Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast search method for vector quantization by simultaneously using two subvectors

Encoding speed is one of the key issues in vector quantization (VQ). In order to effectively reduce computational complexity, before actually computing the expensive real Euclidean distance in VQ, it is possible to estimate the Euclidean distance first by using the statistical features of sum and variance of a k-D vector. The IEENNS method has been proposed to reject most unlikely candidate codewords for the input vector. Furthermore, by partitioning a k-D vector in half to construct its two (k/2)-D subvectors and then apply IEENNS method again to each of the two subvectors separately, SIEENNS method has been reported as well. The SIEENNS method is the most essential subvector-based search method for VQ but it failed to deal with the two subvectors at the same time, which degrades the search performance obviously. This paper aims at generalizing and enhancing state-of-the-art SIEENNS method by means of simultaneously instead of separately using the two subvectors so as to reject more unlikely candidate codewords for the input vector. Mathematical analysis and experimental results confirmed that the proposed method in this paper can significantly improve the search efficiency to 68.3%~82.2% compared to the SIEENNS method.
Target-cancer-cell-specific activatable fluorescence imaging probes: rational design and in vivo applications.

Conventional imaging methods, such as angiography, computed tomography (CT), magnetic resonance imaging (MRI), and radionuclide imaging, rely on contrast agents (iodine, gadolinium, and radioisotopes, for example) that are "always on. " Although these indicators have proven clinically useful, their sensitivity is lacking because of inadequate target-to-background signal ratio. A unique aspect of optical imaging is that fluorescence probes can be designed to be activatable, that is, only "turned on" under certain conditions. These probes are engineered to emit signal only after binding a target tissue; this design greatly increases sensitivity and specificity in the detection of disease. Current research focuses on two basic types of activatable fluorescence probes. The first developed were conventional enzymatically activatable probes. These fluorescent molecules exist in the quenched state until activated by enzymatic cleavage, which occurs mostly outside of the cells. However, more recently, researchers have begun designing target-cell-specific activatable probes. These fluorophores exist in the quenched state until activated within targeted cells by endolysosomal processing, which results when the probe binds specific receptors on the cell surface and is subsequently internalized. In this Account, we present a review of the rational design and in vivo applications of target-cell-specific activatable probes. In engineering these probes, researchers have asserted control over a variety of factors, including photochemistry, pharmacological profile, and biological properties. Their progress has recently allowed the rational design and synthesis of target-cell-specific activatable fluorescence imaging probes, which can be conjugated to a wide variety of targeting molecules. Several different photochemical mechanisms have been utilized, each of which offers a unique capability for probe design. These include self-quenching, homo- and hetero-fluorescence resonance energy transfer (FRET), H-dimer formation, and photon-induced electron transfer (PeT). In addition, the repertoire is further expanded by the option for reversibility or irreversibility of the signal emitted through these mechanisms. Given the wide range of photochemical mechanisms and properties, target-cell-specific activatable probes have considerable flexibility and can be adapted to specific diagnostic needs. A multitude of cell surface molecules, such as overexpressed growth factor receptors, are directly related to carcinogenesis and thus provide numerous targets highly specific for cancer. This discussion of the chemical, pharmacological, and biological basis of target-cell-specific activatable imaging probes, and methods for successfully designing them, underscores the systematic, rational basis for further developing in vivo cancer imaging.
Treatment of juxtapapillary choroidal melanoma

Purpose: To compare different treatment for juxtapapillary choroidal melanomas. Methods: Retrospective study comparing recurrence, survival and complications in 14 patients treated with proton beam treatment, 11 patients treated with stereotactic radiotherapy and 28 patients treated with Ruthenium brachytherapy in combination with transpupillary thermotherapy. Results: Mean follow-up time was 45.3 months, in which 4 patients died due to their melanoma. There was a significant faster decrease of the tumour prominence in the Ruthenium group. Earlier radiation retinopathy (from 6 months onward) in the Ruthenium group, but no significant more radiation retinopathy after 5 years. The vision after 5 years was significant lower in the stereotactic radiotherapy group, but this was also due to the fact that there were more patients with a juxtapapillary melanoma on the macular side in this group. Conclusions: A prospective randomised study is neaded to determine which therapy is best in treating juxtapapillary melanomas. In this retrospective study, there was no difference in local recurrence or survival in the 3 treatment groups.
Association of Type D personality with unhealthy lifestyle, and estimated risk of coronary events in the general Icelandic population

Background: Type D personality is associated with an increased morbidity and mortality risk in cardiovascular disease patients, but the mechanisms explaining this risk are unclear. We examined whether Type D was associated with coronary artery disease (CAD) risk factors, estimated risk of developing CAD, and previous cardiac events. Design: Cross-sectional study in the general Icelandic population. Methods: A random sample of 4753 individuals (mean age 49.1 ± 12.0 years; 49% men) from the REFINE-Reykjavik study completed assessments for Type D personality and conventional CAD risk factors. Ten-year risk of developing CAD was estimated with the Icelandic risk calculator. Results: Type D personality (22% of sample) was associated with a higher prevalence of hypertension (35 vs. 31%, p = 0.009), but less use of hypertension medication (58 vs. 65%, p = 0.013) in hypertensives, more diabetes (6 vs. 4%, p = 0.023), wider waist circumference (p = 0.007), and elevated body mass index (p = 0.025) and blood lipids (p < 0.05). Type D individuals reported less physical exercise (p = 0.000) and more current (26 vs. 21%, p = 0.003) and former smoking (48 vs. 44%, p = 0.036). Estimates of 10-year risk of CAD were higher in Type D individuals (12.4%, 95% CI 1.9 to 23.8%), and Type Ds reported more previous cardiac events than non-Type Ds (5 vs. 3%, p < 0.01; OR 1.71, 95% CI 1.21 to 2.42). Conclusions: In the general Icelandic population, Type D personality was associated with differences in lifestyle-related CAD risk factors, a higher estimated risk of developing CAD, and higher incidence of previous cardiac events. Unhealthy lifestyles may partly explain the adverse cardiovascular effect of Type D personality.
Real-time MVC viewer for free viewpoint navigation

A real-time MVC viewer for free-viewpoint navigation is demonstrated. MVC, a video coding standard for multi-view video, is an extension of the state-of-the-art H.264/AVC. Realizing parallel decoding and view synthesis is essential to develop real-time viewers. A new decoder architecture is introduced for the proposed viewer. In addition, a file format for MVC is introduced. View synthesis is performed entirely within GPU. It is demonstrated that the MVC viewer can decode a MVC bitstream and generate a virtual camera image in real-time.
Mucosal and Peripheral Lin− HLA-DR+ CD11c/123− CD13+ CD14− Mononuclear Cells Are Preferentially Infected during Acute Simian Immunodeficiency Virus Infection

ABSTRACT Massive infection of memory CD4 T cells is a hallmark of early simian immunodeficiency virus (SIV) infection, with viral infection peaking at day 10 postinfection (p.i.), when a majority of memory CD4 T cells in mucosal and peripheral tissues are infected. It is not clear if mononuclear cells from the monocyte and macrophage lineages are similarly infected during this early phase of explosive HIV and SIV infections. Here we show that, at day 10 p.i. , Lin− HLA-DR+ CD11c/123− CD13+ CD14− macrophages in the jejunal mucosa were infected, albeit at lower levels than CD4 memory T cells. Interestingly, Lin− HLA-DR+ CD11c/123− CD13+ CD14− macrophages in peripheral blood, like their mucosal counterparts, were preferentially infected compared to Lin− HLA-DR+ CD11c/123− CD13+ CD14+ monocytes, suggesting that differentiated macrophages were selectively infected by SIV. CD13+ CD14− macrophages expressed low levels of CD4 compared to CD4 T cells but expressed similar levels of CCR5 as lymphocytes. Interestingly, CD13+ CD14− macrophages expressed Apobec3G at lower levels than CD13+ CD14+ monocytes, suggesting that intracellular restriction may contribute to the differential infection of mononuclear subsets. Taken together, our results suggest that CD13+ CD14− macrophages in mucosal and peripheral tissues are preferentially infected very early during the course of SIV infection.
Bandwidth-rate-distortion optimized motion estimation

Motion estimation process is the most computational and memory intensive component in video encoders. However, traditional motion estimation algorithms focus on rate and distortion performance and do not take memory bandwidth into consideration. As a result, its performance will be degraded under bandwidth constraint environment. In this paper, a bandwidth-rate-distortion optimized motion estimation algorithm is introduced to solve the above issue. Simulation results show that the proposed method could achieve similar performance as the bandwidth unconstrained method with up to 70% bandwidth saving.
The Chromosomes in Human Cancer and Leukemia

The past decade has witnessed significant advances in our understanding of some aspects of cancer biology, especially the genetic changes in cancer cells. During this period, the critical role of chromosome changes in the complex process of malignant transformation has received further recognition. For years, the cytogenetic database has been tapped by molecular biologists who have used the information as a starting point to tackle problems at the molecular level. Cytogenetic analysis was the key to defining two major categories of genetic rearrangements, namely, recurring chromosomal translocations and consistent deletions. These abnormalities have now been shown to contribute to the oncogenic process through either the modification and activation of cellular protooncogenes or the inactivation of tumor suppressor genes. Clinicians have also used cytogenetic information to assign prognosis in acute leukemia, lymphoma, and certain solid tumors. Thus, the karyotypic picture of any particular tumor has become of value to clinicians, biologists,
Isoflavone Agonists of IRF-3 Dependent Signaling Have Antiviral Activity against RNA Viruses

ABSTRACT There is a growing need for novel antiviral therapies that are broad spectrum, effective, and not subject to resistance due to viral mutations. Using high-throughput screening methods, including computational docking studies and an interferon-stimulated gene 54 (ISG54)-luciferase reporter assay, we identified a class of isoflavone compounds that act as specific agonists of innate immune signaling pathways and cause activation of the interferon regulatory factor (IRF-3) transcription factor. The isoflavone compounds activated the ISG54 promoter, mediated nuclear translocation of IRF-3, and displayed highly potent activity against hepatitis C virus (HCV) and influenza virus. Additionally, these agonists efficiently activated IRF-3 in the presence of the HCV protease NS3-4A, which is known to blunt the host immune response. Furthermore, genomic studies showed that discrete innate immune pathways centered on IRF signaling were regulated following agonist treatment without causing global changes in host gene expression. Following treatment, the expression of only 64 cellular genes was significantly induced. This report provides the first evidence that innate immune pathways dependent on IRF-3 can be successfully targeted by small-molecule drugs for the development of novel broad-spectrum antiviral compounds.
Induction of the Cellular MicroRNA, Hs_154, by West Nile Virus Contributes to Virus-Mediated Apoptosis through Repression of Antiapoptotic Factors

ABSTRACT MicroRNAs (miRNAs) are a class of noncoding small RNAs that regulate multiple cellular processes, as well as the replication and pathogenesis of many DNA viruses and some RNA viruses. Examination of cellular miRNA profiles in West Nile virus (WNV)-infected HEK293 and SK-N-MC cells revealed increased expression of multiple miRNA species. One of these miRNAs, Hs_154, was significantly induced not only in WNV-infected neuronal cells in culture but also in the central nervous system tissues of infected mice and, upon transfection, caused a significant reduction in viral replication. Analysis of mRNA transcripts enriched through immunoprecipitation of the RNA-induced silencing complex identified several transcripts that contain seed sequence matches to Hs_154 in their 3′ untranslated regions (UTRs). Two of these targets, the CCCTC-binding factor (CTCF) and the epidermal growth factor receptor (EGFR)-coamplified and overexpressed protein (ECOP/VOPP1) proteins display reduced expression in WNV-infected cells, and the 3′ UTRs of these transcripts were sufficient to cause downregulation of expression in infected cells or in cells transfected with Hs_154, findings consistent with miRNA targeting of these transcripts. CTCF and ECOP have been shown to be associated with cell survival, implicating miRNA-directed repression of these targets in WNV-induced cell death. Consistent with this hypothesis, expression of these genes in WNV-infected cells results in a reduction in the number of cells undergoing apoptosis. These observations suggest that induction of Hs_154 expression after WNV infection modulates the apoptotic response to WNV and that cellular miRNA expression can be quickly altered during WNV infection to control aspects of the host response.
Detection and management of asymptomatic myocardial injury after noncardiac surgery

Surgery and the subsequent recovery are serious circulatory stress tests that may result in symptomatic cardiac events in vulnerable patients. Despite efforts to prevent the occurrence of postoperative adverse events, myocardial infarction following noncardiac surgery remains common. Even more worrisome, the typical symptoms of myocardial ischaemia, such as chest pain, are easily masked by postoperative pain treatment including opioids. As a consequence, the clinical course of postoperative myocardial infarction is mainly silent. Yet, cardiac morbidity and mortality rates in patients with asymptomatic postoperative myocardial infarction reportedly are similar to those among patients with a clinical diagnosis of myocardial infarction. As postoperative myocardial infarction may go largely undetected, the available evidence further indicates significant elevations of risk in postoperative patients with increases in circulating biomarkers reflecting cardiac cell damage, such as troponin, but without a conventional clinical diagnosis of myocardial infarction. Silent myocardial injury, as documented by elevated cardiac biomarkers, may occur in 10–20% of the patients undergoing noncardiac surgery. A metaanalysis of studies in such patients showed isolated troponin elevations to be a strong independent predictor of mortality within the first year after surgery. Moreover, the VISION study, including over 15,000 noncardiac surgery patients, showed a strong association between any troponin elevation after surgery, which occurred in 11% of the patients, and 30-day mortality. After implementing routine postoperative troponin monitoring in elderly noncardiac surgery patients at our institution, we found similar results: 19% of the patients had a troponin elevation following surgery and such elevation was significantly associated with 30-day mortality. These patients go largely undetected, and if detected, clinical guidelines for the management of isolated increases in cardiac biomarkers do presently not exist. Coronary plaque rupture
Novel projector calibration approaches of multi-resolution display

This paper proposes convenient and useful approaches to automatically calibrate the projectors of a multi-resolution display. The proposed approaches estimate both the keystone effect and misalignment of the projections with an assistance of a color camera. Structured light patterns are employed to construct the geometric relationship between projectors and the projection surface, and then pre-warp the images so that they appear undistorted as a result. Experimental results demonstrate that the proposed approaches successfully reduce the human-effort and lower the calibration time of multi-resolution display calibration task.
Hepatitis C Virus (HCV) Induces Formation of Stress Granules Whose Proteins Regulate HCV RNA Replication and Virus Assembly and Egress

ABSTRACT Stress granules (SGs) are cytoplasmic structures that are induced in response to environmental stress, including viral infections. Here we report that hepatitis C virus (HCV) triggers the appearance of SGs in a PKR- and interferon (IFN)-dependent manner. Moreover, we show an inverse correlation between the presence of stress granules and the induction of IFN-stimulated proteins, i.e., MxA and USP18, in HCV-infected cells despite high-level expression of the corresponding MxA and USP18 mRNAs, suggesting that interferon-stimulated gene translation is inhibited in stress granule-containing HCV-infected cells. Finally, in short hairpin RNA (shRNA) knockdown experiments, we found that the stress granule proteins T-cell-restricted intracellular antigen 1 (TIA-1), TIA1-related protein (TIAR), and RasGAP-SH3 domain binding protein 1 (G3BP1) are required for efficient HCV RNA and protein accumulation at early time points in the infection and that G3BP1 and TIA-1 are required for intracellular and extracellular infectious virus production late in the infection, suggesting that they are required for virus assembly. In contrast, TIAR downregulation decreases extracellular infectious virus titers with little effect on intracellular RNA content or infectivity late in the infection, suggesting that it is required for infectious particle release. Collectively, these results illustrate that HCV exploits the stress granule machinery at least two ways: by inducing the formation of SGs by triggering PKR phosphorylation, thereby downregulating the translation of antiviral interferon-stimulated genes, and by co-opting SG proteins for its replication, assembly, and egress.
Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

ABSTRACT Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890–3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the “GENETIC classification”). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.
Content-aware auto-soundtracks for personal photo music slideshows

We present a novel slideshow generation concept based on content-aware photo-music mapping. Current technologies for automated personal photo slideshow generation primarily focus on photo presentations and visual effects. These solutions utilize either a manually chosen single song or preset slideshow songs. Our technology focuses on an automatic soundtrack generation process that attempts to comprehend what the photos depict and choose music accordingly. The process comprises analyzing a photo album, composing an auto-soundtrack by dynamically mapping song segments to photo events, and automatically choosing content-aware transitions and visual effects appropriate for the presentation.
Foamy Virus Envelope Glycoprotein-Mediated Entry Involves a pH-Dependent Fusion Process

ABSTRACT In general, enveloped viruses use two different entry strategies and are classified accordingly into pH-dependent and pH-independent viruses. Different members of the retrovirus family use one or the other strategy. Little is known about the uptake of foamy viruses (FV), a special group of retroviruses, into the target cells. In this study, we examined the pH dependence of FV entry by analyzing FV envelope glycoprotein (Env)-mediated infection of target cells with murine leukemia virus or FV vector pseudotypes in the presence of various lysosomotropic agents. Similar to vesicular stomatitis virus glycoprotein G (VSV-G)-mediated uptake, FV Env-mediated entry was inhibited by various lysosomotropic agents, suggesting a pH-dependent endocytic pathway. However, in contrast to its effect on VSV-G pseudotypes, chloroquine failed to reduce the infectivity of FV Env pseudotypes, implying that the pathway is different from that of VSV-G. Glycoproteins of various other FV species showed inhibition profiles similar to that of the prototype FV (PFV) Env. Analysis of the pH dependence of the FV Env-mediated fusion process in a cell-to-cell fusion assay revealed an induction of syncytium formation by a short exposure to acidic pH, peaking around pH 5.5. Interestingly, of all FV Env species analyzed, only the PFV Env had a significant fusion activity at neutral pH. Taken together, these data suggest a pH-dependent endocytic pathway for infection of target cells by FV.