Miracle-dz/UniFAR-FTUs huggingface dataset:
Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance

Endogenous retrotransposons have caused extensive genomic variation within mammalian species, but the functional implications of such mobilization are mostly unknown. We mapped thousands of endogenous retrovirus (ERV) germline integrants in highly divergent, previously unsequenced mouse lineages, facilitating a comparison of gene expression in the presence or absence of local insertions. Polymorphic ERVs occur relatively infrequently in gene introns and are particularly depleted from genes involved in embryogenesis or that are highly expressed in embryonic stem cells. Their genomic distribution implies ongoing negative selection due to deleterious effects on gene expression and function. A polymorphic, intronic ERV at Slc15a2 triggers up to 49-fold increases in premature transcriptional termination and up to 39-fold reductions in full-length transcripts in adult mouse tissues, thereby disrupting protein expression and functional activity. Prematurely truncated transcripts also occur at Polr1a, Spon1, and up to ∼5% of other genes when intronic ERV polymorphisms are present. Analysis of expression quantitative trait loci (eQTLs) in recombinant BxD mouse strains demonstrated very strong genetic associations between the polymorphic ERV in cis and disrupted transcript levels. Premature polyadenylation is triggered at genomic distances up to >12.5 kb upstream of the ERV, both in cis and between alleles. The parent of origin of the ERV is associated with variable expression of nonterminated transcripts and differential DNA methylation at its 5′-long terminal repeat. This study defines an unexpectedly strong functional impact of ERVs in disrupting gene transcription at a distance and demonstrates that ongoing retrotransposition can contribute significantly to natural phenotypic diversity.
Discovery : Fine-Grained Classification of X-ray Scattering Images

We explore the use of computer vision methods for organizing, searching, and classifying x-ray scattering images. X-ray scattering is a technique that shines an intense beam of x-rays through a sample of interest. By recording the intensity of x-ray deflection as a function of angle, scientists can measure the structure of materials at the molecular and nano-scale. Current and planned synchrotron instruments are producing x-ray scattering data at an unprecedented rate, making the design of automatic analysis techniques crucial for future research. In this paper, we devise an attribute-based approach to recognition in x-ray scattering images and demonstrate applications to image annotation and retrieval.
Mindfulness in counseling and psychotherapy: A literature review and quantitative investigation of mindfulness competencies.

approved: Dale-Elizabeth Pehrsson There is substantial interest in the application of mindfulness in counseling and psychotherapy. The appeal of mindfulness training and mindfulness-based interventions has increased as research continues to demonstrate benefits. Mindfulness practice has not only been effective in clinical applications with clients, but has also been conceptualized as beneficial for counselors and psychotherapists. Counselors are required to adhere to the ethical codes and standards of counseling related professional associations by practicing in a new specialty area only after appropriate education and training experience. With the desire to apply this new specialty area of counseling, educational opportunities are being offered by academic institutions, training programs and literature geared to counseling and psychotherapy professionals. Recommendations and qualifications can be found in the literature for specific mindfulness training programs and therapies, however, no set of competencies for mindfulness training have been proposed for the general or integrative practices of counseling and psychotherapy. The purpose of this dissertation study is to produce two manuscripts related to mindfulness in counseling and psychotherapy, and importantly, explore what it means to be competent to provide mindfulness training to clients. The dissertation investigated to what extent experts (N=52) agreed with a proposed set of 16 mindfulness competency statements. The mindfulness competency survey was investigated for reliability and validity. In conjunction with recommendations in the professional literature on mindfulness trainer qualifications, this research suggests that experts on mindfulness in counseling and psychotherapy, in general, agree with the 16 proposed competency statements.
Cerebral Venous Thrombosis: A Descriptive Multicenter Study of Patients in Pakistan and Middle East

Background and Purpose— The natural history, causative factors, and outcomes of patients with cerebral venous thrombosis from Asia and Middle East have not been well described. This descriptive multicenter study describes the results for cerebral venous thrombosis patients in South Asia and the Middle East. Methods— The retrospective and prospective data of patients with radiologically confirmed cerebral venous thrombosis were collected from 4 centers located in Pakistan and United Arab Emirates. The demographic, clinical, radiological, and outcome data were recorded and analyzed. Primary outcome was death or dependency (modified Rankin score >2) at the time of hospital discharge. Results— This study included 109 patients with cerebral venous thrombosis; the presenting features most commonly being observed were headache (81%), focal motor deficits (45%), seizures (39%), and mental status changes (37%). Important predisposing factors included systemic and central nervous system infection (18%), postpartum state (17%), hyperhomocystinemia (9%), genetic thrombophilia (5%), and oral contraceptive pill use (3%). Ninety-six (67%) patients received therapeutic anticoagulation. Seven patients died and 43 had poor outcome at discharge. Focal motor deficits (OR, 2.93; 95% CI, 1.2–7.5; P=0.018) and hemorrhagic infarctions (OR, 2.81; 95% CI, 1.04–7.85; P=0.041) were independent predictors of unfavorable outcome at discharge. Hemorrhagic infarction was the most significant factor of long-term unfavorable outcome (OR, 5.87; 95% CI, 1.49–23.02; P=0.011). Conclusions— Infections and postpartum state were the most common predisposing factors for cerebral venous thrombosis in this cohort. Most patients (67%) were treated with anticoagulation therapy. Almost 50% of patients were dead or disabled at discharge.
Acquisition and visualization of colored 3D objects

This paper presents a complete system for scanning the geometry and surface color of a 3D object and for displaying realistic images of the object from arbitrary viewpoints. A stereo system with active light produces several views of dense range and color data. The data is registered and a surface that approximates the data is constructed. The surface estimate can be fairly coarse, as the appearance of fine detail is recreated by view-dependent texturing of the surface using color images.
Isolation of Multipotent Neural Precursors Residing in the Cortex of the Adult Human Brain

Multipotent precursors able to generate neurons, astrocytes, and oligodendrocytes have previously been isolated from human brain embryos and recently from neurogenic regions of the adult human brains. The isolation of multipotent neural precursors from adult human should open new perspectives to study adult neurogenesis and for brain repair. The present study describes the in vitro isolation from adult human brains of a progenitor responsive to both epidermal and basic fibroblast growth factors that forms spheres as it proliferates. Single spheres derived from various regions of the brain generate in vitro neurons, astrocytes, and oligodendrocytes. The clonal origin of the spheres was revealed by genomic viral insertion using lentiviral vector. Interestingly, this vector appears to be a potent tool for gene transfer into human neural progeny. Ninety-six percent of the spheres investigated were multipotent. Multipotent precursors were isolated from all brain regions studied, including the temporal and the frontal cortex, the amygdala, the hippocampus, and the ventricular zone. This study is the first evidence that primitive precursors such as multipotent precursors exist in the adult human cortex and can reside far from the ventricles. Neurogenesis derived from adult human progenitors differ to murine neurogenesis by the requirement of laminin for oligodendrocyte generation and by the action of basic-fibroblast growth factor and platelet derived growth factor that prevented the formation of oligodendrocytes and neurons. Moreover, the differentiation of human adult precursors seems to differ from fetal ones: adult precursors do not necessitate the removal of mitogen for differentiation. These results indicate that the study of adult multipotent precursors is a new platform to study adult human neurogenesis, potentially generate neural cells for transplantation, and design protocols for in vivo stimulation.
"Why 6?" Defining the operational limits of stide, an anomaly-based intrusion detector

Anomaly-detection techniques have considerable promise for two difficult and critical problems in information security and intrusion detection: detecting novel attacks, and detecting masqueraders. One of the best-known anomaly detectors used in intrusion detection is stide. Developed at the University of New Mexico, stide aims to detect attacks that exploit processes that run with root privileges. The original work on stide presented empirical results indicating that data sequences of length six and above were required for effective intrusion detection. This observation has given rise to the long-standing question, "why six? " accompanied by related questions regarding the conditions under which six may or may not be appropriate. This paper addresses the "why six" issue by presenting an evaluation framework that maps out stide's effective operating space, and identifies the conditions that contribute to detection capability, particularly detection blindness. A theoretical justification explains the effectiveness of sequence lengths of six and above, as well as the consequences of using other values. In addition, results of an investigation are presented, comparing stide's anomaly-detection capabilities with those of a competing detector.
IFITM Proteins Inhibit Entry Driven by the MERS-Coronavirus Spike Protein: Evidence for Cholesterol-Independent Mechanisms

The interferon-inducible transmembrane (IFITM) proteins 1, 2 and 3 inhibit the host cell entry of several enveloped viruses, potentially by promoting the accumulation of cholesterol in endosomal compartments. IFITM3 is essential for control of influenza virus infection in mice and humans. In contrast, the role of IFITM proteins in coronavirus infection is less well defined. Employing a retroviral vector system for analysis of coronavirus entry, we investigated the susceptibility of human-adapted and emerging coronaviruses to inhibition by IFITM proteins. We found that entry of the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) is sensitive to inhibition by IFITM proteins. In 293T cells, IFITM-mediated inhibition of cellular entry of the emerging MERS- and SARS-CoV was less efficient than blockade of entry of the globally circulating human coronaviruses 229E and NL63. Similar differences were not observed in A549 cells, suggesting that cellular context and/or IFITM expression levels can impact inhibition efficiency. The differential IFITM-sensitivity of coronaviruses observed in 293T cells afforded the opportunity to investigate whether efficiency of entry inhibition by IFITMs and endosomal cholesterol accumulation correlate. No such correlation was observed. Furthermore, entry mediated by the influenza virus hemagglutinin was robustly inhibited by IFITM3 but was insensitive to accumulation of endosomal cholesterol, indicating that modulation of cholesterol synthesis/transport did not account for the antiviral activity of IFITM3. Collectively, these results show that the emerging MERS-CoV is a target of the antiviral activity of IFITM proteins and demonstrate that mechanisms other than accumulation of endosomal cholesterol can contribute to viral entry inhibition by IFITMs.
Low rate common control channel based AODV routing protocol for cognitive radio ad-hoc networks

In Cognitive Radio Ad-hoc Networks, dynamic spectrum Access (DSA) and opportunistic routing introduces concurrent channel-path selection with appropriate PU free spectrum hole (white space) to cater end-to-end connectivity for application data transmission. Most state-of-the-art cognitive routing protocols either uses 2.4 GHz unlicensed dedicated common control channel (CCC) or licensed PU free CCC for channel-path selection and CR node co-ordination message exchange. With licensed CCC, channel-path selection and CR node co-ordination time will be high due to sequential or group based CCC coverage whereas dedicated 2.4GHz unlicensed CCC is subject to saturation and interference with other services. Hence, there is a greater extent for 2.4 GHz CCC to be congested which increases link failures and routing control overhead that successively degrade the performance of routing protocol. Several small slices of unlicensed frequencies (433MHz/868 MHz/902-928 MHz) are existing in lower spectral bands which are not efficiently utilized. Our Proposed work make use of low unlicensed spectrum band (902-928 MHz) as a low rate AODV common control channel for broadcasting route control(channel-path) and CR coordination messages which abbreviates hop count, link failures, routing overhead and end-to-end data transmission delay. Simulation (NS-2.31) results shows that performance of low rate common control channel based AODV routing protocol outperforms compared with 2.4GHz saturated AODV control channel especially for delay sensitive CR networks.
A SENTENCE COMPLETION TASK FOR ELICITING PERSONAL CONSTRUCTS IN SPECIFIC DOMAINS

A novel sentence completion task was developed to assess how individuals view themselves and others in different domains of experience. This task was incorp orated into a repertory grid and evaluated in two studies. In the first study, ratings obtained from the grid procedure were shown to be internally consistent and reliable over time in two distinct domains of experience: mathematics and athletics. Moreover, ratings for oneself in the grids for each domain were found to be highly correlated with corresponding subscale scores from a popular multidimensional measure of self-concept. In the second study, the repertory grid ratings were again shown to be internally consistent and to yield information that was truly distinct across the domains of mathematics and athletics. Positive ratings for oneself in the grids were again shown to correlate highly with corresponding subscale scores from the same multidimensional measure of self-concept. The theoretical and methodological implications of these results and new procedures were discussed.
Equalization concepts for EDGE

An equalization concept for the novel radio access scheme Enhanced Data rates for GSM Evolution (EDGE) is proposed by which high performance can be obtained at moderate computational complexity. Because high-level modulation is employed in EDGE, optimum equalization as usually performed in Global System for Mobile Communications (GSM) receivers is too complex and suboptimum schemes have to be considered. It is shown that delayed decision-feedback sequence estimation (DDFSE) and reduced-state sequence estimation (RSSE) are promising candidates. For various channel profiles, approximations for the bit error rate of these suboptimum equalization techniques are given and compared with simulation results for DDFSE. It turns out that a discrete-time prefilter creating a minimum-phase overall impulse response is indispensable for a favorable tradeoff between performance and complexity. Additionally, the influence of channel estimation and of the receiver input filter is investigated and the reasons for performance degradation compared to the additive white Gaussian noise channel are indicated. Finally, the overall system performance attainable with the proposed equalization concept is determined for transmission with channel coding.
Combined Stent Insertion and High-intensity Focused Ultrasound Ablation for Patients With Malignant Obstructive Jaundice

Purpose: We aimed to determine the clinical effectiveness of combined stent insertion and high-intensity focused ultrasound (HIFU) ablation for patients with malignant obstructive jaundice (MOJ). Materials and Methods: From June 2013 to May 2015, consecutive patients with inoperable MOJ underwent biliary stent with or without HIFU ablation in our center. Treatment-related complications, stent patency time, and survival time were compared between 2 groups. Results: During the enrolled time, a total of 51 patients with MOJ underwent biliary stent with HIFU ablation (n=24) or biliary stent only (n=27) in our center. There was no significant difference in baseline data between 2 groups. Relief of jaundice was achieved in all patients in both groups. Cholangitis was observed in 2 patients in stent with HIFU ablation group and 1 patient in stent only group (P=0.483). Reobstruction of stent was observed in 4 patients in stent with HIFU ablation group and 8 patients in stent only group (P=0.276). The mean stent patency time was 367±41 days in stent with HIFU ablation group and 257±35 days in stent only group (P=0.037). The mean overall survival was 238±31 days in stent with HIFU ablation group and 152±20 days in stent only group (P=0.014). Conclusions: Combined biliary stent insertion and HIFU ablation is a safe and easy method for patients with MOJ, and seems to extend stent patency time and survival when compared with biliary stent only.
Automated immunostaining of cell smears: an alternative to flow cytometry

Aims: To assess the applicability of an automated tissue immunostainer machine for the phenotypic analysis of peripheral blood and bone marrow aspirate smears. Methods: Air-dried smears of peripheral blood and bone marrow from normal individuals and 14 patients with haematological malignancies were stained, following fixation, with a range of antibodies to haemopoietic antigens using both immunoperoxidase and immuno-alkaline phosphatase methods on the Bond-maX (Leica Microsystems) automated immunostaining machine. Results: Automated protocols used for staining formalin-fixed paraffin-embedded tissue could be applied to cell smears, giving high quality staining with excellent cytological detail and antigenic preservation for an extensive antibody panel. Optimal quality (morphological preservation and antigen detection without background staining) was obtained with an alkaline phosphatase method and Fast Red chromogenic substrate. Both cell surface and intracellular (cytoplasmic and nuclear) antigens could be detected and gave the expected reactivity. Conclusions: Automated immunostaining is possible for haematological smears. It generates consistent high quality staining, with the exception of surface immunoglobulin, and is applicable to haematological and, potentially, cytological smears. It provides a practical alternative to flow cytometry and will have particular application when smears are available and there is no suitable sample for flow cytometry.
23 problems in systems neuroscience

Part I How have brains evolved? 1. Shall we ever understand the fly's brain? 2. Can we understand the action of brain in natural environments? 3. Hemisphere dominance of brain function-which functions are lateralized and why? Part II How is the cerebral cortex organized? 4. What is the function of the thalamus? 5. What is a neuronal map, how does it arise, and what is it good for? 6. What is fed back? Part III How do neurons interact? 7. How Can the Brain be so Fast? 8. What is the Neural Code? 9. Are single cortical neurons independent or are they obedient members of a huge orchestra? 10. What is the other 85% of V1 doing? Part IV What can brains compute? 11. Which computation runs in visual cortical columns? 12. Are neurons adapted for specific computations? Examples from temporal coding in the auditory system 13. How is time represented in the brain? 14. How general are neural codes in sensory systems? 15. How does the hearing system perform auditory scene analysis? 16. How does our visual system achieve shift and size invariance? 17. What is reflected in sensory neocortical activity: External stimuli or what the cortex does with them? 18. Do perception and action result from different brain circuits? The three visual systems hypothesis 19. What are the projective fields of cortical neurons? 20. How are the features of objects integrated into perceptual wholes that are selected by attention? 21. Where are the switches on this thing? 22. Synesthesia: What does it tell us about the emergence of qualia, metaphor, abstract thought and language? 23. What are the neural correlates of consciousness?
Bounds to Fair Rate Allocation and Communication Strategies in Source/Relay Wireless Networks

We analyze the achievable data rate of cooperative relaying strategies in networks where nodes operate in half-duplex mode. Nodes have to deliver their data to a gateway, at a certain rate, and may have limited energy capabilities, as in the case of energy-harvesting communication networks. Both the requested data rate and the available energy capabilities may vary from node to node. Under such constraints, we take an information-theoretic approach and derive cut-set upper bounds to the achievable rate. Furthermore, we devise two kinds of communication strategies, each aiming at a different objective. The former ensures a fair rate allocation to the network nodes, but it neglects their energy constraints. The latter does consider energy constraints by meeting the requirements on the average power consumption at each node and by providing fairness in the data rate allocation. We show the performance of the aforementioned communication strategies, highlighting their effectiveness and providing useful insights on the system behavior.
KUNLPLab:Sentiment Analysis on Twitter Data

This paper presents the system submitted by KUNLPLab for SemEval-2014 Task9 - Subtask B: Message Polarity on Twitter data. Lexicon features and bag-of-words features are mainly used to represent the datasets. We trained a logistic regression classifier and got an accuracy of 6% increase from the baseline feature representation. The effect of pre-processing on the classifier’s accuracy is also discussed in this work.
Correlation Between Gel Structural Properties and Drug Release Pattern in Scleroglucan Matrices

The drug delivery behavior of scleroglucan hydrogels was correlated with the structural features found by means of steady-state fluorescence studies. Theophylline at 0.4% in weight was used as the model drug and its release was measured using a Franz cell device. The results were fitted with a semi-empirical power law equation, finding significant differences between the 0.5% and higher than 0.8% scleroglucan concentrations (w/w). Four molecular fluorescent probes were used to test microenvironmental properties of the gel cavities, which will play a key role on the release of the pharmaceutical drugs. The results found by the fluorescence analysis are in good agreement with the ones obtained by release kinetics.