Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the Mechanism of Defective Interfering RNA (DI RNA) Biogenesis Reveals That a Viral Protein and the DI RNA Act Antagonistically in Virus Infection

ABSTRACT Potato mop-top virus (PMTV) produces a defective RNA (D RNA) encompassing the 5′-terminal 479 nucleotides (nt) and 3′-terminal 372 nt of RNA-TGB (where TGB is triple gene block). The mechanism that controls D RNA biogenesis and the role of D RNA in virus accumulation was investigated by introducing deletions, insertions, and point mutations into the sequences of the open reading frames (ORFs) of TGB1 and the 8-kilodalton (8K) protein that were identified as required for efficient production of the D RNA. Transient expression of RNA-TGB in the absence of RNA-Rep (which encodes the replicase) did not result in accumulation of D RNA, indicating that its production is dependent on PMTV replication. The D RNA could be eliminated by disrupting a predicted minus-strand stem-loop structure comprising complementary sequences of the 5′ TGB1 ORF and the 3′ 8K ORF, suggesting intramolecular template switching during positive-strand synthesis as a mechanism for the D RNA biogenesis. Virus accumulation was reduced when the 8K ORF was disrupted but D RNA was produced. Conversely, the virus accumulated at higher titers when the 8K ORF was intact and D RNA production was blocked. These data demonstrate that the D RNA interferes with virus infection and therefore should be referred to as a defective interfering RNA (DI RNA). The 8K protein was shown to be a weak silencing suppressor. This study provides an example of the interplay between a pathogen and its molecular parasite where virus accumulation was differentially regulated by the 8K protein and DI RNA, indicating that they play antagonistic roles and suggesting a mechanism by which the virus can attenuate replication, decreasing viral load and thereby enhancing its efficiency as a parasite.
Anisotropic photon migration in human skeletal muscle

It is demonstrated in the short head of the human biceps brachii of 16 healthy subjects (12 males and 4 females) that near infrared photon migration is anisotropic. The probability for a photon to travel along the direction of the muscle fibres is higher (∼0.4) than that of travelling along a perpendicular axis (∼0.3) while in the adipose tissue the probability is the same (∼0.33) in all directions. Considering that the muscle fibre orientation is different depending on the type of muscle considered, and that inside a given skeletal muscle the orientation may change, the present findings in part might explain the intrasubject variability observed in the physiological parameters measured by near infrared spectroscopy techniques. In other words, the observed regional differences might not only be physiological differences but also optical artefacts.
A reduced reference approach based on bidimensional empirical mode decomposition for image quality assessment

In this paper, we present a reduced reference method for image quality assessment (RRIQA). This method is based on statistical properties of the bidimensional empirical mode decomposition (BEMD) components, called intrinsic mode function (IMF). First we decompose both reference and distorted images to IMFs, then we compute the distance between marginal probability distributions of each IMF coefficients of the reference image, and its corresponding IMF of the distorted image using the Kullback Leibler divergence (KLD) as a measure of image distortion. To summarize the histogram of each IMF coefficients of the reference image, we use the Generalized Gaussian density model (GGD), in order that only a vector of few features will be needed for the image quality assessment(IQA) purpose. This method is simple to implement and it outperforms some existing results especially for the blur and the white noise distortion.
Influence of comorbidities and age on risk of death without recurrence: a retrospective analysis of the Arimidex, Tamoxifen Alone or in Combination trial.

PURPOSE The Arimidex, Tamoxifen Alone or in Combination (ATAC) study was a double-blind randomized trial in which postmenopausal women with early-stage breast cancer were assigned to receive anastrozole, tamoxifen, or the combination. We have conducted a retrospective analysis to examine the effects of comorbidities and age on treatment received, breast cancer-related mortality, and competing causes of mortality. PATIENTS AND METHODS The current analyses were based on 10-year median follow-up data in the two monotherapy arms (anastrozole, n = 3,092; tamoxifen, n = 3,094) of the ATAC study. Baseline comorbidities and tumor and treatment characteristics were compared between women age less than 70 years and women age ≥ 70 years. The cumulative incidence of breast cancer-related and non-breast cancer-related mortality was assessed according to age and comorbidities. RESULTS One thousand six hundred sixty-two patients (27%) were age ≥ 70 years at study entry. Older women were more likely to undergo mastectomy (odds ratio [OR], 1.92; 95% CI, 1.71 to 2.16) and less likely to receive radiotherapy (OR, 0.49; 95% CI, 0.44 to 0.55) or chemotherapy (OR, 0.24; 95% CI, 0.18 to 0.29). Women age ≥ 70 years had an increased risk of recurrence compared with women age less than 70 years (hazard ratio [HR], 1.21; 95% CI, 1.08 to 1.37) and a substantially increased risk of death without recurrence (HR, 4.13; 95% CI, 3.53 to 4.83). The risk of death without recurrence increased with comorbidity score (10-year estimates of 8.4%, 20.0%, and 30.4% for Satariano score 0, 1, and 2+, respectively; P < .001). CONCLUSION Age influences the risk of recurrence, and age and comorbidities significantly influence the risk of death without recurrence. Formal assessment of comorbidities should be incorporated into decisions regarding adjuvant therapies.
Inter-Subject Correlation of Brain Hemodynamic Responses During Watching a Movie: Localization in Space and Frequency

Cinema is a promising naturalistic stimulus that enables, for instance, elicitation of robust emotions during functional magnetic resonance imaging (fMRI). Inter-subject correlation (ISC) has been used as a model-free analysis method to map the highly complex hemodynamic responses that are evoked during watching a movie. Here, we extended the ISC analysis to frequency domain using wavelet analysis combined with non-parametric permutation methods for making voxel-wise statistical inferences about frequency-band specific ISC. We applied these novel analysis methods to a dataset collected in our previous study where 12 subjects watched an emotionally engaging movie “Crash” during fMRI scanning. Our results suggest that several regions within the frontal and temporal lobes show ISC predominantly at low frequency bands, whereas visual cortical areas exhibit ISC also at higher frequencies. It is possible that these findings relate to recent observations of a cortical hierarchy of temporal receptive windows, or that the types of events processed in temporal and prefrontal cortical areas (e.g., social interactions) occur over longer time periods than the stimulus features processed in the visual areas. Software tools to perform frequency-specific ISC analysis, together with a visualization application, are available as open source Matlab code.
DNA vaccination with a single-plasmid construct coding for viruslike particles protects mice against infection with a highly pathogenic avian influenza A virus.

BACKGROUND With seasonal outbreaks affecting millions of people each year and devastating pandemics, human influenza is a major health concern. The pandemic threat includes highly pathogenic avian influenza viruses (HPAIVs) that gained the ability to infect humans in Asia and quickly spread throughout the world. Major concerns have been raised regarding today's vaccine production systems against influenza viruses, and new strategies to design efficient vaccines are under intensive investigation. METHODS We demonstrated elsewhere that viruslike particles (VLPs) incorporating HPAIV hemagglutinin induce strong humoral immune response when injected in mice. In the current study, we evaluated a novel strategy that combines the immunogenicity of influenza VLPs and the advantages of DNA vaccines. RESULTS We developed minimal expression vectors encoding all genetic information necessary to produce H7N1 influenza VLPs. We showed that mice vaccinated with small DNA amounts developed specific, high-titer neutralizing antibodies against homologous H7N1 strain and were protected against lethal doses of an antigenically distinct H7N7 HPAIV. Moreover, using some of these constructs, we were able to raise cross-neutralizing antibodies against an unrelated H5N1 HPAIV. CONCLUSIONS DNA vaccination with constructs coding for influenza VLP production is a promising strategy to induce protection against different influenza viruses.
Link Level Design Issues for IP based Multi-Hop Communication Systems

In this paper we outline our future research activities in the area of wireless multi‐hop communication systems. Our focus is on the link level design issues for IP based multi‐hop communication systems using code division multiple access with pseudo‐noise spreading sequences. We employ pseudo noise sequences to keep the signalling overhead low. In particular, we report on our initial design considerations and evaluations of a low complexity power control mechanism for multi‐hop CDMA systems. Our Interference controlled transmit power control relies on pilot tone transmissions and adjusts the power based on the interference levels measured from the pilot tones. A rule derived from the Cocktail Party problem is used to set the transmit power level. Our preliminary simulation results indicate that our initial design increases the capacity in the center of the network, which is most frequently traversed. Also, our design reduces the overall consumed power. On the downside our design reduces the overall capacity in the network. In our ongoing work we study the trade‐offs between capacity and consumed power as well as the areas of increased/reduced capacity/connectivity and their impact on the overall QoS provided by the network in more detail and refine our design to achieve optimal trade‐offs.
On Large-Scale Retrieval: Binary or n-ary Coding?

The growing amount of data available in modern-day datasets makes the need to efficiently search and retrieve information. To make large-scale search feasible, Distance Estimation and Subset Indexing are the main approaches. Although binary coding has been popular for implementing both techniques, n-ary coding (known as Product Quantization) is also very effective for Distance Estimation. However, their relative performance has not been studied for Subset Indexing. We investigate whether binary or n-ary coding works better under different retrieval strategies. This leads to the design of a new n-ary coding method, "Linear Subspace Quantization (LSQ)" which, unlike other n-ary encoders, can be used as a similarity-preserving embedding. Experiments on image retrieval show that when Distance Estimation is used, n-ary LSQ outperforms other methods. However, when Subset Indexing is applied, interestingly, binary codings are more effective and binary LSQ achieves the best accuracy.
The Significance of Positive Margins in Loop Electrosurgical Cone Biopsies

Objective: To determine the interpretability and significance of the endocervical margins of cervical cone biopsy specimens removed by the loop electrosurgical excision procedure (LEEP). Methods: Loop electrosurgical cervical conization was performed on 57 women with biopsy-confirmed, high-grade dysplasias in whom the extent of the lesion could not be determined by colposcopic visualization. Internal endocervical margins of the resected specimens were marked with ink by the operating physician and evaluated microscopically by the pathologist. Endocervical curettage (ECC) was done in all instances, and all subjects were followed for 1 year after the procedure. Results: Histologic evaluation of the inked endocervical margins was possible for all 57 resected specimens and was in no instance hindered by thermal artifact. In 19 patients, dysplasia was present in the inked core margin, the ECC, or both. Each patient had re-excisions of the endocervical area; 12 of the 19 (63%) had dysplasia in the specimen. Of 12 cases in which dysplasia was present in both the endocervical margin and the ECC, nine had residual dysplasia. Two of four patients with positive margins but a negative ECC had residual dysplasia, but only one of three patients with a negative endocervical margin and a positive ECC showed residual dysplasia. In the 38 patients with negative inked margins and a negative ECC, there was only one instance of dysplasia demonstrated during the 1-year follow-up period. Conclusion: Endocervical margins of cone biopsies removed by LEEP can be accurately assessed pathologically and can help predict the presence of persistent dysplasia. (Obstet Gynecol 1994;84:996-1000)
Robust Decentralized Virtual Coordinate Systems in Adversarial Environments

Virtual coordinate systems provide an accurate and efficient service that allows hosts on the Internet to determine the latency to arbitrary hosts without actively monitoring all of the nodes in the network. Many of the proposed systems were designed with the assumption that all of the nodes are altruistic. However, this assumption may be violated by compromised nodes acting maliciously to degrade the accuracy of the coordinate system. As numerous peer-to-peer applications come to rely on virtual coordinate systems to achieve good performance, it is critical to address the security of such systems. In this work, we demonstrate the vulnerability of decentralized virtual coordinate systems to insider (or Byzantine) attacks. We propose techniques to make the coordinate assignment robust to malicious attackers without increasing the communication cost. We use both spatial and temporal correlations to perform context-sensitive outlier analysis to reject malicious updates and prevent unnecessary and erroneous adaptations. We demonstrate the attacks and mitigation techniques in the context of a well-known virtual coordinate system using simulations based on three representative, real-life Internet topologies of hosts and corresponding Round Trip Times (RTT). We show the effects of the attacks and the utility of the mitigation techniques on the virtual coordinate system as seen by higher-level applications, elucidating the utility of deploying robust virtual coordinate systems as network services.
A framework for unifying presentation space

Making effective use of the available display space has long been a fundamental issue in user interface design. We live in a time of rapid advances in available CPU power and memory. However, the common sizes of our computational display spaces have only minimally increased or in some cases, such as hand held devices, actually decreased. In addition, the size and scope of the information spaces we wish to explore are also expanding. Representing vast amounts of information on our relatively small screens has become increasingly problematic and has been associated with problems in navigation, interpretation and recognition. User interface research has proposed several differing presentation approaches to address these problems. These methods create displays that vary considerably, visually and algorithmically. We present a unified framework that provides a way of relating seemingly distinct methods, facilitating the inclusion of more than one presentation method in a single interface. Furthermore, it supports extrapolation between the presentation methods it describes. Of particular interest are the presentation possibilities that exist in the ranges between various distortion presentations, magnified insets and detail-in-context presentations, and between detail-in-context presentations and a full-zooming environment. This unified framework offers a geometric presentation library in which presentation variations are available independently of the mode of graphic representation. The intention is to promote the ease of exploration and experimentation into the use of varied presentation combinations.
Erythrocyte aggregation tendency and cellular properties in horse , human , and rat : a comparative study

Baskurt, Oguz K. , Robert A. Farley, and Herbert J. Meiselman. Erythrocyte aggregation tendency and cellular properties in horse, human, and rat: a comparative study. Am. J. Physiol. 273 (Heart Circ. Physiol. 42): H2604–H2612, 1997. —Horse blood has a higher tendency to form red blood cell (RBC) aggregates compared with human blood, with this enhanced aggregation previously attributed to differences in plasma factors. Our results confirm this observation and further indicate that washed horse RBC also have a significantly higher aggregation tendency in dextran 70 solutions (i.e., horse RBC have a higher ‘‘aggregability’’). In contrast, the aggregation tendency of rat RBC, both in autologous plasma and in dextran 70, is significantly less compared with human and horse RBC. Other rheological findings for horse and rat RBC include smaller changes in RBC deformation indexes over the same shear stress range and a lower RBC shape recovery time constant. Rat RBC also had higher two-phase aqueous polymer partition coefficients, suggesting a higher surface charge. Membrane protein analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed marked differences: 1) band 4.2 protein was lacking in horse RBC membranes, and 2) carbohydrate groups have different distributions in human, rat, and horse RBC, as indicated by different patterns in periodic acid-Schiff-stained protein bands. Our results clearly indicate significant differences in RBC aggregability among the three species and indicate that cellular factors contribute importantly to these differences. Furthermore, they suggest that systematic studies of blood and RBC from different species should provide insight into the mechanism(s) of RBC aggregation.
Representative Factor Generation for the Interactive Visual Analysis of High-Dimensional Data

Datasets with a large number of dimensions per data item (hundreds or more) are challenging both for computational and visual analysis. Moreover, these dimensions have different characteristics and relations that result in sub-groups and/or hierarchies over the set of dimensions. Such structures lead to heterogeneity within the dimensions. Although the consideration of these structures is crucial for the analysis, most of the available analysis methods discard the heterogeneous relations among the dimensions. In this paper, we introduce the construction and utilization of representative factors for the interactive visual analysis of structures in high-dimensional datasets. First, we present a selection of methods to investigate the sub-groups in the dimension set and associate representative factors with those groups of dimensions. Second, we introduce how these factors are included in the interactive visual analysis cycle together with the original dimensions. We then provide the steps of an analytical procedure that iteratively analyzes the datasets through the use of representative factors. We discuss how our methods improve the reliability and interpretability of the analysis process by enabling more informed selections of computational tools. Finally, we demonstrate our techniques on the analysis of brain imaging study results that are performed over a large group of subjects.
Alternation and redundancy analysis of the intersection problem

The intersection of sorted arrays problem has applications in search engines such as Google. Previous work has proposed and compared deterministic algorithms for this problem, in an adaptive analysis based on the encoding size of a certificate of the result (cost analysis). We define the alternation analysis, based on the nondeterministic complexity of an instance. In this analysis we prove that there is a deterministic algorithm asymptotically performing as well as any randomized algorithm in the comparison model. We define the redundancy analysis, based on a measure of the internal redundancy of the instance. In this analysis we prove that any algorithm optimal in the redundancy analysis is optimal in the alternation analysis, but that there is a randomized algorithm which performs strictly better than any deterministic algorithm in the comparison model. Finally, we describe how these results can be extended beyond the comparison model.
An Introduction to Statistical Spoken Language Understanding

1 Introduction Besides dictation, there are many other practical applications for speech recognition, including command and control, spoken dialog systems [1, 2], speech-to-speech translation [3], and multi-modal interaction [4-6]. The success of these applications relies on the correct recognition of not only what is said, but also what is meant. In contrast to automatic speech recognition (ASR), which converts a speaker's spoken utterance into a text string, spoken language understanding (SLU) consists in interpreting user's intentions from their speech utterances. Traditionally, this has been accomplished by writing context free (CFG) or unification grammars (UG) by hand. The manual grammar authoring process is laborious, expensive and requires a lot of expertise. In recent years, many data-driven models have been proposed for this problem. The main purpose of this overview paper is to provide an introduction to the statistical framework common in spoken language understanding, which has not been widely exposed to signal processing readers in the past. SLU is closely related to natural language understanding (NLU), a field that has been studied for half a century. However, the problem of SLU has its own characteristics. Unlike general domain NLU, SLU is, in the current state of technology, focused only on specific application domains. Hence, many domain-specific constraints can be included in the understanding model. Ostensibly, this may make the problem easier to solve. Unfortunately, spoken language is much noisier than written language. The inputs to a SLU system are not as well-formed as those to an NLU system. They often do not comply with rigid syntactic constraints. Disfluencies such as false starts, repairs, and hesitations are pervasive, especially in conversational speech, and errors made by speech recognizers are inevitable. Therefore, robustness is one of the most important issues in SLU. On the other hand, a robust solution tends to over-generalize and introduce ambiguities, leading to reduction of understanding accuracy. A major challenge to SLU is thus to strike an optimal balance between the robustness and the constraints that prevent over-generalizations and reduce ambiguities. 2 The study of SLU started in the 1970's in the DARPA Speech Understanding Research (SUR) and then the Resource Management (RM) tasks. At this early stage, NLU techniques like finite state machine (FSM) and augmented transition networks (ATNs) were applied for SLU [7]. The study of SLU surged in the 90's, with the DARPA sponsored Air Travel Information System (ATIS) evaluations [8]. Many of the SLU technologies …