Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembly Properties of Human Immunodeficiency Virus Type 1 Gag-Leucine Zipper Chimeras: Implications for Retrovirus Assembly

ABSTRACT Expression of the retroviral Gag protein leads to formation of virus-like particles in mammalian cells. In vitro and in vivo experiments show that nucleic acid is also required for particle assembly. However, several studies have demonstrated that chimeric proteins in which the nucleocapsid domain of Gag is replaced by a leucine zipper motif can also assemble efficiently in mammalian cells. We have now analyzed assembly by chimeric proteins in which nucleocapsid of human immunodeficiency virus type 1 (HIV-1) Gag is replaced by either a dimerizing or a trimerizing zipper. Both proteins assemble well in human 293T cells; the released particles lack detectable RNA. The proteins can coassemble into particles together with full-length, wild-type Gag. We purified these proteins from bacterial lysates. These recombinant “Gag-Zipper” proteins are oligomeric in solution and do not assemble unless cofactors are added; either nucleic acid or inositol phosphates (IPs) can promote particle assembly. When mixed with one equivalent of IPs (which do not support assembly of wild-type Gag), the “dimerizing” Gag-Zipper protein misassembles into very small particles, while the “trimerizing” protein assembles correctly. However, addition of both IPs and nucleic acid leads to correct assembly of all three proteins; the “dimerizing” Gag-Zipper protein also assembles correctly if inositol hexakisphosphate is supplemented with other polyanions. We suggest that correct assembly requires both oligomeric association at the C terminus of Gag and neutralization of positive charges near its N terminus.
Reducing Energy at the Minimum Energy Operating Point Via Statistical Error Compensation

This paper demonstrates that statistical error compensation reduces the energy consumption Emin at the minimum energy operating point (MEOP), which is known to occur in the subthreshold regime. In particular, the impact of algorithmic noise-tolerance (ANT) [1], in conjunction with frequency overscaling (FOS) and voltage overscaling, is studied in the context of an eight-tap finite impulse response (FIR) filter in a 45-nm CMOS process. At the nominal process corner and using low-Vt devices, we show that the ANT-based FIR filter achieves 20%-47% reduction in Emin and a 1.8×-2.25× increase in the frequency of operation over a conventional (error free) filter operating at its MEOP. This result is achieved via the ability of ANT to compensate for a precompensation error rate of 70%-85%. The use of high-Vt devices reduces Emin by 10%. This is due to the reduced effectiveness of FOS and increased sensitivity of delay to voltage variations. In the presence of process variations, the ANT-based FIR filter reduces Emin by 54% over a transistor up-sized design while meeting a fixed throughput constraint, and a parametric yield of 99.7%.
Improved Analytical Delay Models for RC-Coupled Interconnects

As process technologies scale into deep submicrometer region, crosstalk delay is becoming increasingly severe, especially for global on-chip buses. To cope with this problem, accurate delay models of coupled interconnects are needed. In particular, delay models based on analytical approaches are desirable, because they are not only largely transparent to technology, but also explicitly establish the connections between delays of coupled interconnects and transition patterns, thereby enabling crosstalk alleviating techniques such as crosstalk avoidance codes. Unfortunately, existing analytical delay models, such as the widely cited model in [1], have limited accuracy and do not account for loading capacitance. In this brief, we propose analytical delay models for coupled interconnects that address these disadvantages.
Texture modeling and classification in wavelet feature space

One difficulty of texture analysis and classification in the past was the lack of adequate tools to characterize textures over different scales. Previous developments in multiresolution analysis, such as the wavelet transform, promise ways to overcome this difficulty. We present a texture classification algorithm based on Markov modeling of intrascale and interscale statistical regularities of textures in the wavelet domain. The model provides an accurate multiscale texture representation and underlies a classification algorithm with a high classification rate.
Analyzing the Efficiency of L1 Caches for Reliable Hybrid-Voltage Operation Using EDC Codes

The increasing demand for highly miniaturized battery-powered ultralow cost systems (e.g., below 1 dollar) in emerging applications such as body, urban life and environment monitoring, and so on, has introduced many challenges in chip design. Such applications require high performance occasionally and very little energy consumption during most of the time to extend battery lifetime. In addition, they require real-time guarantees. Caches have been shown to be the most critical blocks in these systems due to their high energy/area consumption and hard-to-predict behavior. New, simple, hybrid-voltage operation (high Vcc and ultralow Vcc), single-Vcc domain L1 cache architectures based on replacing energy-hungry bitcells (e.g., 10T) by more energy-efficient and smaller cells (e.g., 8T) enhanced with error detection and correction codes have been recently proposed. Such designs provide significant energy and area efficiency without jeopardizing reliability levels to still provide strong performance guarantees. In this brief, we analyze the efficiency of these designs during ultralow voltage operation. We identify the limits of such approaches by finding an energy-optimal voltage region through experimental models. The experimental results show that area efficiency is always achieved in the range 200-400 mV, whereas both energy and area gains occur above 250 mV, i.e., in near-threshold regime.
New rule-based framework for post-processing merging in video sequence segmentation

This paper addresses the problem of semantic object segmentation in a video sequence for multimedia applications. It presents a new framework to generate a segmentation from multiple segmentations of an image (e.g. using intensity, motion, motion projections from past frames, etc.). We define a rule processor that applies a set of merging and splitting conditions to the segmentations. Each condition is model by a rule which is characterized by two functions, one to verify compliance, and the other to apply the rule. This framework is flexible since rules can be easily added or removed from the processor. Results obtained with two sets of simple rules show the possibilities offered by this framework.
Determinants of the Establishment of Human Immunodeficiency Virus Type 1 Latency

ABSTRACT Recent research has emphasized the notion that human immunodeficiency virus type 1 (HIV-1) latency is controlled by a restrictive histone code at, or DNA methylation of, the integrated viral promoter (long terminal repeat [LTR]). The present concept of HIV-1 latency has essentially been patterned from the principles of cellular gene regulation. Here we introduce an experimental system that allows for the qualitative and quantitative kinetic study of latency establishment and maintenance at the population level. In this system, we find no evidence that HIV-1 latency establishment is the consequence of downregulation of initial active infection followed by the establishment of a restrictive histone code at the viral LTR. Latent infection was established following integration of the virus in the absence of viral gene expression (silent integration) and was a function of the NF-κB activation level in the host cell at the time of infection. In the absence of a role for epigenetic regulation, we demonstrate that transcriptional interference, a mechanism that has recently been suggested to add to the stabilization of HIV-1 latency, is the primary mechanism to govern latency maintenance. These findings provide direct experimental evidence that the high number of viral integration events (>90%) found in actively expressed genes of CD4+ memory T cells from highly active antiretroviral therapy-suppressed patients represent indeed latent infection events and that transcriptional interference may be the primary mechanism to control HIV-1 latency in vivo. HIV-1 latency may thus not be governed by the principles of cellular gene regulation, and therapeutic strategies to deplete the pool of latently HIV-1-infected cells should be reconsidered.
A 0.325 V, 600-kHz, 40-nm 72-kb 9T Subthreshold SRAM with Aligned Boosted Write Wordline and Negative Write Bitline Write-Assist

This brief presents a two-port disturb-free 9T subthreshold static random access memory (SRAM) cell with independent single-ended read bitline and write bitline (WBL) and cross-point data-aware write structure to facilitate robust subthreshold operation and bit-interleaving architecture for enhanced soft error immunity. The design employs a variation-tolerant line-up write-assist scheme where the timing of areaefficient boosted write wordline and negative WBL are aligned and triggered/initiated by the same low-going global WBL to maximize the write-ability enhancement. A 72-kb test chip is implemented in United Microelectronics Corp. 40-nm low-power (40LP) CMOS. Full functionality is achieved for VDD ranging from 1.5 to 0.32 V without redundancy. The measured maximum operation frequency is 260 MHz (450 kHz) at 1.1 V (0.32 V) and 25 °C. At 0.325 V and 25 °C, the chip operates at 600 kHz with 5.78 μW total power and 4.69 μW leakage power, offering 2× frequency improvement compared with 300 kHz of our previous 72-kb 9T subthreshold SRAM design in the same 40LP technology. The energy efficiency (power/frequency/IO) at 0.325 V and 25 °C is 0.267 pJ/bit, a 23.7% improvement over the 0.350 pJ/bit of our previous design.
Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children

ABSTRACT Cardioviruses cause enteric infections in mice and rats which when disseminated have been associated with myocarditis, type 1 diabetes, encephalitis, and multiple sclerosis-like symptoms. Cardioviruses have also been detected at lower frequencies in other mammals. The Cardiovirus genus within the Picornaviridae family is currently made up of two viral species, Theilovirus and Encephalomyocarditis virus. Until recently, only a single strain of cardioviruses (Vilyuisk virus within the Theilovirus species) associated with a geographically restricted and prevalent encephalitis-like condition had been reported to occur in humans. A second theilovirus-related cardiovirus (Saffold virus [SAFV]) was reported in 2007 and subsequently found in respiratory secretions from children with respiratory problems and in stools of both healthy and diarrheic children. Using viral metagenomics, we identified RNA fragments related to SAFV in the stools of Pakistani and Afghani children with nonpolio acute flaccid paralysis (AFP). We sequenced three near-full-length genomes, showing the presence of divergent strains of SAFV and preliminary evidence of a distant recombination event between the ancestors of the Theiler-like viruses of rats and those of human SAFV. Further VP1 sequencing showed the presence of five new SAFV genotypes, doubling the reported genetic diversity of human and animal theiloviruses combined. Both AFP patients and healthy children in Pakistan were found to be excreting SAFV at high frequencies of 9 and 12%, respectively. Further studies are needed to examine the roles of these highly common and diverse SAFV genotypes in nonpolio AFP and other human diseases.
Antiviral Stilbene 1,2-Diamines Prevent Initiation of Hepatitis C Virus RNA Replication at the Outset of Infection

ABSTRACT The recent development of a cell culture model of hepatitis C virus (HCV) infection based on the JFH-1 molecular clone has enabled discovery of new antiviral agents. Using a cell-based colorimetric screening assay to interrogate a 1,200-compound chemical library for anti-HCV activity, we identified a family of 1,2-diamines derived from trans-stilbene oxide that prevent HCV infection at nontoxic, low micromolar concentrations in cell culture. Structure-activity relationship analysis of ∼300 derivatives synthesized using click chemistry yielded compounds with greatly enhanced low nanomolar potency and a >1,000:1 therapeutic ratio. Using surrogate models of HCV infection, we showed that the compounds selectively block the initiation of replication of incoming HCV RNA but have no impact on viral entry, primary translation, or ongoing HCV RNA replication, nor do they suppress persistent HCV infection. Selection of an escape variant revealed that NS5A is directly or indirectly targeted by this compound. In summary, we have identified a family of HCV inhibitors that target a critical step in the establishment of HCV infection in which NS5A translated de novo from an incoming genomic HCV RNA template is required to initiate the replication of this important human pathogen.
Temporomandibular Joint Magnetic Resonance Imaging Analysis in Adults with Steinert's Myotonic Dystrophy

El objetivo de este estudio, fue analizar las caracteristicas de la articulacion temporomandibular (ATM) en un grupo de pacientes adultos portadores de distrofia muscular de Steinert (DM1). Fueron evaluados 42 pacientes adultos, con edades entre 21 y 69 anos (Media=38,7619; DE=12,74) diagnosticados con DM1. Se realizo un estudio por RNM de ATM mediante imagenes sagitales de ATM derecha e izquierda en posicion de maxima intercuspidacion (MIC) y apertura maxima sin dolor, y se analizaron a) la calidad de las corticales de la fosa mandibular, tuberosidad y cabeza mandibular, b) la relacion cabeza mandibular- disco- tuberosidad articular en MIC, c) la forma anatomica del disco articular. Todos los pacientes presentaron alteraciones en la forma y superficie de las corticales de la fosa mandibular, tuberosidad articular y cabeza mandibular. Con respecto a la relacion de la CM en la FM, el 41% se encontro en la region 2B, el 29% 1B, 18% 1A, 9% 2A y 3% 2C de la ATM. El 49% de los discos en MIC se encontraron sobre la cabeza mandibular, 26% estaban desplazados anteriormente, 14% presentaron un dislocamiento anterior. El 38% presento alteraciones de la forma del disco y 30% presentaron conservada la forma anatomica. El 98% de los discos presentaron hiposenal en T1 y T2. La disminucion de la actividad muscular en los pacientes con DMS genera cambios degenerativos en la ATM visibles con RNM.
The Posterior Medial Blind Spot of the Distal Tibia

The distal tibial blind spot represents an area where improperly measured long screws may pose a risk to surrounding anatomic structures and is not well visualized on AP, mortise, and lateral radiographs. Awareness of this area as well as the use of a 45° external rotation oblique view when placing fixation in this area may prevent iatrogenic injury. Levels of Evidence: Level V, Expert Opinion
Source Coding and Preemphasis for Double-Edged Pulsewidth Modulation Serial Communication

Double-edged pulsewidth modulation (DPWM) is less sensitive to frequency-dependent losses in electrical chip-to-chip interconnects. However, the DPWM scheme instantaneously transmits information at a different rate than a synchronous source. This paper presents an 8-/9-bit line-coding scheme to compensate for the timing skew between the DPWM and synchronous clock domains while limiting the size of buffering required in the transmitter and receiver. Furthermore, preemphasis is introduced and analyzed as a means to improve the signal integrity of a DPWM signal. A multiphase-based, time interleaving receiver architecture using a sense amplifier is presented for high-speed data recovery. The DPWM transceiver is implemented in a 45-nm CMOS Silicon on insulator and operates at 10 Gbit/s with 10-12 bit error rate and consumes 96 mW. The power consumption of the 8-/9-bit coding hardware is 1.5 mW at 10 Gbit/s demonstrating low-power overhead.
A high-resolution image acquisition method with defect-pixel recovery for solid-state image sensors

For super-high-resolution image acquisition beyond HDTV, a CMOS image sensor is the most promising. At present, a CMOS image sensor with spatial resolution of 3K/spl times/4K and temporal resolution of 30 fps is being developed. The serious problem in fabricating such a super-high-resolution CMOS image sensor is a tremendously low yield rate, which is caused by occurrence of defect pixels. If defect pixels are recovered by some post-processing, we can improve the yield rate dramatically. From this point of view, we propose a new high-resolution image acquisition method which makes it possible to utilize a CMOS image sensor having many defect pixels. Our method deliberately takes a defocused image using an image sensor having defect pixels, applies a certain image recovery algorithm to it, and thus produces its focused and repaired version. We study the frequency response of our method using one-dimensionally sinusoidally changing chart images, and perform some experimental simulations on real images.
Design of Modified Second-Order Frequency Transformations Based Variable Digital Filters With Large Cutoff Frequency Range and Improved Transition Band Characteristics

The frequency transformation based filters (FT filters) provide an absolute control over the cutoff frequency. However, the cutoff frequency range (Ω<sub>c_range</sub>) of the FT filters is limited. The second-order frequency transformations combined with coefficient decimation technique based filter (FTCDM filter) has wider Ω<sub>c_range</sub> compared with the FT filter; however, the ratio of transition bandwidth of the transformed filter to that of the prototype filter, tbw<sub>FT</sub>/tbw<sub>mod</sub>, is large over a significant portion of Ω<sub>c_range</sub>. In this paper, we propose a novel idea of relaxing the one-to-one mapping condition between the frequency variables, to overcome the issue of limited Ω<sub>c_range</sub> for tbw<sub>FT</sub> ≤ tbw<sub>mod</sub>. In the proposed modified second-order frequency transformation based filter (MSFT filter), we relax the one-to-one mapping condition between the frequency variables and use low-pass to high-pass transformation on the prototype filter to achieve wider Ω<sub>c_range</sub> with tbw<sub>FT</sub> ≤ tbw<sub>mod</sub>. Design example shows that the MSFT filter provides 3 and 1.22 times wider Ω<sub>c_range</sub> compared to FT and FTCDM filters, respectively.
Progesterone-Based Contraceptives Reduce Adaptive Immune Responses and Protection against Sequential Influenza A Virus Infections

ABSTRACT In addition to their intended use, progesterone (P4)-based contraceptives promote anti-inflammatory immune responses, yet their effects on the outcome of infectious diseases, including influenza A virus (IAV) infection, are rarely evaluated. To evaluate their impact on immune responses to sequential IAV infections, adult female mice were treated with placebo or one of two progestins, P4 or levonorgestrel (LNG), and infected with a mouse-adapted H1N1 (maH1N1) virus. Treatment with P4 or LNG reduced morbidity but had no effect on pulmonary virus titers during primary H1N1 infection compared to placebo treatment. In serum and bronchoalveolar lavage fluid, total anti-IAV IgG and IgA titers and virus-neutralizing antibody titers but not hemagglutinin stalk antibody titers were lower in progestin-treated mice than placebo-treated mice. Females were challenged 6 weeks later with either an maH1N1 drift variant (maH1N1dv) or maH3N2 IAV. The level of protection following infection with the maH1N1dv was similar among all groups. In contrast, following challenge with maH3N2, progestin treatment reduced survival as well as the numbers and activity of H1N1- and H3N2-specific memory CD8+ T cells, including tissue-resident cells, compared with placebo treatment. In contrast to primary IAV infection, progestin treatment increased the titers of neutralizing and IgG antibodies against both challenge viruses compared with those achieved with placebo treatment. While the immunomodulatory properties of progestins protected immunologically naive female mice from the severe outcomes from IAV infection, it made them more susceptible to secondary challenge with a heterologous IAV, despite improving their antibody responses against a secondary IAV infection. Taken together, the immunomodulatory effects of progestins differentially regulate the outcome of infection depending on exposure history. IMPORTANCE The impact of hormone-based contraceptives on the outcome of infectious diseases outside the reproductive tract is rarely considered. Using a mouse model, we have made the novel observation that treatment with either progesterone or a synthetic analog found in hormonal contraceptives, levonorgestrel, impacts sequential influenza A virus infection by modulating antibody responses and decreasing the numbers and activity of memory CD8+ T cells. Progestins reduced the antibody responses during primary H1N1 virus infection but increased antibody titers following a sequential infection with either an H1N1 drift variant or an H3N2 virus. Following challenge with an H3N2 virus, female mice treated with progestins experienced greater mortality with increased pulmonary inflammation and reduced numbers and activity of CD8+ T cells. This study suggests that progestins significantly affect adaptive immune responses to influenza A virus infection, with their effect on the outcome of infection depending on exposure history.