bluuebunny/crossref_metadata_2025_split huggingface dataset:
Filtered backprojection proton CT reconstruction along most likely paths
Authors: Rit Simon , Dedes George , Freud Nicolas , Sarrut David , Létang Jean Michel 
Published: March 2013

Purpose:Proton CT (pCT) has the potential to accurately measure the electron density map of tissues at low doses but the spatial resolution is prohibitive if the curved paths of protons in matter is not accounted for. The authors propose to account for an estimate of the most likely path of protons in a filtered backprojection (FBP) reconstruction algorithm.Methods:The energy loss of protons is first binned in several proton radiographs at different distances to the proton source to exploit the depth‐dependency of the estimate of the most likely path. This process is named the distance‐driven binning. A voxel‐specific backprojection is then used to select the adequate radiograph in the distance‐driven binning in order to propagate in the pCT image the best achievable spatial resolution in proton radiographs. The improvement in spatial resolution is demonstrated using Monte Carlo simulations of resolution phantoms.Results:The spatial resolution in the distance‐driven binning depended on the distance of the objects from the source and was optimal in the binned radiograph corresponding to that distance. The spatial resolution in the reconstructed pCT images decreased with the depth in the scanned object but it was always better than previous FBP algorithms assuming straight line paths. In a water cylinder with 20 cm diameter, the observed range of spatial resolutions was 0.7 − 1.6 mm compared to 1.0 − 2.4 mm at best with a straight line path assumption. The improvement was strongly enhanced in shorter 200° scans.Conclusions:Improved spatial resolution was obtained in pCT images with filtered backprojection reconstruction using most likely path estimates of protons. The improvement in spatial resolution combined with the practicality of FBP algorithms compared to iterative reconstruction algorithms makes this new algorithm a candidate of choice for clinical pCT.
Micro‐CT artifacts reduction based on detector random shifting and fast data inpainting
Authors: Zhu Yining , Zhao Mengliu , Li Hongwei , Zhang Peng 
Published: March 2013

Purpose:In Micro‐CT systems based on optical coupling detectors, the defects of scintillator or CCD‐camera would lead to heavy artifacts in reconstructed CT images. Meanwhile, different detector units usually suffer from inhomogeneous response, which also leads to artifacts in the CT images. Detector shifting is a simple and efficient method to remove the artifacts due to inhomogeneous responses of detector units. However, it does not work well for heavy artifacts due to defects in scintillator or CCD. The purpose of this paper is to develop a data preprocessing method to reduce both kinds of artifacts.Methods:A hybrid method which involves detector random shifting and data inpainting is proposed to correct the projection data, so as to suppress the artifacts in the reconstructed CT images. The defects in scintillator or CCD‐camera lead to data lost in some areas of the projection data. The Criminisi algorithm is employed to recover the lost data. By detector random shifting, the location of the lost data in one view might be shifted away in adjacent views. This feature is utilized to design the search window, such that the best match patch shall be searched across adjacent views. By this way, the best match patches should really enjoy high similarity. As a result, the heavy artifacts due to defects of scintillator or CCD‐camera should be suppressed. Furthermore, a multiscale tessellation method is proposed to locate the defects and similarity patches, which makes the Criminisi algorithm very fast.Results:The authors tested the proposed method on both simulated projection data and real projection data. Experiments show that the proposed method could correct the bad data in the projections quite well. Compared to other popular methods, such as linear interpolation, wavelet combining Fourier transform, and TV‐inpainting, experimental results suggest that the CT images reconstructed from the preprocessed data sets by our method is significantly better in quality.Conclusions:They have proposed a hybrid method for projection data preprocessing which fits well to typical Micro‐CT systems. The hybrid method could suppress the ring artifacts in the reconstructed CT images efficiently, while the spatial resolution is not reduced even with a critical eye.
Genome Sequence of
Methanobrevibacter
sp. Strain JH1, Isolated from Rumen of Korean Native Cattle
Authors: Lee Jong-Hwan , Rhee Moon-Soo , Kumar Sanjay , Lee Geun-Hye , Chang Dong-Ho , Kim Dae-Soo , Choi Sang-Haeng , Lee Dong-Woo , Yoon Min-Ho , Kim Byoung-Chan 
Published: March 2013

ABSTRACT

The
Methanobrevibacter
sp. strain JH1 was isolated from the rumen of Korean native cattle (HanWoo;
Bos taurus
coreanae
). Here, we provide a 2.06-Mb draft genome sequence of strain JH1 that might provide more information about the lifestyle of rumen methanogens and about the genes and proteins that can be targeted to curb methane emissions.
Draft Genome Sequence of
Brevibacillus
sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture
Authors: Joshi M. N. , Sharma A. , Pandit A. S. , Pandya R. V. , Saxena A. K. , Bagatharia S. B. 
Published: March 2013

ABSTRACT

A Gram-positive bacterium,
Brevibacillus
sp. strain BAB-2500, was isolated as a lab contaminant in Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses genes for the reduction of arsenate and aluminum. These findings might provide insights into the utilization of this strain for improving crop production.
Genome Sequence of Enterobacter cancerogenus YZ1
Authors: Wei Yifeng , Yang Yu , Zhou Lisha , Liu Zhangyi , Wang Xiangyan , Yang Rentao , Su Qingqing , Zhou Yuping , Zhao Jiao , Yang Jun 
Published: March 2013

ABSTRACT

Enterobacter cancerogenus
is usually known as an opportunistic human pathogen. Recently, it has attracted great attention for its capability to produce bioemulsifier, degrade xenobiotics, and resist alkalis and antibiotics. Here we report the complete genome of
Enterobacter cancerogenus
YZ1, isolated from a bran-feeding
Coleoptera
insect's frass.
Genome Sequence of Lawsonia intracellularis Strain N343, Isolated from a Sow with Hemorrhagic Proliferative Enteropathy
Authors: Sait Michelle , Aitchison Kevin , Wheelhouse Nick , Wilson Kim , Lainson F. Alex , Longbottom David , Smith David G. E. 
Published: March 2013

ABSTRACT

Lawsonia intracellularis
is the etiological agent of proliferative enteropathy (PE), causing mild or acute hemorrhagic diarrhea in infected animals. Here we report the genome sequence of strain N343, isolated from a sow that died of hemorrhagic PE. N343 contains 24 single nucleotide polymorphisms and 90 indels compared to the reference strain PHE/MN1-00.
Draft Genome Sequence of
Fusarium fujikuroi
B14, the Causal Agent of the Bakanae Disease of Rice
Authors: Jeong Haeyoung , Lee Seunghoon , Choi Gyung Ja , Lee Theresa , Yun Sung-Hwan 
Published: March 2013

ABSTRACT

Here, we present the genome sequence of a Korean strain (B14) of
Fusarium fujikuroi
, a fungal rice pathogen. The final assembly consists of 455 contigs with 43,810,516 bp and 14,017 predicted genes. Comparison with the
F. verticillioides
7600 genome revealed a reference coverage of 83% (66.3% of reads mapped).
Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R
Authors: Remus-Emsermann Mitja N. P. , Kim Eun Bae , Marco Maria L. , Tecon Robin , Leveau Johan H. J. 
Published: March 2013

ABSTRACT

Bacteria belonging to the genus
Pantoea
are common colonizers of plant leaf surfaces. Here, we present the draft genome sequence of
Pantoea agglomerans
299R, a phyllosphere isolate that has become a model strain for studying the ecology of plant leaf-associated bacterial commensals.
The Nonstructural Protein 2C of a Picorna-Like Virus Displays Nucleic Acid Helix Destabilizing Activity That Can Be Functionally Separated from Its ATPase Activity
Authors: Cheng Zhenyun , Yang Jie , Xia Hongjie , Qiu Yang , Wang Zhaowei , Han Yajuan , Xia Xiaoling , Qin Cheng-Feng , Hu Yuanyang , Zhou Xi 
Published: March 2013

ABSTRACT

Picorna-like viruses in the
Picornavirales
order are a large group of positive-strand RNA viruses that include numerous important pathogens for plants, insects, and humans. In these viruses, nonstructural protein 2C is one of the most conserved proteins and contains ATPase activity and putative RNA helicase activity. Here we expressed 2C protein of
Ectropis obliqua
picorna-like virus (EoV; genus
Iflavirus
, family
Iflaviridae
, order
Picornavirales
) in a eukaryotic expression system and determined that EoV 2C displays ATP-independent nucleic acid helix destabilizing and strand annealing acceleration activity in a concentration-dependent manner, indicating that this picornaviral 2C is more like an RNA chaperone than like the previously predicted RNA helicase. Our further characterization of EoV 2C revealed that divalent metal ions, such as Mg
2+
and Zn
2+
, inhibit 2C-mediated helix destabilization to different extents. Moreover, we determined that EoV 2C also contains ATPase activity like that of other picornaviral 2C proteins and further assessed the functional relevance between its RNA chaperone-like and ATPase activities using mutational analysis as well as their responses to Mg
2+
. Our data show that, when one of the two 2C activities was dramatically inhibited or almost abolished, the other activity could remain intact, showing that the RNA chaperone-like and ATPase activities of EoV 2C can be functionally separated. This report reveals that a picorna-like virus 2C protein displays RNA helix destabilizing and strand annealing acceleration activity, which may be critical for picornaviral replication and pathogenesis, and should foster our understanding of picorna-like viruses and viral RNA chaperones.
KIR2DL4Copy Number Variation Is Associated with CD4+T-Cell Depletion and Function of Cytokine-Producing NK Cell Subsets in SIV-InfectedMamu-A*01-Negative Rhesus Macaques
Authors: Hellmann Ina , Letvin Norman L. , Schmitz Jörn E. 
Published: March 2013

ABSTRACTHere, we demonstrate thatKIR2DL4copy number variation (CNV) is associated with CD4+T-cell decline and functionality of cytokine-producing NK cells during primary simian immunodeficiency virus (SIV) infection inMamu-A*01−Indian-origin rhesus macaques, with higherKIR2DL4copy numbers being associated with a better preservation of CD4+T cells and an increased gamma interferon (IFN-γ) production from stimulated cytokine-producing NK cell subsets during acute SIVmac251 infection. These findings underscore the crucial role of activating killer-cell immunoglobulin-like receptors (KIRs) in NK cell-mediated SIV responses during early SIV infection.
Robust Immunity to an Auxotrophic Mycobacterium bovis BCG-VLP Prime-Boost HIV Vaccine Candidate in a Nonhuman Primate Model
Authors: Chege Gerald K. , Burgers Wendy A. , Stutz Helen , Meyers Ann E. , Chapman Rosamund , Kiravu Agano , Bunjun Rubina , Shephard Enid G. , Jacobs William R. , Rybicki Edward P. , Williamson Anna-Lise 
Published: March 2013

ABSTRACTWe previously reported that a recombinant pantothenate auxotroph ofMycobacterium bovisBCG expressing human immunodeficiency virus type 1 (HIV-1) subtype C Gag (rBCGpan-Gag) efficiently primes the mouse immune system for a boost with a recombinant modified vaccinia virus Ankara (rMVA) vaccine. In this study, we further evaluated the immunogenicity of rBCGpan-Gag in a nonhuman primate model. Two groups of chacma baboons were primed or mock primed twice with either rBCGpan-Gag or a control BCG. Both groups were boosted with HIV-1 Pr55gagvirus-like particles (Gag VLPs). The magnitude and breadth of HIV-specific cellular responses were measured using a gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISPOT) assay, and the cytokine profiles and memory phenotypes of T cells were evaluated by polychromatic flow cytometry. Gag-specific responses were detected in all animals after the second inoculation with rBCGpan-Gag. Boosting with Gag VLPs significantly increased the magnitude and breadth of the responses in the baboons that were primed with rBCGpan-Gag. These responses targeted an average of 12 Gag peptides per animal, compared to an average of 3 peptides per animal for the mock-primed controls. Robust responses of Gag-specific polyfunctional T cells capable of simultaneously producing IFN-γ, tumor necrosis alpha (TNF-α), and interleukin-2 (IL-2) were detected in the rBCGpan-Gag-primed animals. Gag-specific memory T cells were skewed toward a central memory phenotype in both CD4+and CD8+T cell populations. These data show that the rBCGpan-Gag prime and Gag VLP boost vaccine regimen is highly immunogenic, inducing a broad and polyfunctional central memory T cell response. This report further indicates the feasibility of developing a BCG-based HIV vaccine that is safe for childhood HIV immunization.
Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Empty Capsids
Authors: Halder Sujata , Nam Hyun-Joo , Govindasamy Lakshmanan , Vogel Michèle , Dinsart Christiane , Salomé Nathalie , McKenna Robert , Agbandje-McKenna Mavis 
Published: March 2013

ABSTRACT

The structure of single-stranded DNA (ssDNA) packaging H-1 parvovirus (H-1PV), which is being developed as an antitumor gene delivery vector, has been determined for wild-type (wt) virions and noninfectious (empty) capsids to 2.7- and 3.2-Å resolution, respectively, using X-ray crystallography. The capsid viral protein (VP) structure consists of an α-helix and an eight-stranded anti-parallel β-barrel with large loop regions between the strands. The β-barrel and loops form the capsid core and surface, respectively. In the wt structure, 600 nucleotides are ordered in an interior DNA binding pocket of the capsid. This accounts for ∼12% of the H-1PV genome. The wt structure is identical to the empty capsid structure, except for side chain conformation variations at the nucleotide binding pocket. Comparison of the H-1PV nucleotides to those observed in canine parvovirus and minute virus of mice, two members of the genus
Parvovirus
, showed both similarity in structure and analogous interactions. This observation suggests a functional role, such as in capsid stability and/or ssDNA genome recognition for encapsulation. The VP structure differs from those of other parvoviruses in surface loop regions that control receptor binding, tissue tropism, pathogenicity, and antibody recognition, including VP sequences reported to determine tumor cell tropism for oncotropic rodent parvoviruses. These structures of H-1PV provide insight into structural features that dictate capsid stabilization following genome packaging and three-dimensional information applicable for rational design of tumor-targeted recombinant gene delivery vectors.
Human Cell Tropism and Innate Immune System Interactions of Human Respiratory Coronavirus EMC Compared to Those of Severe Acute Respiratory Syndrome Coronavirus
Authors: Zielecki Florian , Weber Michaela , Eickmann Markus , Spiegelberg Larissa , Zaki Ali Moh , Matrosovich Mikhail , Becker Stephan , Weber Friedemann 
Published: March 2013

ABSTRACT
Infections with human coronavirus EMC (HCoV-EMC) are associated with severe pneumonia. We demonstrate that HCoV-EMC resembles severe acute respiratory syndrome coronavirus (SARS-CoV) in productively infecting primary and continuous cells of the human airways and in preventing the induction of interferon regulatory factor 3 (IRF-3)-mediated antiviral alpha/beta interferon (IFN-α/β) responses. However, HCoV-EMC was markedly more sensitive to the antiviral state established by ectopic IFN. Thus, HCoV-EMC can utilize a broad range of human cell substrates and suppress IFN induction, but it does not reach the IFN resistance of SARS-CoV.
H2AX Phosphorylation Is Important for LANA-Mediated Kaposi's Sarcoma-Associated Herpesvirus Episome Persistence
Authors: Jha Hem Chandra , Upadhyay Santosh Kumar , AJ Mahadesh Prasad , Lu Jie , Cai Qiliang , Saha Abhik , Robertson Erle S. 
Published: March 2013

ABSTRACT
The DNA damage response (DDR) of host cells is utilized by a number of viruses to establish and propagate their genomes in the infected cells. We examined the expression of the DDR genes during Kaposi's sarcoma-associated herpesvirus (KSHV) infection of human peripheral blood mononuclear cells (PBMCs). The genes were mostly downregulated, except H2AX, which was upregulated during infection. H2AX is important for gammaherpesvirus infectivity, and its phosphorylation at serine 139 is crucial for maintenance of latency during mouse gamma-herpesvirus 68 (MHV-68) infection. We now also observed phosphorylation of H2AX at serine 139 during KSHV infection. H2AX is a histone H2A isoform shown to interact with the latency-associated nuclear antigen (LANA) encoded by KSHV. Here, we show that LANA directly interacted with H2AX through domains at both its N and C termini. The phosphorylated form of H2AX (γH2AX) was shown to colocalize with LANA. Chromatin immunoprecipitation (ChIP) assays showed that a reduction in H2AX levels resulted in reduced binding of LANA with KSHV terminal repeats (TRs). Binding preferences of H2AX and γH2AX along the KSHV episome were examined by whole-episome ChIP analysis. We showed that γH2AX had a higher relative binding activity along the TR regions than that of the long unique region (LUR), which highlighted the importance of H2AX phosphorylation during KSHV infection. Furthermore, knockdown of H2AX resulted in decreased KSHV episome copy number. Notably, the C terminus of LANA contributed to phosphorylation of H2AX. However, phosphorylation was not dependent on the ability of LANA to drive KSHV-infected cells into S-phase. Thus, H2AX contributes to association of LANA with the TRs, and phosphorylation of H2AX is likely important for its increased density at the TRs.
Evidence HDAC9 Genetic Variant Associated With Ischemic Stroke Increases Risk via Promoting Carotid Atherosclerosis
Authors: Markus Hugh S. , Mäkelä Kari-Matti , Bevan Steve , Raitoharju Emma , Oksala Niku , Bis Joshua C. , O’Donnell Chris , Hainsworth Atticus , Lehtimäki Terho 
Published: March 2013

Background and Purpose—
A novel association between a single nucleotide polymorphism on chromosome 7p21.1 and large-vessel ischemic stroke was recently identified. The most likely underlying gene is histone deacetylase 9 (HDAC9). The mechanism by which HDAC9 increases stroke risk is not clear; both vascular and neuronal mechanisms have been proposed.

Methods—
We determined whether the lead single nucleotide polymorphisms were associated with asymptomatic carotid plaque (N=25 179) and carotid intima-media thickness (N=31 210) detected by carotid ultrasound in a meta-analysis of population-based and community cohorts. Immunohistochemistry was used to determine whether HDAC9 was expressed in healthy human cerebral and systemic arteries. In the Tampere Vascular Study, we determined whether HDAC9 mRNA expression was altered in carotid (N=29), abdominal aortic (N=15), and femoral (N=24) atherosclerotic plaques compared with control (left internal thoracic, N=28) arteries.

Results—

Both single nucleotide polymorphisms (rs11984041 and rs2107595) were associated with common carotid intima-media thickness (rs2107595;
P
=0.0018) and with presence of carotid plaque (rs2107595;
P
=0.0022). In both cerebral and systemic arteries, HDAC9 labeling was seen in nuclei and cytoplasm of vascular smooth muscle cells, and in endothelial cells. HDAC9 expression was upregulated in carotid plaques compared with left internal thoracic controls (
P
=0.00000103). It was also upregulated in aortic and femoral plaques compared with controls, with mRNA expression increased in carotid compared with femoral plaques (
P
=0.0038).

Conclusions—
Our results are consistent with the 7p21.1 association acting via promoting atherosclerosis, and consistent with alterations in HDAC9 expression mediating this increased risk. Further studies in experimental models are required to confirm this link.
Reporting of Aspiration Pneumonia or Choking as a Cause of Death in Patients Who Died With Stroke
Authors: Chang Chia-Yu , Cheng Tain-Junn , Lin Ching-Yih , Chen Jen-Yin , Lu Tsung-Hsueh , Kawachi Ichiro 
Published: March 2013

Background and Purpose—
It is not known how many stroke patients die from fatal pulmonary complications such as aspiration pneumonia (AP) and choking each year in the United States. This study aimed to determine the frequency of reporting of AP or choking as a cause of death on death certificates with mention of stroke in the United States as a proxy measure of the incidence of dying from AP or choking among patients with stroke.

Methods—

We used multiple-cause mortality data for the years 2001 to 2010 to identify death certificates with mention of stroke (
International Classification of Diseases, Tenth Revision
code I60–I69), AP (
International Classification of Diseases, Tenth Revision
code J69), and choking (
International Classification of Diseases, Tenth Revision
code W78–W80) for analysis.

Results—
Of 2 424 379 death certificates with mention of stroke in the United States between 2001 and 2010, 5.1% (n=124 503) reported AP as a cause of death, and 1.5% (n=36 997) reported choking as a cause of death. However, if we confined the analysis to autopsy-confirmed cases, the frequency decreased to 1.3% (555/42 732) and 1.3% (541/42 732), respectively. The adjusted odds ratios of reporting AP or choking as a cause of death were higher among men, increased with age, and were higher among decedents who died in a nursing home/long-term care.

Conclusions—
The estimated incidence of dying from AP and choking among patients who died with stroke was 5% (~12 000 deaths per year) and 1% (~3700 deaths per year) according to information reported on death certificates. Efforts are needed to reduce the number of deaths from these 2 preventable complications.