Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletions of the Hypervariable Region (HVR) in Open Reading Frame 1 of Hepatitis E Virus Do Not Abolish Virus Infectivity: Evidence for Attenuation of HVR Deletion Mutants In Vivo

ABSTRACT Hepatitis E virus (HEV) is an important human pathogen, although little is known about its biology and replication. Comparative sequence analysis revealed a hypervariable region (HVR) with extensive sequence variations in open reading frame 1 of HEV. To elucidate the role of the HVR in HEV replication, we first constructed two HVR deletion mutants, hHVRd1 and hHVRd2, with in-frame deletion of amino acids (aa) 711 to 777 and 747 to 761 in the HVR of a genotype 1 human HEV replicon. Evidence of HEV replication was detected in Huh7 cells transfected with RNA transcripts from mutant hHVRd2, as evidenced by expression of enhanced green fluorescent protein. To confirm the in vitro results, we constructed three avian HEV mutants with various HVR deletions: mutants aHVRd1, with deletion of aa 557 to 585 (Δ557-585); aHVRd2 (Δ612-641); and aHVRd3 (Δ557-641). Chickens intrahepatically inoculated with capped RNA transcripts from mutants aHVRd1 and aHVRd2 developed active viral infection, as evidenced by seroconversion, viremia, and fecal virus shedding, although mutant aHVRd3, with complete HVR deletion, was apparently attenuated in chickens. To further verify the results, we constructed four additional HVR deletion mutants using the genotype 3 swine HEV as the backbone. Mutants sHVRd2 (Δ722-781), sHVRd3 (Δ735-765), and sHVRd4 (Δ712-765) were shown to tolerate deletions and were infectious in pigs intrahepatically inoculated with capped RNA transcripts from the mutants, whereas mutant sHVRd1 (Δ712-790), with a nearly complete HVR deletion, exhibited an attenuation phenotype in infected pigs. The data from these studies indicate that deletions in HVR do not abolish HEV infectivity in vitro or in vivo, although evidence for attenuation was observed for HEV mutants with a larger or nearly complete HVR deletion.
Varicella-Zoster Virus Open Reading Frame 48 Encodes an Active Nuclease

ABSTRACT Based on a DNA sequence and relative genomic position similar to those other herpesviruses, varicella-zoster virus (VZV) open reading frame 48 (ORF48) is predicted to encode an alkaline nuclease. Here we report the cloning, expression, purification, and characterization of recombinant VZV ORF48 protein and a VZV ORF48 point mutation (T172P). Protein encoded by wild-type ORF48, but not mutant protein, displayed both endo- and exonuclease activity, identifying ORF48 as a potential therapeutic target in VZV disease since efficient viral replication requires viral nuclease activity.
A 1.2-V Piecewise Curvature-Corrected Bandgap Reference in 0.5 $\mu$m CMOS Process

A 1.2-V piecewise curvature-corrected CMOS bandgap reference (BGR) is proposed. It features in utilizing piecewise nonlinear curvature-corrected current and rail-to-rail operational amplifier to a conventional first-order current-mode BGR. The corrected current is zero, exponential with temperature and proportional to the squared temperature in the lower, middle and higher temperature range (TR). The rail-to-rail operational amplifier biased by a current proportional to absolute temperature (PTAT) helps to provide negative feedback for the proposed BGR. Measured results indicate that the proposed BGR achieves temperature coefficient (TC) of 8.9 ppm/°C in the TR of -40°C-110°C without trimming, power supply rejection (PSR) of - 58 dB and line regulation of 2.4 mV/V in the supply range of 1.2-3.2 V. It is fabricated in CSMC 0.5-μ m mixed-signal CMOS process with power consumption of 48 μW and effective chip area of 0.1 mm2 .
Inhibition of Marburg Virus Budding by Nonneutralizing Antibodies to the Envelope Glycoprotein

ABSTRACT The envelope glycoprotein (GP) of Marburg virus (MARV) and Ebola virus (EBOV) is responsible for virus entry into host cells and is known as the only target of neutralizing antibodies. While knowledge about EBOV-neutralizing antibodies and the mechanism for the neutralization of infectivity is being accumulated gradually, little is known about antibodies that can efficiently regulate MARV infectivity. Here we show that MARV GP-specific monoclonal antibodies AGP127-8 (IgG1) and MGP72-17 (IgM), which do not inhibit the GP-mediated entry of MARV into host cells, drastically reduced the budding and release of progeny viruses from infected cells. These antibodies similarly inhibited the formation of virus-like particles (VLPs) consisting of GP, the viral matrix protein, and nucleoprotein, whereas the Fab fragment of AGP127-8 showed no inhibitory effect. Morphological analyses revealed that filamentous VLPs were bunched on the surface of VLP-producing cells cultured in the presence of the antibodies. These results demonstrate a novel mechanism of the antibody-mediated inhibition of MARV budding, in which antibodies arrest unformed virus particles on the cell surface. Our data lead to the idea that such antibodies, like classical neutralizing antibodies, contribute to protective immunity against MARV and that the “classical” neutralizing activity is not the only indicator of a protective antibody that may be available for prophylactic and therapeutic use.
A new edge detection algorithm using data fusion approaches

A robust edge detection algorithm for gray scale noisy images using data fusion approaches is presented. Two sets of multi-scale linear weighted gradient operators that show different directional properties with respect to impulse-type noise are utilized in the proposed algorithm. The complementary responses of the used operators are combined effectively to obtain a high level of edge localization and insensitivity with respect to noise. This is in contrast to conventional edge detection algorithms employing a single gradient operator that are very sensitive to noise. Simulation results obtained using a variety of noisy images to demonstrate the robustness of the proposed algorithm are presented.
A statistically efficient method for ellipse detection

In this paper, we introduce a statistically efficient method for detecting ellipses in an image. Given a set of digital arc segments, we introduce geometric criteria to select possible pairs of arc segments belonging to the same ellipse. The selected arc pairs are subsequently validated or rejected based on certain statistical criteria via hypothesis testing. The advantages of the technique include: 1) the proposed criteria are scale-invariant; and 2) they can automatically adapt to the noise characteristics of each image and do not need to be adjusted empirically. Performance evaluation of the technique with real images demonstrates its good performance.
Crystal Structure of Herpes Simplex Virus 2 gD Bound to Nectin-1 Reveals a Conserved Mode of Receptor Recognition

ABSTRACT Herpes simplex virus 1 (HSV-1) and HSV-2 are among the most prevalent human pathogens. Both viruses can recognize, via the surface envelope glycoprotein D (gD), human nectin-1 as a functional receptor. Previous studies have successfully elucidated the molecular basis of the binding between HSV-1 gD and nectin-1 by cocrystallography. Despite a high sequence identity between HSV-1 and HSV-2 gDs, the atomic intermolecule details for the HSV-2-gD/nectin-1 interaction remain elusive. Here, we report the crystal structures of both the unbound and the nectin-1-bound HSV-2 gDs. The free-gD structure expectedly comprises an IgV-like core and the surface-exposed terminal extensions as observed in its HSV-1 counterpart but lacks traceable electron densities for a large portion of the terminal elements. These terminal residues were clearly traced in the complex structure as a definitive loop in the N terminus and an α-helix in the C terminus, thereby showing a conserved nectin-1-binding mode as reported for HSV-1 gD. The interface residues in nectin-1 were further mutated and tested for the gD interaction by surface plasmon resonance. The resultant binding patterns were similar for HSV-1 and HSV-2 gDs, further supporting a homologous receptor-binding basis by the two viruses for nectin-1. These data, together with a cell-based fusion assay showing a cross-inhibition of the gD/nectin-1-mediated cell-cell fusion by soluble HSV-1 and HSV-2 gDs, provided solid structural and functional evidence that HSV-1 and HSV-2 recognize nectin-1 via the same binding mode. Finally, we also demonstrated that nectin-1 I80 is an important residue involved in gD interaction. IMPORTANCE Despite intensified studies, a detailed picture of the molecular features in the HSV-2-gD/nectin-1 interaction remains unavailable. Previous work focused on HSV-1 gD, which folds into an IgV-like core with large terminal extensions and utilizes the extension elements to engage nectin-1. Here, we report the crystal structures of HSV-2 gD in both the free and the nectin-1-bound forms. The atomic intermolecule details for HSV-2-gD/nectin-1 interaction are clearly presented. The observed binding mode is identical to that reported for its HSV-1 counterpart. This structural observation was further supported by our comparative functional assays showing that nectin-1 mutations similarly affect the ligand-receptor interaction of both virus gDs. Taken together, we provide comprehensive structural and functional data demonstrating a conserved receptor-binding mode between HSV-1 and HSV-2 for nectin-1. Our results also indicate that the tropism difference between the two viruses likely arises from aspects other than the gD/nectin-1 binding features.
Complete Genome Sequence of a Monosense Densovirus Infecting the Cotton Bollworm, Helicoverpa armigera

ABSTRACT Densoviruses (DNVs) infecting arthropods are members of the family Parvoviridae. Here we report the complete genome sequence of a novel DNV with a monosense genome that infects cotton bollworms (Helicoverpa armigera), named HaDNV-1. Alignment and phylogenetic analysis revealed that HaDNV-1 showed high identity with the genus Iteravirus.
Live Attenuated Influenza Viruses Containing NS1 Truncations as Vaccine Candidates against H5N1 Highly Pathogenic Avian Influenza

ABSTRACT Due to the high mortality associated with recent, widely circulating strains of H5N1 influenza virus in poultry, the recurring introduction of H5N1 viruses from birds to humans, and the difficulties in H5N1 eradication by elimination of affected flocks, an effective vaccine against HPAI (highly pathogenic avian influenza) is highly desirable. Using reverse genetics, a set of experimental live attenuated vaccine strains based on recombinant H5N1 influenza virus A/Viet Nam/1203/04 was generated. Each virus was attenuated through expression of a hemagglutinin protein in which the polybasic cleavage site had been removed. Viruses were generated which possessed a full-length NS1 or a C-terminally truncated NS1 protein of 73, 99, or 126 amino acids. Viruses with each NS genotype were combined with a PB2 polymerase gene which carried either a lysine or a glutamic acid at position 627. We predicted that glutamic acid at position 627 of PB2 would attenuate the virus in mammalian hosts, thus increasing the safety of the vaccine. All recombinant viruses grew to high titers in 10-day-old embryonated chicken eggs but were attenuated in mammalian cell culture. Induction of high levels of beta interferon by all viruses possessing truncations in the NS1 protein was demonstrated by interferon bioassay. The viruses were each found to be highly attenuated in a mouse model. Vaccination with a single dose of any virus conferred complete protection from death upon challenge with a mouse lethal virus expressing H5N1 hemagglutinin and neuraminidase proteins. In a chicken model, vaccination with a single dose of a selected virus encoding the NS1 1-99 protein completely protected chickens from lethal challenge with homologous HPAI virus A/Viet Nam/1203/04 (H5N1) and provided a high level of protection from a heterologous virus, A/egret/Egypt/01/06 (H5N1). Thus, recombinant influenza A/Viet Nam/1203/04 viruses attenuated through the introduction of mutations in the hemagglutinin, NS1, and PB2 coding regions display characteristics desirable for live attenuated vaccines and hold potential as vaccine candidates in poultry as well as in mammalian hosts.
Asynchronous Fine-Grain Power-Gated Logic

This paper presents a novel low-power logic family, called asynchronous fine-grain power-gated logic (AFPL). Each pipeline stage in the AFPL circuit is comprised of efficient charge recovery logic (ECRL) gates, which implement the logic function of the stage, and a handshake controller, which handles handshaking with the neighboring stages and provides power to the ECRL gates. In the AFPL circuit, ECRL gates acquire power and become active only when performing useful computations, and idle ECRL gates are not powered and thus have negligible leakage power dissipation. The partial charge reuse (PCR) mechanism can be incorporated in the AFPL circuit. With the PCR mechanism, part of the charge on the output nodes of an ECRL gate entering the discharge phase can be reused to charge the output nodes of another ECRL gate about to evaluate, reducing the energy dissipation required to complete the evaluation of an ECRL gate. Moreover, AFPL-PCR adopts an enhanced C-element, called C*-element, in its handshake controllers such that an ECRL gate in AFPL-PCR can enter the sleep mode early once its output has been received by the downstream pipeline stage. To mitigate the hardware overhead of the AFPL circuit, two techniques of circuit simplification have been developed.
Visual embedding of wavelet transform coefficients

In wavelet image compression using embedded quantization, visual quality can be improved by limiting the number of bits used to refine each significant coefficient to some maximum which is different for each sub-band. At a fixed bit rate, the bits saved are used to augment the number of coefficients coded. In this work, a refinement strategy for just noticeable degradation is obtained experimentally for a 5-scale wavelet decomposition, giving a specification for visually lossless quantization. For a range of higher compression ratios, psychovisual experimentation to determine viewer preferences produces a scheme for the allocation of refinement bits at low bit rates. The results are consistent between subjects and across a range of standard test images. The work is a step towards wavelet image coding in which the data stream is fully embedded for optimum visual quality.
Does the Design of Settings Where Acute Care Is Delivered Meet the Needs of Older People? Perspectives of Patients, Family Carers, and Staff

Background: Older people with an acute illness, many of whom are also frail, form a significant proportion of the acute hospital inpatient population. Attention is focusing on ways of improving the physical environment to optimize health outcomes and staff efficiency. Purpose: This article explores the effects of the physical environment in three acute care settings: acute hospital site, in-patient rehabilitation hospital, and intermediate care provision (a nursing home with some beds dedicated to intermediate care) chosen to represent different steps on the acute care pathway for older people and gain the perspectives of patients, family carers, and staff. Methods: Semi structured interviews were undertaken with 40 patient/carer dyads (where available) and three staff focus groups were conducted in each care setting with a range of staff. Results: Multiple aspects of the physical environment were reported as important by patients, family carers, and staff. For example, visitors stressed the importance of access and parking, patients valued environments where privacy and dignity were protected, storage space was poor across all sites, and security was important to patients but visitors want easy access to wards. Conclusions: The physical environment is a significant component of acute care for older people, many of whom are also frail, but often comes second to organization of care, or relationships between actors in an episode of care.
Functional Characterization of Bovine Viral Diarrhea Virus Nonstructural Protein 5A by Reverse Genetic Analysis and Live Cell Imaging

ABSTRACT Nonstructural protein 5A (NS5A) of bovine viral diarrhea virus (BVDV) is a hydrophilic phosphoprotein with RNA binding activity and a critical component of the viral replicase. In silico analysis suggests that NS5A encompasses three domains interconnected by two low-complexity sequences (LCSs). While domain I harbors two functional determinants, an N-terminal amphipathic helix important for membrane association, and a Zn-binding site essential for RNA replication, the structure and function of the C-terminal half of NS5A are still ill defined. In this study, we introduced a panel of 10 amino acid deletions covering the C-terminal half of NS5A. In the context of a highly efficient monocistronic replicon, deletions in LCS I and the N-terminal part of domain II, as well as in domain III, were tolerated with regard to RNA replication. When introduced into a bicistronic replicon, only deletions in LCS I and the N-terminal part of domain II were tolerated. In the context of the viral full-length genome, these mutations allowed residual virion morphogenesis. Based on these data, a functional monocistronic BVDV replicon coding for an NS5A variant with an insertion of the fluorescent protein mCherry was constructed. Live cell imaging demonstrated that a fraction of NS5A-mCherry localizes to the surface of lipid droplets. Taken together, this study provides novel insights into the functions of BVDV NS5A. Moreover, we established the first pestiviral replicon expressing fluorescent NS5A-mCherry to directly visualize functional viral replication complexes by live cell imaging.
Compound PCA-ICA neural network model for enhancement and feature extraction of multi-frequency polarimetric SAR imagery

Through its demixing operation, the potential use of independent components analysis (ICA) for multi-frequency polarimetric SAR imagery enhancement and feature extraction is demonstrated. A compound PCA-ICA neural network model is proposed, which consists of two levels of processing. The first one is the simultaneous diagonalization of the signal and signal-dependent noise covariance matrices using PCA transforms. The goal is to provide the PC images that are decorrelated and in which the SNR is improved. The second one consists of separating the noise from these images by providing new IC images in which the speckle is reduced. These images approach the PC ones and may be different only in their order and contrast. As a quantitative criterion, the contrast ratio is used, which value is smaller when the speckle is reduced. The model has been applied to the SIR-C data. The extracted features are quite effective for scene interpretation.
Faults Affecting Energy-Harvesting Circuits of Self-Powered Wireless Sensors and Their Possible Concurrent Detection

We analyze the effects of faults on an energy-harvesting circuit (EHC) providing power to a wireless biomedical multisensor node. We show that such faults may prevent the EHC from producing the power supply voltage level required by the multisensor node. Then, we propose a low-cost (in terms of power consumption and area overhead) additional circuit monitoring the voltage level produced by the EHC continuously, and concurrently with the normal operation of the device. Such a monitor gives an error indication if the generated voltage falls below the minimum value required by the sensor node to operate correctly, thus allowing the activation of proper recovery actions to guarantee system fault tolerance. The proposed monitor is self-checking with regard to the internal faults that can occur during its in-field operation, thus providing an error signal when affected by faults itself.
A histogram-based method for detection of faces and cars

We describe a statistical method for 3D object detection. We represent the statistics of both object appearance and "non-object" appearance using a product of histograms. Each histogram represents the joint statistics of a subset of wavelet coefficients and their position on the object. Our approach is to use many such histograms representing a wide variety of visual attributes. Using this method, we have developed the first algorithm that can reliably detect human faces that vary from frontal view to full profile view and the first algorithm that can reliably detect cars over a wide range of viewpoints.
Nine Complete Genome Sequences of Cutaneous Human Papillomavirus Genotypes Isolated from Healthy Skin of Individuals Living in Rural He Nan Province, China

ABSTRACT Nine novel human papillomavirus (HPV) types were isolated from healthy skin of individuals in rural Anyang, China. All of these isolates belong to the genus Gammapapillomavirus. These data will provide us with useful information for a better understanding of PV evolution and the relationship of PV with the host.
Extra-articular Ankle Stabilization

Maintenance of the foot at 90° to the lower leg following posterior calf lengthening or to prevent an equinus contracture in situations in which splint, cast, or external fixation is deemed inappropriate is a challenge. The author presents an observational case series involving 9 extra-articular ankle stabilizations performed in 9 consecutive patients. Each patient underwent his or her index surgery followed by percutaneous placement of 2 smooth 2.8-mm or larger diameter Steinmann pins extra-articular to the ankle joint. There were 6 men and 3 women with a mean age of 56.1 years (range, 31-73 years). Five patients had diabetes with peripheral neuropathy, 2 had critical limb ischemia, 1 had alcohol-induced neuropathy, 1 had lupus, and 1 was an active smoker. Eight patients had posterior calf lengthening, and 1 had open metatarsal fractures with severe soft-tissue disruption with an inability to use splint immobilization. Three patients had a transmetatarsal amputation, 2 patients had Chopart amputations, 2 patients had forefoot plastic surgery reconstructive procedures, 1 had a complex Charcot reconstruction, and 1 had a splittibialis anterior tendon transfer. Extra-articular ankle stabilization fixation was retained for a mean of 5.5 weeks (range, 2-10 weeks). Mean follow-up was 12 months (range, 1-17 months). All extra-articular stabilization procedures were deemed successful. When properly performed, extra-articular stabilization to maintain the foot at 90° to the lower leg represents a safe, simple, reliable, and minimally invasive technique useful in situations in which traditional splint or cast immobilization is not possible and when external fixation is deemed inappropriate.