Miracle-dz/UniFAR-FTUs huggingface dataset:
A Murine Leukemia Virus (MuLV) Long Terminal Repeat Derived from Rhesus Macaques in the Context of a Lentivirus Vector and MuLVgag Sequence Results in High-Level Gene Expression in Human T Lymphocytes

ABSTRACT We constructed human immunodeficiency virus type 1 (HIV-1) vectors that will allow higher levels of gene expression in T cells. Gene expression under the control of an internal cytomegalovirus (CMV) immediate-early promoter in a self-inactivating lentiviral vector (CSCG) is 4- to 15-fold lower in T-cell lines (SUPT1 and CEMX174) than in non-lymphoid-cell lines (HeLa and 293T). This is in contrast to a Moloney murine leukemia virus (MoMLV)-based retrovirus vector (SRαLEGFP). We therefore replaced the internal CMV promoter of CSCG with three different murine oncoretroviral long terminal repeat (LTR) promoters—murine sarcoma virus (MSV), MoMLV (MLV), and the LTR (termed Rh-MLV) that is derived from the ampho-mink cell focus-forming (AMP/MCF) retrovirus in the serum of one rhesus macaque monkey that developed T-cell lymphoma following autologous transplantation of enriched bone marrow stem cells transduced with a retrovirus vector preparation containing replication-competent viruses (E. F. Vanin, M. Kaloss, C. Broscius, and A. W. Nienhuis, J. Virol. 68:4241–4250, 1994). We found that the combination of Rh-MLV LTR and a partial gag sequence of MoMLV (Δgag 871–1612) in CS-Rh-MLV-E gave the highest level of enhanced green fluorescent protein (EGFP) gene expression compared with MLV, MSV LTR, phosphoglycerate kinase, and CMV promoters in T-cell lines, as well as activated primary T cells. Interestingly, there was a further two- to threefold increase in EGFP expression (thus, 10-fold-higher expression than with CMV) when the Rh-MLV promoter and Δgag 871–1612 were used in a self-inactivating-vector setting that has a further deletion in the U3 region of the HIV-1 LTR. These hybrid vectors should prove useful in gene therapy applications for T cells.
Incremental mining of frequent sequences from a window sliding over a stream of itemsets

We introduce the problem of mining frequent sequences in a window sliding over a stream of itemsets. To address this problem, we present a complete and correct incremental algorithm based on a representation of frequent sequences inspired by the PSP algorithm and a method for counting the minimal occurrences of a sequence. The experiments were conducted on simulated data and on real instantaneous power consumption data. The results show that our incremental algorithm significantly improves the computation time compared to a non-incremental approach.
Lectures on Effective Field Theories for Nuclei, Nuclear Matter and Dense Matter

This note is based on four lectures that I gave at the 10th Taiwan Nuclear Spring School held at Hualien, Taiwan in January 2002. It aims to correlate the old notion of Cheshire Cat Principle developed for elementary baryons to the modern notion of quark-baryon and gluon-meson "continuities" or "dualities" in dilute and dense many-body systems and predict what would happen to mesons when squeezed by nuclear matter to high density as possibly realized in compact stars. Using color-flavor locking in QCD, the vector mesons observed at low density can be described as the Higgsed gluons dressed by cloud of collective modes, i.e., pions just as they are in superdense matter, thus showing the equivalence between hidden $flavor$ gauge symmetry and explicit $color$ gauge symmetry. Instead of going into details of well-established facts, I focus on a variety of novel ideas -- some solid and some less -- that could be confirmed or ruled out in the near future.
Electrical Impedance Tomography

Employment of technical equipment and devices increased intensely in anaesthesiology and intensive care medicine respectively during the last decades. Regarding mechanical ventilation, which is of outstanding clinical value up to date, lots of modes, parameters and features have been developed and technically implemented in modern respirators [1]. Although the ARDS network encouraged scientific projects concerning concepts of protective artificial respiration during the past ten years, there is still a major deficiency regarding monitoring of ventilation [2]. Up to date, there are just global and very imprecise modalities to monitor injurious impacts of ventilation to lung tissue at bedside. Since CT and MRI scans are associated with high resource consumption, the central method for controlling ventilatory settings and further treatment still is blood gas analysis and predefined algorithms (e.g. according to the ARDS network protocol).
Delay optimization of wireless networks with network coding

We address the problem of minimum average packet delay of Multi-hop Wireless Networks (MWN) which uses network coding. Our objective is to allocate capacities to different wireless nodes in a way that the average packet delay in the network is minimized under the assumption that the network topology, the traffic matrix in the network, and routing are given. Exploiting queueing theory as well as wireless interference modeling, we present an optimization that performs a non-linear search for the minimum average delay of a network. The proposed formulation, moreover, is valid both in the presence and the absence of opportunistic listening mechanisms for any pattern of flow. Our numerical results show that significant performance improvement can be achieved by using network coding.
Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation

Yan is an ETS-domain transcription factor responsible for maintaining Drosophila eye cells in a multipotent state. Yan is at the core of a regulatory network that determines the time and place in which cells transit from multipotency to one of several differentiated lineages. Using a fluorescent reporter for Yan expression, we observed a biphasic distribution of Yan in multipotent cells, with a rapid inductive phase and slow decay phase. Transitions to various differentiated states occurred over the course of this dynamic process, suggesting that Yan expression level does not strongly determine cell potential. Consistent with this conclusion, perturbing Yan expression by varying gene dosage had no effect on cell fate transitions. However, we observed that as cells transited to differentiation, Yan expression became highly heterogeneous and this heterogeneity was transient. Signals received via the EGF Receptor were necessary for the transience in Yan noise since genetic loss caused sustained noise. Since these signals are essential for eye cells to differentiate, we suggest that dynamic heterogeneity of Yan is a necessary element of the transition process, and cell states are stabilized through noise reduction. DOI: http://dx.doi. org/10.7554/eLife.08924. 001
Sampling with polyominoes

We present a new general-purpose method for fast hierarchical importance sampling with blue-noise properties. Our approach is based on self-similar tiling of the plane or the surface of a sphere with rectifiable polyominoes. Sampling points are associated with polyominoes, one point per polyomino. Each polyomino is recursively subdivided until the desired local density of samples is reached. A numerical code generated during the subdivision process is used for thresholding to accept or reject the sample. The exact position of the sampling point within the polyomino is determined according to a structural index, which indicates the polyomino's local neighborhood. The variety of structural indices and associated sampling point positions are computed during the offline optimization process, and tabulated. Consequently, the sampling itself is extremely fast. The method allows both deterministic and pseudo-non-deterministic sampling. It can be successfully applied in a large variety of graphical applications, where fast sampling with good spectral and visual properties is required. The prime application is rendering.
Factors Related to Quality of Life in Non-Hispanic White Adults

The objective of this study was to compare quality of life (QoL) and factors which relate to QoL in non-Hispanic white adults with and without type II diabetes (DM). This cross sectional study included thirty-eight participants: 19 adults aged 18 - 75 with type II diabetes and 19 healthy control adults without diabetes. Socio-demographic information was collected on age, ethnicity, marital status, education level, employment, and current health. Participants completed self-report questionnaires on activity limitations, community integration, emotional/social function, and global and specific quality of life. Performance-based tests were administered to measure grip and pinch strength, dexterity, and upper and lower extremity joint motion. t -tests were done to compare the participants with and without DM on the demographic variables, self-report questionnaires and performance based tests. Spearman rho correlation coefficients were done to determine relationships between QoL and other variables. The DM group had significantly lower levels of current health than the HC group, but there were no significant differences between other demographic variables. The DM group had significantly lower present and past QoL and specific QoL than healthy controls. The DM group also had more pain and joint limitations, decreased dexterity, poorer emotional/social function, more activity limitations and less community integration than healthy controls. In the DM group, age, pain, joint motion, emotional/social, functional disability, and community integration correlated with specific QoL. In contrast, in the HC group, pain, emotional/social, health and functional disability correlated with the specific QoL.
An exploratory qualitative study of values issues associated with training and practice in pluralistic counselling

Background A pluralistic model of practice has become increasingly influential in recent years. A distinctive feature of this approach is its explicit grounding within a philosophical and moral perspective. Aim The aim of this study was to investigate issues and challenges that pluralistic counsellors experience in relation to values dilemmas that arise in practice. Methodology Twelve practitioners, of various experience levels, who identified as pluralistic counsellors, were invited to take part in semi-structured interviews. Transcripts were analysed using a method of thematic analysis. Findings Participants viewed their personal values to be compatible with the values that they perceived pluralistic counselling to hold, and reported that they chose pluralism as a modality because they found a similarity between their personal values and the values of pluralistic counselling. Core values associated with pluralistic practice included the following: the importance of connection, ‘there is no one right way to be’, equality (not taking an expert role), honesty, and willingness to make use of research evidence. Participants also described value dilemmas, and their use of supervision in dealing with value issues. Implications The implications of these findings for training, research and practice are discussed.
Extrinsic calibration of a 2d laser-rangefinder and a camera based on scene corners

Robots are often equipped with 2D laser-rangefinders (LRFs) and cameras since they complement well to each other. In order to correctly combine measurements from both sensors, it is required to know their relative pose, that is, to solve their extrinsic calibration. In this paper we present a new approach to such problem which relies on the observations of orthogonal trihedrons which are profusely found as corners in human-made scenarios. Thus, the method does not require any specific pattern, which turns the calibration process fast and simpler to perform. The estimated relative pose has proven to be also very precise since it uses two different types of constraints, line-to-plane and point-to-plane, as a result of a richer configuration than previous proposals that relies on plane or V-shaped patterns. Our approach is validated with synthetic and real experiments, showing better performance than the state-of-art methods.
An adaptive unequal error protection strategy for uncompressed video transmission over 60GHz WPAN systems

Uncompressed HD (high-definition) video transmission via wireless personal area network (WPAN) is a promising application at the 60 GHz mmWave band. In this paper, we design a four-level UEP scheme which not only pays attention to the luminance and chrominance components' unequal effects on the reconstructed video quality, but also considers the differences between the two chrominance components. Furthermore, an adaptive UEP mode selection strategy based on multi-level partition is also proposed in order to achieve better video quality and higher transmission efficiency. Simulation results show the four-level UEP scheme outperforms the conventional two-level UEP scheme in terms of the average peak-signal-to-noise (PSNR) at moderate SNRs, and the proposed adaptive UEP strategy can achieve better visual quality and the optimal transmission efficiency in the varying wireless channel environment.
Querying Natural Logic Knowledge Bases

This paper describes the principles of a system applying natural logic as a knowledge base language. Natural logics are regimented fragments of natural language employing high level inference rules. We advocate the use of natural logic for knowledge bases dealing with querying of classes in ontologies and class-relationships such as are common in life-science descriptions. The paper adopts a version of natural logic with recursive restrictive clauses such as relative clauses and adnominal prepositional phrases. It includes passive as well as active voice sentences. We outline a prototype for partial translation of natural language into natural logic, featuring further querying and conceptual path finding in natural logic knowledge bases.
Troublesome concepts in statistics: a student perspective on what they are and how to learn them

The notion of threshold concepts (Meyer and Land 2002; 2004) has sparked renewed interest in examining what is important for students to learn, and the challenges they may encounter whilst learning (see for example Meyer and Land 2006). Most of these discussions have emerged from the perspective of disciplinary academics, many of whom nominate and exemplify the ‘threshold concepts’ within their discipline or field of study. We felt that the student’s experience of what is ‘threshold’ (Davies 2006) and equally of what seems troublesome (Perkins 2006) was also of significance, and would be potentially informative for the design of teaching, assessment and feedback. In this modest study we sought to take an initial step in this direction. The study is focused on an introductory statistics course, which typically attracts between 300-500 students each semester. Our primary concern was to gain access to the student’s view of what constituted significant learning within the course, and the concepts they found particularly tricky or challenging. We were particularly interested to see if the concepts nominated as ‘important’ or significant in some way by the students aligned in any way with those nominated by the PASS (Peer Assisted Study Session) leaders and the lecturer. We were also keen to consider the types of difficulties students indicated they experienced, as this could inform future course design and teaching strategies.
Secrecy capacity of MISO Gaussian wiretap channel with a cooperative jammer

We study the Gaussian MISO wiretap channel with a transmitter, a legitimate receiver, an eavesdropper and an external helper, where the transmitter and the helper have an arbitrary number of antennas but the intended receiver and the eavesdropper have only one antenna. The transmitter sends confidential messages to its intended receiver, while the helper transmits jamming signals independent of the source message to confuse the eavesdropper. The jamming signal is assumed to be treated as noise at both the intended receiver and the eavesdropper. Assuming Gaussian signaling at the helper, we obtain the optimal beamformers at the transmitter and the helper that achieve the secrecy capacity.
A New Approach to Relationships in Live Music: Redefining Emotional Content and Meaning

Live music is a social and artistic activity where all its participants establish a set of relationships in real time, mediated by different musical, social, psychological and environmental factors. The aim of this research is to study the relationships between audiences and musicians and their influence in the processes that lead to the generation of emotions and the creation of meaning. By taking a transdisciplinary view, I am trying to bridge some of the divides that frequently appear in music research (object-activity, aesthetic-social, etc.) and so I want to go beyond common artificial investigations about emotions and meaning in music by reflecting on the complex nature of real music experiences. The methodological approach is mainly qualitative — based on observations, and interviews; however, some quantitative data from a survey have also been taken into account. The research has been carried out as a case study that had the concerts of El Teatre Instrumental, an orchestra that specialises in the repertoire of the classical period, as its object.
Automatic verification of hybrid systems: an audio control protocol

The work is concerned with formal approaches to specification and verification for a better development in systems design. Automatic verification is a solution for validating highly critical systems, like controlling robots or supervising electronical devices. Important efforts have been realized in industry and education for supporting its development. Nevertheless, technical problems keep arising due to the size of specifications, in some cases requiring too much effort to obtain some results. We present the specification of the EEL communication protocol, used by Phillips in its audio components. This protocol verifies the correct communication between an audio system and its remote control, and is a typical case for studying hybrid systems. Hybrid systems are specified by finite automata enriched with a set of real variables. Properties to prove are usually written in some temporal logic. Automatic verification tools solve the "model checking" problem: does property /spl pi/ hold in system S? To solve difficulties associated to the size of systems, different tools have implemented techniques such as symbolic model checking, "on the fly" analysis, modularization and clock reduction. We believe that there are still ways to improve these tools: diminish redundancy in modelling, optimization for data management and storage, randomization of algorithms.
Elasticity in evaluations of criminal evidence: Exploring the role of cognitive dissonance

Purpose. Previous experiments have demonstrated asymmetrical scepticism in investigators' judgments of criminal evidence - evidence inconsistent (vs. consistent) with the dominant hypothesis about a case is judged as less reliable. In addition, some types of evidence (e.g., witness testimony) are more susceptible to asymmetrical scepticism than others (e.g., DNA evidence), indicating varying degrees of elasticity. This article proposes that inconsistent evidence arouses cognitive dissonance, and that the dissonance can be reduced through either asymmetrical scepticism (for high-elasticity evidence) or belief change (for low-elasticity evidence). The hypotheses are tested in two experiments.Methods. In both experiments, law students made a preliminary judgment about the guilt of a suspect in a homicide case, and subsequently received a piece of DNA or witness evidence which was either consistent or inconsistent with the preliminary judgment. The extent to which participants changed their guilt judgments, judged the additional evidence as reliable, and felt dissonance served as the main dependent variables.Results. Inconsistent (vs. consistent) evidence did arouse stronger dissonance, but only for witness (and not DNA) evidence. Experienced dissonance (Experiment 1) and dissonance reduction (Experiment 2) accounted for the effect of the evidence on changes in guilt judgments, but not for the effect on reliability judgments. The greatest dissonance reduction was observed among participants who received inconsistent witness evidence but did not change their guilt judgments accordingly.Conclusions. It appears that dissonance plays a significant, although complex, role in investigative judgments of guilt and reliability. Alternative dissonance-reducing mechanisms that can account for the findings and practical implications are discussed. Language: en
CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice

Significance Assigning biological relevance and molecular function to large catalogues of mutated genes in cancer is a major challenge. Likewise, pinpointing drivers among thousands of transcriptionally or epigenetically dysregulated genes within a cancer is complex and limited by the lack of tools for high-throughput functional cancer genomic analyses. We show here for the first time, to our knowledge, application of the CRISPR/Cas9 genome engineering system for simultaneous (multiplexed) mutagenesis of large gene sets in adult mice, allowing high-throughput discovery and validation of cancer genes. We characterized applications of CRISPR/Cas9 multiplexing, resulting tumor phenotypes, and limitations of the methodology. By using defined genetic or environmental predisposing conditions, we also developed, to our knowledge, the first mouse models of CRISPR/Cas9-induced hepatocellular carcinoma and show how multiplexed CRISPR/Cas9 can facilitate functional genomic analyses of hepatobiliary cancers. Here, we show CRISPR/Cas9-based targeted somatic multiplex-mutagenesis and its application for high-throughput analysis of gene function in mice. Using hepatic single guide RNA (sgRNA) delivery, we targeted large gene sets to induce hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC). We observed Darwinian selection of target genes, which suppress tumorigenesis in the respective cellular/tissue context, such as Pten or Cdkn2a, and conversely found low frequency of Brca1/2 alterations, explaining mutational spectra in human ICC/HCC. Our studies show that multiplexed CRISPR/Cas9 can be used for recessive genetic screening or high-throughput cancer gene validation in mice. The analysis of CRISPR/Cas9-induced tumors provided support for a major role of chromatin modifiers in hepatobiliary tumorigenesis, including that of ARID family proteins, which have recently been reported to be mutated in ICC/HCC. We have also comprehensively characterized the frequency and size of chromosomal alterations induced by combinatorial sgRNA delivery and describe related limitations of CRISPR/Cas9 multiplexing, as well as opportunities for chromosome engineering in the context of hepatobiliary tumorigenesis. Our study describes novel approaches to model and study cancer in a high-throughput multiplexed format that will facilitate the functional annotation of cancer genomes.
User-mode per-process name spaces for the AP1000 file system

The perceived simplicity of interprocess cooperation is strongly influenced by the type of name space in which the processes involved execute. If multiple processes share a common name space, they are more likely to cooperate effectively than if each operates in a distinct name space. This paper argues that, especially where specialized resources, such as a supercomputer, are involved, per-process name spaces are the optimum way to provide common name spaces across arbitrary domain boundaries. This paper also argues that such name spaces are best implemented in user mode. The user-mode per-process name spaces supported by the AP1000 File System are then described, as are some of the file system types supported on the AP1000. The performance implications of the user-mode implementation are also examined.