Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and Dynamics of Adeno-Associated Virus Serotype 1 VP1-Unique N-Terminal Domain and Its Role in Capsid Trafficking

ABSTRACT The importance of the phospholipase A2 domain located within the unique N terminus of the capsid viral protein VP1 (VP1u) in parvovirus infection has been reported. This study used computational methods to characterize the VP1 sequence for adeno-associated virus (AAV) serotypes 1 to 12 and circular dichroism and electron microscopy to monitor conformational changes in the AAV1 capsid induced by temperature and the pHs encountered during trafficking through the endocytic pathway. Circular dichroism was also used to monitor conformational changes in AAV6 capsids assembled from VP2 and VP3 or VP1, VP2, and VP3 at pH 7.5. VP1u was predicted (computationally) and confirmed (in solution) to be structurally ordered. This VP domain was observed to undergo a reversible pH-induced unfolding/refolding process, a loss/gain of α-helical structure, which did not disrupt the capsid integrity and is likely facilitated by its difference in isoelectric point compared to the other VP sequences assembling the capsid. This study is the first to physically document conformational changes in the VP1u region that likely facilitate its externalization from the capsid interior during infection and establishes the order of events in the escape of the AAV capsid from the endosome en route to the nucleus.
Complete Genome Sequence of a Recombinant Nephropathogenic Infectious Bronchitis Virus Strain in China

ABSTRACT Recently, nephropathogenic infectious bronchitis virus (IBV) outbreaks have occurred in commercial broiler flocks and have been associated with a high incidence and morbidity in China. The CK/CH/Zhejiang/06/10 strain (IBV-YX10) was isolated from a 12-day-old broiler chicken in a flock of chickens with swollen speckled kidneys and distended ureters filled with uric acid in China in 2010. Here we reported the complete genomic sequence of the IBV-YX10 which was a natural recombinant nephropathogenic infectious bronchitis virus strain. These findings will contribute additional insights into the molecular characteristics of evolving IBV genomes and the need for effective control of IBV in China.
A Standard Ionization Chamber for Grenz Rays

Abstract A special type of chamber has been designed to measure the ionization produced by from 3 to 12 K.V. x-rays in a known volume of unrestricted air, thus making it possible to express the intensity of the x-ray beam in roentgens per minute. By the use of a very small guarded field ionization chamber (5 × 5 cm.), the air absorption correction is reduced several fold, and hence errors in its determination are not so serious in the final result sought. It is shown that air absorption corrections must be determined separately for each beam of radiation used, and the chamber is so designed that the necessary corrections may be determined without recourse to other special apparatus. Examples are given showing in detail the methods of making measurements with the chamber described. Compared at higher voltages (from 40 to 90 K.V.) with a large primary standard ionization chamber, the small type here described shows a divergence of about ±0.5 per cent which is believed to be the over-all error present in its.
Complete Genome Sequence of Equine Herpesvirus Type 9

ABSTRACT Equine herpesvirus type 9 (EHV-9), which we isolated from a case of epizootic encephalitis in a herd of Thomson's gazelles (Gazella thomsoni) in 1993, has been known to cause fatal encephalitis in Thomson's gazelle, giraffe, and polar bear in natural infections. Our previous report indicated that EHV-9 was similar to the equine pathogen equine herpesvirus type 1 (EHV-1), which mainly causes abortion, respiratory infection, and equine herpesvirus myeloencephalopathy. We determined the genome sequence of EHV-9. The genome has a length of 148,371 bp and all 80 of the open reading frames (ORFs) found in the genome of EHV-1. The nucleotide sequences of the ORFs in EHV-9 were 86 to 95% identical to those in EHV-1. The whole genome sequence should help to reveal the neuropathogenicity of EHV-9.
Surgical Preparation for Articular Cartilage Regeneration in the Osteoarthritic Knee Joint

Purpose: Autologous chondrocyte implantation (ACI) is a treatment option even in early osteoarthritis (OA). Surgical preparation for ACI should avoid penetration of the subchondral bone plate to prevent hemorrhage, fibrin clot formation, and subsequent activation of the inflammatory response. Hypothesis: Current surgical procedures with ring curettes preserve the integrity of the subchondral bone plate, even in patients with OA. Methods: Subchondral femoral bone plates (n = 40) of OA knees undergoing total knee arthroplasty were prepared in vivo using standard, non–brute-force debridement for ACI. To approach regular wear/early OA, only cartilage with maximally grade 3A International Cartilage Repair Society score was prepared. Effects were analyzed by light microscopy. Results: In 87.5% of the specimens (35/40), standard debridement did not violate the tide mark, except for occasional minor openings with a smooth edge (diameter approximately 20 µm). In contrast, 5/40 samples (12.5%) showed one large area with a missing bone plate and an open bone marrow space. Twenty-eight specimens (70%) showed at least remnants of uncalcified cartilage. Conclusion: On the basis of size/fine structure, the occasional minor openings are likely due to increased vascular penetration through the tide mark in the pathologically altered bone-cartilage interface in OA. The consequences of limited hemorrhage through minor openings or selected large defects following in vivo debridement are still unknown. Thus, standard debridement appears suitable for cartilage regeneration even in OA defects.
Light Absorptive Properties of Articular Cartilage, ECM Molecules, Synovial Fluid, and Photoinitiators as Potential Barriers to Light-Initiated Polymer Scaffolding Procedures

Objective Many in vivo procedures to repair chondral defects use ultraviolet (UV)-photoinitiated in situ polymerization within the cartilage matrix. Chemical species that absorb UV light might reduce the effectiveness of these procedures by acting as light absorption barriers. This study evaluated whether any of the individual native biochemical components in cartilage and synovial fluid interfered with the absorption of light by common scaffolding photosensitizers. Materials UV-visible spectroscopy was performed on each major component of cartilage in solution, on bovine synovial fluid, and on four photosensitizers, riboflavin, Irgacure 2959, quinine, and riboflavin-5′-phosphate. Molar extinction and absorption coefficients were calculated at wavelengths of maximum absorbance and 365 nm. Intact articular cartilage was also examined. Results The individual major biochemical components of cartilage, Irgacure 2959, and quinine did not exhibit a significant absorption at 365 nm. Riboflavin and riboflavin-5′-phosphate were more effectual light absorbers at 365 nm, compared with the individual native species. Intact cartilage absorbed a significantly greater amount of UV light in comparison with the native species. Conclusion Our results indicate that none of the individual native species in cartilage will interfere with the absorption of UV light at 365 nm by these commonly used photoinitiators. Intact cartilage slices exhibited significant light absorption at 365 nm, while also having distinct absorbance peaks at wavelengths less than 300 nm. Determining the UV absorptive properties of the biomolecules native to articular cartilage and synovial fluid will aid in optimizing scaffolding procedures to ensure sufficient scaffold polymerization at a minimum UV intensity.
Interfacing liquid metals with stretchable metal conductors.

UNLABELLED Highly stretchable conductors are essential components in deformable electronics. Owing to their high stretchability and conductivity, liquid metals have attracted significant attention for use as circuits and interconnections. However, their poor wettability to stretchable metal electrodes prevents the formation of stable electrical connections. This study examined two approaches for creating a stable interface between a liquid metal (EGaIn) and stretchable metal electrodes via: (i) the use of honeycomb-structured stretchable metal electrodes and (ii) the addition of a conducting polymer interlayer. The line width of the honeycomb had a significant influence on the formation of a stable interface. The liquid metal formed a stable film layer on honeycomb metal electrodes, which have line widths of less than 50 μm. Coating PEDOT PSS with a nonionic surfactant lowered the interfacial energy of EGaIn with flat stretchable metal surfaces; hence EGaIn was coated uniformly on the stretchable metal surfaces. Strain sensors were fabricated as a demonstrative example of an application that utilizes the stable interface.
Whole-Genome Characterization and Genotyping of Global WU Polyomavirus Strains

ABSTRACT Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.
Impact of Human Immunodeficiency Virus Type 1 Resistance to Protease Inhibitors on Evolution of Resistance to the Maturation Inhibitor Bevirimat (PA-457)

ABSTRACT The maturation inhibitor bevirimat [3-O-(3′,3′dimethysuccinyl)betulinic acid; BVM; also known as PA-457 or DSB] potently inhibits human immunodeficiency virus type 1 (HIV-1) replication by blocking protease (PR)-mediated cleavage at the junction between capsid (CA) and spacer peptide 1 (SP1) in Gag. We previously isolated a panel of single-amino-acid substitutions that confer resistance to BVM in vitro (C. S. Adamson, S. D. Ablan, I. Boeras, R. Goila-Gaur, F. Soheilian, K. Nagashima, F. Li, K. Salzwedel, M. Sakalian, C. T. Wild, and E. O. Freed, J. Virol. 80:10957-10971, 2006). The BVM resistance mutations cluster at or near the CA-SP1 cleavage site. Because BVM likely will be used clinically in patients harboring viruses resistant to PR inhibitors (PIs), in this study we evaluated the interplay between a PI-resistant (PIR) PR and the BVM resistance mutations in Gag. As expected, the PIR mutations had no effect on inhibition by BVM; however, we observed general processing defects and a slight delay in viral replication in Jurkat T cells associated with the PIR mutations, even in the absence of compound. When combined, most BVM resistance and PIR mutations acted additively to impair viral replication, particularly in the presence of BVM. The BVM-resistant mutant SP1-A1V was an exception, as it supported robust replication in the context of either wild-type (WT) or PIR PR, even at high BVM concentrations. Significantly, the emergence of BVM resistance was delayed in the context of the PIR PR, and the SP1-A1V mutation was acquired most frequently with either WT or PIR PR. These results suggest that resistance to BVM is less likely to emerge in patients who have failed PIs than in patients who are PI naïve. We predict that the SP1-A1V substitution is the most likely to emerge in vivo, as this mutant replicates robustly independently of PR mutations or BVM. These findings offer insights into the effect of PIR mutations on the evolution of BVM resistance in PI-experienced patients.
Complete Genome Sequence of a Subgenotype VIId Newcastle Disease Virus Circulating Predominantly in Chickens in China

ABSTRACT At least 11 genotypes of class II viruses have been identified since the discovery of Newcastle disease virus (NDV) in 1926. Here, we reported the complete genome sequence of a prevalent NDV variant from China, belonging to subgenotype VIId in class II. The similar viruses have been the predominant strains circulating in China for the past decade, which occupied over 80% of Chinese prevalent strains and were phylogenetically different from currently available vaccines.
Production of Nanopowders of Metal Oxides Using Pulsed Electron Beam in Low Pressure Gas

The installation for production of metal oxide nanopowders was created. The method involves evaporation of the target by a pulsed-electron beam, condensation of the vapors of the material in a low-pressure gas, and deposition of nanopowders on a cold large-area crystallizer. In a new installation, a higher-power electron gun with a hollow cathode, which ensures the formation of the current pulse of the electron beam with amplitude up to 1 A and a duration of 100 μs, and a crystallizer of a larger diameter (0.3 m) and length (0.5 m), which makes it possible to decrease the agglomeration, were used. The results of the evaporation of targets made of YSZ, C e G d O 𝑥 , Zn-ZnO, Al 2O 3, and ZnO were presented. Room-temperature ferromagnetism has been observed in YSZ, Zn-ZnO, and Cu(Al)-doped Al 2O 3. The proposed method makes it possible to obtain nanopowders of oxides with a characteristic particle size of 3–5 nm and agglomerates consisting of them 20–600 nm in size, specific surfaces of up 338 m 2/g, productivity of up to 12 g/h, and a specific power consumption ≥112 (W h)/g.
Pediatric cervical spine

pediatric cervical spine is steadily growing. This issue of Neurosurgical Focus is intended to augment that knowledge base by concentrating exclusively on issues regarding the subaxial pediatric cervical spine. A number of authors have contributed their expertise so that a wide variety of important topics are covered. The topics range from managing traumatic injuries of the pediatric cervical spine to evaluating difficult deformity problems after spinal cord tumor resection. Original and review articles are included to give the reader both historical perspective and cuttingedge knowledge of pediatric cervical spine management principles. It is hoped that this issue of Neurosurgical Focus and its contents will be a springboard toward further understanding of this important and fascinating topic. Neurosurg Focus 20 (2):Intro, 2006
Cytomegalovirus Proteins vMIA and m38.5 Link Mitochondrial Morphogenesis to Bcl-2 Family Proteins

ABSTRACT Apoptosis is a host defense mechanism against viruses that can be subverted by viral gene products. Human cytomegalovirus encodes viral mitochondria-localized inhibitor of apoptosis (vMIA; also known as pUL37x1), which is targeted to mitochondria and functions as a potent cell death suppressor by binding to and inhibiting proapoptotic Bcl-2 family members Bax and Bak. vMIA expression also dramatically alters mitochondrial morphology, causing the fragmentation of these organelles. A potential ortholog of vMIA, m38.5, which was identified in murine cytomegalovirus, has been shown to localize to mitochondria and protect against chemically induced apoptosis by unknown mechanisms. Despite sharing negligible homology with vMIA and no region detectably corresponding to the vMIA Bax-binding domain, we find that m38.5, like vMIA, binds to Bax and recruits Bax to mitochondria. Interestingly, m38.5 and vMIA appear to block Bax downstream of translocation to mitochondria and after an initial stage of Bax conformational change. In contrast to vMIA, m38.5 neither binds to Bak nor causes mitochondrial fragmentation. Consistently with Bax-selective inactivation by m38.5, m38.5 fragments mitochondria in Bak knockout (KO) cells and protects Bak KO cells from apoptosis better than Bax KO cells. Thus, vMIA and m38.5 share some, but not all, features of apoptosis regulation through Bcl-2 family interaction and allow the dissection of Bax translocation into discrete steps.
OFDM With Iterative Blind Channel Estimation

A new blind channel estimation technique is presented for uncoded orthogonal frequency-division multiplexing (OFDM) systems. Instead of using pilots to sound the channel, a decision algorithm first makes primary estimates of the data symbol for each subcarrier based on a constrained linear minimum mean square error (MMSE) criterion. Then, these estimates are applied to optimal MMSE channel estimation. The technique requires only one value from the time-frequency correlation of the channel transfer function. Performance is evaluated by simulation so that comparison can be made with known optimal coherent/differential detection. Compared with known decision-directed Kalman-based estimation and two pilot-aided OFDM schemes (block pilots and comb pilots), the presented technique performs better for regions with mid to high signal-to-noise ratios (SNRs). Its robustness to the time variation of the channel is also quantified by simulation, showing only small degradation in performance relative to the quasistatic case of wireless local area network (WLAN) systems. Finally, the impact of covariance assumptions in the channel modeling is quantified using simulation, offering a feel for the performance with mismatch between the channel model and the receiver assumptions.
Novel Power Adaptation Strategy for Space–Time-Coded Multiantenna Systems With Imperfect Channel State Information

This paper presents a strategy for allocating power in both space and time for beamforming space-time-coded multiantenna systems with imperfect channel state information at the transmitter (CSIT) over flat and quasi-static Rayleigh fading channels. We first develop a closed-form spatial-only (S-O) power allocation scheme based on a newly defined compressed signal-to-noise ratio (CSNR) criterion. The derived power allocation formula has a parameter (compression factor) that can be used to minimize the conditional bit error rate (BER). The BER performance of the new CSNR-based power allocation scheme is almost identical to the previous optimal S-O power allocation schemes, whereas its computation is more efficient. Using the CSNR-based power adaptation, we derive a joint spatio-temporal (S-T) power allocation method to minimize the average BER subject to a long-term (time) average of the transmit power constraint, which provides a large BER performance gain over the S-O power strategies and the existing S-T method. The practical issue of peak power constraint is also addressed.
Hepatitis B Virus Regulates Apoptosis and Tumorigenesis through the MicroRNA-15a-Smad7-Transforming Growth Factor Beta Pathway

ABSTRACT Hepatitis B virus (HBV) infection causes chronic hepatitis in hundreds of millions of people worldwide, which can eventually lead to hepatocellular carcinoma (HCC). Previously, we found that HBV mRNAs can absorb microRNA-15a (miR-15a) to affect apoptosis through the Bcl-2 pathway. We asked whether HBV could inhibit apoptosis and promote tumorigenesis through different pathways. In this study, we found that the transforming growth factor β (TGF-β) pathway-inhibitory factor Smad7 is a novel target of miR-15a. We demonstrated that HBV can upregulate the level of Smad7 by downregulating miR-15a. Furthermore, we examined the level of Smad7 in liver samples from HBV-infected HCC patients and found that HBV mRNAs are positively correlated with the level of Smad7. By taking the approach of using immunoblotting and luciferase reporter assays, we revealed that HBV can abrogate TGF-β signaling via upregulating Smad7. By using annexin V staining and caspase 3/7 activity assays, we found that HBV can inhibit TGF-β-induced apoptosis of HepG2 cells. We also showed that HBV can promote tumor growth in BALB/c nude mice through upregulating the expression of Smad7. In conclusion, we demonstrated that HBV can upregulate Smad7 expression and inhibit TGF-β signaling, which makes the cells resistant to TGF-β-induced apoptosis and promotes tumorigenesis. IMPORTANCE Hepatitis B virus (HBV) infection causes chronic hepatitis, which can eventually lead to hepatocellular carcinoma (HCC). TGF-β signaling is closely linked to liver fibrosis, cirrhosis, and subsequent HCC progression and plays a unique role in the pathogenesis of HCC. At the early stage of tumor formation, TGF-β functions as a tumor suppressor that inhibits cell proliferation and induces apoptosis. Previously, we found that HBV mRNAs can sponge off miR-15a to affect apoptosis through the Bcl-2 pathway. In this study, we identified that the TGF-β-inhibitory factor Smad7 is a novel target of miR-15a. We reveal that HBV can abrogate TGF-β signaling via upregulating Smad7, inhibit TGF-β-induced apoptosis, as well as promote tumor development. Our study provides evidence to support the idea that viral RNAs can exert their functions as competing endogenous RNAs (ceRNAs) toward microRNA and participate in important cellular processes.
Opportunistic Multiple Relay Selection With Outdated Channel State Information

The quality of channel state information (CSI) plays a significant role in the performance of relay selection (RS) schemes in cooperative communications. Particularly in a highly mobile environment when there exists delay between the selection and data transmission instants, the quality of CSI often degrades, given to what is known as outdated CSI phenomena. In this paper, we first outline several single RS schemes that achieve full diversity when using perfect CSI and prove that the diversity order of these schemes reduces to unity if outdated CSI exists. To deal with the performance deterioration due to the outdated CSI phenomena, we propose a new multiple RS scheme for both amplify-and-forward (AaF) and decode-and-forward (DaF) relay systems, namely, the plus normalized threshold opportunistic RS . In particular, we first opportunistically select best relays from all candidate relays with respect to end-to-end signal-to-noise ratios (SNRs) for AaF and relay-to-destination SNRs for DaF. Then, the ratios of the SNRs on the rest of the candidate relays to that of the th highest SNR are tested against a normalized threshold , and only those relays passing this test are selected in addition to the best relays. The performance of the scheme is theoretically analyzed in terms of outage probability, and its asymptotic diversity order is also examined. In addition, we outline a distributed selection protocol that makes no assumption of the global CSI at each relay. Numerical results confirm the analysis and show the advantage of the proposed scheme against existing counterparts in highly dynamic networks.
Enhanced Road Boundary and Obstacle Detection Using a Downward-Looking LIDAR Sensor

Detection of road boundaries and obstacles is essential for autonomous vehicle navigation. In this paper, we propose a road boundary and obstacle detection method using a downward-looking light detection and ranging sensor. This method extracts line segments from the raw data of the sensor in polar coordinates. After that, the line segments are classified into road and obstacle segments. To enhance the classification performance, the estimated roll and pitch angles of the sensor relative to the scanning road surface in the previous time step are then used. The classified road line segments are applied to track the road boundaries, roll, and pitch angles by using an integrated probabilistic data association filter. The proposed method was evaluated with the autonomous vehicle A1, which was the winner of the 2010 Autonomous Vehicle Competition in Korea organized by the Hyundai-Kia automotive group. The proposed method using the estimated roll and pitch angles can detect road boundaries and roadside, as well as road obstacles under various road conditions, including paved and unpaved roads and intersections.