-fgr, the data indicate a possible role of c-fgr expression in B-lymphocyte immortalization by EBV and a mechanism by which EBNA-2 contributes to the immortalizing activity of EBV.
Regrets Associated with Providing Healthcare: Qualitative Study of Experiences of Hospital-Based Physicians and Nurses

Background Regret is an unavoidable corollary of clinical practice. Physicians and nurses perform countless clinical decisions and actions, in a context characterised by time pressure, information overload, complexity and uncertainty. Objective To explore feelings associated with regretted clinical decisions or interventions of hospital-based physicians and nurses and to examine how these regrets are coped with. Method Qualitative study of a volunteer sample of 12 physicians and 13 nurses from Swiss University Hospitals using semi-structured interviews and thematic analysis Results All interviewees reported at least one intense regret, which sometimes led to sleep problems, or taking sickness leave. Respondents also reported an accumulation effect of small and large regrets, which sometimes led to quitting one's unit or choosing another specialty. Respondents used diverse ways of coping with regrets, including changing their practices and seeking support from peers and family but also suppression of thoughts related to the situation and ruminations on the situation. Another coping strategy was acceptance of one's limits and of medicine's limits. Physicians reported that they avoided sharing with close colleagues because they felt they could lose their credibility. Conclusions Since regret seems related to both positive and negative consequences, it is important to learn more about regret coping among healthcare providers and to determine whether training in coping strategies could help reduce negative consequences such as sleep problems, absenteeism, or turnover.
Research on the Routing Algorithm Based on QoS Requirement for Cognitive Radio Networks

Cognitive radio network has received increasing attention in recent few years. Cognitive radio network is viewed as a novel network for improving the utilization of a precious natural resource: the radio electromagnetic spectrum. This paper first gives a general overview of the background and concept of cognitive radio network. Then we focus on the routing algorithm based on the QoS requirement. In this paper, the characteristic of QoS requirement and the mathematical model of cognitive radio network are investigated. Finally, a novel term s which considers the effect of the bandwidth and the delay is introduced. We can take into account the term s for the QoS requirement of each session in future work, which means just a fixed value of s, rather than the bandwidth and the delay, will be requested when we provide our QoS requirement for a session.
Impact of country of birth on genetic testing of metastatic lung adenocarcinomas in France: African women exhibit a mutational spectrum more similar to Asians than to Caucasians

Background Limited data are available on the prevalence of oncogenic driver mutations in Caucasian populations, and especially in Europeans. Aim To evaluate the targetable mutational spectra in unselected patients with lung adenocarcinoma in routine clinical practice from several French hospitals, using the same molecular platform. Patients and Methods Samples from 2,219 consecutive patients with histologically-proven advanced lung adenocarcinoma were centrally analysed at a referenced and certified diagnostic platform in order to test for activating and resistance mutations in EGFR, KRAS, BRAF, ERBB2 and PI3KCA. Demographic and clinical features were retrieved from the medical charts. Multivariate binary logistic regression was used to determine the independent predictive factors for the occurrence of specific mutations, in the whole study population or in selected subgroups. Findings The overall respective incidence of EGFR, KRAS, BRAF, ERBB2 and PI3KCA mutations was 10.5%, 0.9%, 25%, 1.5%, 2.1% and 1.4%, in our study sample including 87.4% white Caucasians, 10.8% Africans and 1.8% Asians; 60.6% men, 30.7% never smoker (median age: 68.3 years). Ethnicity was an independent predictor for EGFR, KRAS and ERBB2 gene abnormalities. In all cases, a significantly higher prevalence of targetable EGFR and ERBB2, and a lower prevalence of resistance KRAS mutations were observed in African women as compared to African men or Caucasians. Conclusions In real life conditions of routine genetic testing, we have identified subsets of patients with specific targetable activating somatic mutations according to ethnicity, who could preferentially benefit from anti-EGFR and anti-ERBB2 targeted therapies.
Does rTMS hasten the response to escitalopram, sertraline, or venlafaxine in patients with major depressive disorder? A double-blind, randomized, sham-controlled trial.

BACKGROUND/OBJECTIVE Repetitive transcranial magnetic stimulation (rTMS) has been mainly studied as adjunctive treatment for drug-resistant patients. We assessed the effectiveness of rTMS started concomitantly with antidepressant medications in non-drug-resistant major depressive disorder patients. We also evaluated if, among the 3 antidepressants administered, one had a better synergy with rTMS. METHOD In this 5-week, double-blind, randomized, sham-controlled study, we recruited 99 inpatients suffering from a major depressive episode (DSM-IV criteria). They were randomly assigned to receive venlafaxine, sertraline, or escitalopram in combination with a 2-week period of sham or active 15-Hz rTMS on the left dorso-lateral prefrontal cortex. Data were gathered from February 2004 to June 2005. RESULTS The active rTMS group showed a significantly faster reduction in Hamilton Rating Scale for Depression (HAM-D) scores compared with the sham group (p = .0029). The response and remission rates were significantly greater in the active rTMS group after the stimulation period (p = .002 and p = .003, respectively), but not at the endpoint. We found no significant difference in HAM-D score reduction among the 3 drugs administered, either in the active or in the sham group. CONCLUSION These findings support the efficacy of rTMS in hastening the response to antidepressant drugs in patients with major depressive disorder. The effect of rTMS seems to be unaffected by the specific concomitantly administered drug.
Identification of the Avian Pasteurella multocida phoP Gene and Evaluation of the Effects of phoP Deletion on Virulence and Immunogenicity

Pasteurella multocida (P. multocida) is an animal pathogen of worldwide economic significance that causes fowl cholera in poultry and wild birds. Global gene regulators, including PhoP are important in regulating bacterial virulence and are good targets for developing attenuated vaccines against many pathogenic bacteria. However, the biological significance of phoP gene has not been identified in P. multocida. Here, we identified the phoP gene in P. multocida, and we evaluated the roles of phoP in P. multocida by deleting the phoP gene. The P. multocida phoP mutant exhibited similar growth curves and lipopolysaccharide and outer membrane protein profiles but displayed defective polymyxin resistance in vitro compared with the parent strain. Additionally, the phoP deletion resulted in decreased virulence. The LD50 of the ΔphoP mutant was 32- and 154-fold higher than the parent strain via the oral and intranasal routes, respectively. Transcriptome sequencing analysis showed that 161 genes were up-regulated and 173 genes were down-regulated in the absence of the phoP gene. Finally, the immunogenicity and protective efficacy of the ΔphoP mutant were evaluated. Immunized ducks produced significantly higher levels of serum IgY and bile IgA compared to the control ducks, and immunization with the ΔphoP mutant conferred 54.5% protection efficiency against challenge with the virulent P. multocida. This work provides a platform to dissect the function of phoP and develop a new vaccine against P. multocida.
Concordance between timeline follow-back and single-question assessment of self-reported smoking in a clinical trial

Background: Smoking cessation clinical trials assess tobacco abstinence using self-report and biomarkers. Optimum methods for each are unclear; a common question assesses smoking in the prior 7 days. In contrast, timeline follow-back (TLFB) is another technique often used to assess use of alcohol in treatment trials; it is used less frequently in studies of smoking cessation. The goal of this study was to assess concordance between the 7-day smoking question and a 7-day TLFB. Methods: Secondary analysis of data from a randomized clinical trial of smoking cessation was conducted at a busy, urban hospital emergency department (ED) from October 2010 to December 2012. At 1, 3, and 12 months, subjects were contacted by phone to assess smoking status. Those reporting abstinence at 3 months were asked to return for an in-person measurement of exhaled carbon monoxide. For this analysis, smoking status at 1 month was compared for subjects in response to 2 questions asked concurrently, addressing 7-day point prevalence tobacco use and a 7-day TLFB. Results: Of 780 subjects, 666 (85.4%) were available for 1-month follow-up. Of these, 99 (14.9%) reported no smoking in response to the 7-day question, and 96 (14.4%) reported no smoking in response to the 7-day TLFB. The overall proportionate agreement between the 2 methods was 98.6%, with a kappa of 0.95 (95% confidence interval [CI]: 0.91–0.98). Conclusions: A single question that assesses smoking at 7 days provides excellent concordance with the more detailed TLFB. The single question appears adequate to assess self-reported tobacco use in clinical trials of smoking cessation.
Assessment of multiple cardiac biomarkers in non-ST-segment elevation acute coronary syndromes: observations from the MERLIN-TIMI 36 trial.

AIMS The aim of this study is to simultaneously evaluate the incremental prognostic value of multiple cardiac biomarkers reflecting different underlying pathophysiological processes in a well-characterized population of patients with non-ST-segment acute coronary syndrome (NSTE-ACS). METHODS AND RESULTS We measured cardiac troponin I (cTnI), N-terminal pro B-type natriuretic peptide (NT-proBNP), C-reactive protein, and myeloperodixase (MPO) among 4352 patients with NSTE-ACS in the MERLIN-TIMI 36 (Metabolic Efficiency With Ranolazine for Less Ischaemia in Non-ST Elevation Acute Coronary-Thrombolysis In Myocardial Infarction 36) trial and followed them for a mean of 343 days. When added individually to a multivariable model adjusted for clinical characteristics, the risk of cardiovascular (CV) death rose in a stepwise fashion with increasing quartiles of each biomarker, and when using their pre-defined cut-points [HR(adj) 2.71 (P < 0.001) for cTnI ≥0.03 ng/mL; HR(adj) 3.01 (P < 0.001) for NT-proBNP ≥400 pg/mL; HR(adj) 1.45 (P = 0.019) for high-sensitivity (hs) C-reactive protein ≥15 mg/L; and HR(adj) 1.49 (P = 0.006) for MPO ≥670 pmol/L]. After including all biomarkers, only NT-proBNP and cTnI were independently associated with CV death, and only cTnI with myocardial infarction (MI). The addition of NT-proBNP to a model adjusted for TIMI risk score incorporating cTnI significantly improved both the discrimination and re-classification of the model for CV death and heart failure (HF) while there was no such improvement after the addition of either MPO or hs-C-reactive protein. CONCLUSION In this study of over 4300 patients presenting with NSTEACS, we found that both cTnI and NT-proBNP offer prognostic information beyond that achieved with clinical risk variables for CV death, MI, and HF. Myeloperoxidase and hs-C-reactive protein, while independently associated with some adverse CV outcomes, did not provide substantial incremental prognostic information when evaluated together with cTnI and NT-proBNP.
Composition Measurements near the Second Knee with the Telescope Array Low-Energy Extension ( TALE )

Cosmic rays with energies between 10 and10 eV exhibit a rich range of features. The energy spectrum changes index at at least two points, known as the “se cond knee” and the “ankle”. There may be a composition change in this energy regime as well, perhaps indicati ve of a shift in predominance from galactic to extragalactic sources. The Telescope Array Low -Energy Extension — planned for construction in Millard County, Utah, USA — stands well poised to make decisi ve simultaneous measurements of cosmic ray energy spectra and composition in this transition r egion. Here, we present the results of simulation studies relevant to the design of the TALE detectors, an d estimate the sensitivity of TALE to composition changes in the 10 eV decade.
Matrix compression using the Nyström method

The Nystr\"{o}m method is routinely used for out-of-sample extension of kernel matrices. We describe how this method can be applied to find the singular value decomposition (SVD) of general matrices and the eigenvalue decomposition (EVD) of square matrices. We take as an input a matrix $M\in \mathbb{R}^{m\times n}$, a user defined integer $s\leq min(m,n)$ and $A_M \in \mathbb{R}^{s\times s}$, a matrix sampled from the columns and rows of $M$. These are used to construct an approximate rank-$s$ SVD of $M$ in $O\left(s^2\left(m+n\right)\right)$ operations. If $M$ is square, the rank-$s$ EVD can be similarly constructed in $O\left(s^2 n\right)$ operations. Thus, the matrix $A_M$ is a compressed version of $M$. We discuss the choice of $A_M$ and propose an algorithm that selects a good initial sample for a pivoted version of $M$. The proposed algorithm performs well for general matrices and kernel matrices whose spectra exhibit fast decay.
Introduction to Text Summarization and Other Information Access Technologies

In recent years we have witnessed an explosion of on-line unstructured information in multiple languages, making natural language processing technologies such as automatic text summarization increasingly important for the information society. Text Summarization provides users with condensed descriptions of documents, allowing them to make informed decisions based on text summaries. Text summarization can be combined with Information Retrieval (IR) and Question Answering (QA) to provide users with focus-based or query-based summaries which are targeted towards the users’ speciﬁc needs. When the information a user looks for is spread across multiple sources, text summarization can be used to condense facts and present a non-redundant account of the most relevant facts found across a set of documents. The objective of this IJCNLP 2008 tutorial is to give an overview of a number of technologies in natural language processing for information access including: single and multi-document summarization, cross-lingual summarization; and summarization in the context of question answering. The tutorial will discuss summarization concepts and techniques as well as its relation and relevance to other technologies such as information retrieval and question answering. It will also include description of available resources for development, training and evaluation of summarization components. A summarization (multi-document and multilingual) toolkit will be used for demonstration purposes. A number of question answering components relevant for the creation of deﬁnitional summaries and proﬁles will also be demonstrated.
A Users Guide to the Optimality Interpreter: A Software Tool for Optimality Theoretic Analysis ; CU-CS-734-94

Optimality Theory (Prince & Smolensky 1993) is a constraint-based formalism that has been successfully applied to the explanation of various phenomena of language in the areas of both phonology and syntax. While OT is not inherently computational, it requires some symbol manipulation, and so lends itself to facilitation through software that can aid in the design of optimality theoretic solutions. Such a software application, the Optimality Interpreter, is described in this document. The Interpreter allows for the specification of constraints and competing candidates, as well as valuation of the well-formedness of candidates vis-à-vis the constraints. Constraint orderings can be used to determine the most harmonic candidates, or the Interpreter can determine the existence of a constraint ordering that will force a specified candidate to win. In addition, the interaction of candidate sets can be explored, with implications for the explanation or definition of language typologies. This document describes the functionality of the Optimality Interpreter, provides a detailed tutorial of its application to a problem in syntax from the literature, and discusses the algorithms and data structures underlying the application’s implementation. A user's manual is included as an appendix.
Phenolic alkaloids from Menispermum dauricum inhibits BxPC-3 pancreatic cancer cells by blocking of Hedgehog signaling pathway

Background: The Hedgehog (Hh) signaling pathway plays an important role in pancreatic cancer (PC) cells. Phenolic alkaloids from Menispermum dauricum (PAMD), a traditional Chinese medicine used for the treatment of immune disorders, have been reported to have antitumor activity recently. Objective: To investigate the efficacy and mechanism of PAMD against PC cell BxPC-3. Materials and Methods: F assay was used to assess cell proliferation inhibition of PAMD; the apoptotic induction and cell cycle arrest was detected by flow cytometry; the BxPC-3 xenograft was established to evaluate the tumor growth inhibition of PAMD; hematoxylin-eosin staining was applied to analyze the pathological morphology of tumor tissues; immunohistochemistry (IHC) and Western blot was adopted to detect the protein levels; quantitative real-time polymerase chain reaction was used to determine the mRNA expressions. Results: PAMD shows time-and dose-dependent proliferation inhibition on the BxPC-3 cell, induced G0/G1 phase arrest and cell apoptosis in vitro. PAMD also showed better inhibition of tumor growth and a preferable safety profile compared with chemotherapeutic regimen 5-fluoro-2, 4 (1 H, 3 H) pyrimidinedione in BxPC-3 xenograft in vivo. Furthermore, PAMD directly decreases the protein and mRNA levels of Sonic Hedgehog (Shh) and its downstream transcription factor Gli-1 in the BxPC-3 tumor tissues. Conclusion: The treatment of PAMD displayed Hh signaling pathway blockade through decreasing the protein and mRNA levels of Shh and its downstream transcription factor Gli-1, suggesting a promising strategy in treating human PC.
Interference of the End

The results of three experiments reveal that memory for end enjoyment, rather than beginning enjoyment, of a pleasant gustatory experience determines how soon people desire to repeat that experience. We found that memory for end moments, when people are most satiated, interferes with memory for initial moments. Consequently, end moments are more influential than initial moments when people decide how long to wait until consuming a food again. The findings elucidate the role of memory in delay until repeated consumption, demonstrate how sensory-specific satiety and portion sizes influence future consumption, and suggest one process by which recency effects influence judgments and decisions based on past experiences.
Distribution of Clinically Relevant Borrelia Genospecies in Ticks Assessed by a Novel, Single-Run, Real-Time PCR

ABSTRACT A LightCycler-based PCR protocol was developed which targets the ospA gene for the identification and quantification of the different Borrelia burgdorferi sensu lato species in culture and in ticks, based on the use of a fluorescently labeled probe (HybProbe) and an internally labeled primer. The detection limit of the PCR was 1 to 10 spirochetes. A melting temperature determined from the melting curve of the amplified product immediately after thermal cycling allowed the differentiation of the three different B. burgdorferi sensu lato genospecies (B. burgdorferi sensu stricto, Borrelia garinii, and Borrelia afzelii) that are clinically relevant in Europe in a single PCR run. This method represents a simplified approach to study the association of different Borrelia species in ticks, the risk of Lyme borreliosis, and the putatively species-specific clinical sequelae. To determine the reliability of the real-time PCR protocol, we studied the prevalence of B. burgdorferi sensu lato infection in Ixodes ricinus ticks. A total of 1,055 ticks were collected by flagging vegetation in five different sites in the region of Konstanz (south Germany) and were examined for the distribution of B. burgdorferi species by real-time PCR. The mean infection rate was 35%. Of 548 adult ticks, 40% were positive, and of 507 nymphs, 30% were positive. The predominant genospecies (with 18% mixed infections) in the examined areas was B. afzelii (53%), followed by B. garinii (18%) and B. burgdorferi sensu stricto (11%); 0.8% of the infecting Borrelia could not be identified.
Compressed Sensing via Universal Denoising and Approximate Message Passing

We study compressed sensing (CS) signal reconstruction problems where an input signal is measured via matrix multiplication under additive white Gaussian noise. Our signals are assumed to be stationary and ergodic, but the input statistics are unknown; the goal is to provide reconstruction algorithms that are universal to the input statistics. We present a novel algorithm that combines: (i) the approximate message passing (AMP) CS reconstruction framework, which converts the matrix channel recovery problem into scalar channel denoising; (ii) a universal denoising scheme based on context quantization, which partitions the stationary ergodic signal denoising into independent and identically distributed (i.i.d.) subsequence denoising; and (iii) a density estimation approach that approximates the probability distribution of an i.i. d. sequence by fitting a Gaussian mixture (GM) model. In addition to the algorithmic framework, we provide three contributions: (i) numerical results showing that state evolution holds for non-separable Bayesian sliding-window denoisers; (ii) a universal denoiser that does not require the input signal to be bounded; and (iii) we modify the GM learning algorithm, and extend it to an i.i. d. denoiser. Our universal CS recovery algorithm compares favorably with existing reconstruction algorithms in terms of both reconstruction quality and runtime, despite not knowing the input statistics of the stationary ergodic signal.