Dismantling the ability of CT and MRI to identify the target mismatch profile in patients with anterior circulation large vessel occlusion beyond six hours from symptom onset.

PURPOSE: Patients with large vessel occlusion and target mismatch on imaging may be thrombectomy candidates in the extended time window. However, the ability of imaging modalities including non-contrast CT Alberta Stroke Program Early Computed Tomographic Scoring (CT ASPECTS), CT angiography collateral score (CTA-CS), diffusion-weighted MRI ASPECTS (DWI ASPECTS), DWI lesion volume, and DWI volume with clinical deficit (DWI + NIHSS), to identify mismatch is unknown. METHODS: We defined target mismatch as core infarct (DWI volume) of < 70 mL, mismatch volume (tissue with TMax > 6 s) of ≥ 15 mL, and mismatch ratio of ≥ 1.8. Using experimental dismantling design, ability to identify this profile was determined for each imaging modality independently (phase 1) and then with knowledge from preceding modalities (phase 2). We used a generalized mixed model assuming binary distribution with PROC GLIMMIX/SAS for analysis. RESULTS: We identified 32 patients with anterior circulation occlusions, presenting > 6 h from symptom onset, with National Institute of Health Stroke Scale of ≥ 6, who had CT and MR before thrombectomy. Sensitivities for identifying target mismatch increased modestly from 88% for NCCT to 91% with the addition of CTA-CS, and up to 100% for all MR-based modalities. Significant gains in specificity were observed from successive tests (29, 19, and 16% increase for DWI ASPECTS, DWI volume, and DWI + NIHSS, respectively). CONCLUSIONS: The combination of NCCT ASPECTS and CTA-CS has high sensitivity for identifying the target mismatch in the extended time window. However, there are gains in specificity with MRI-based imaging, potentially identifying treatment candidates who may have been excluded based on CT imaging alone.

Viral species richness and composition in young children with loose or watery stool in Ethiopia.

BACKGROUND: Stool consistency is an important diagnostic criterion in both research and clinical medicine and is often used to define diarrheal disease. METHODS: We examine the pediatric enteric virome across stool consistencies to evaluate differences in richness and community composition using fecal samples collected from children aged 0 to 5 years participating in a clinical trial in the Amhara region of Ethiopia. The consistency of each sample was graded according to the modified Bristol Stool Form Scale for children (mBSFS-C) before a portion of stool was preserved for viral metagenomic analysis. Stool samples were grouped into 29 pools according to stool consistency type. Differential abundance was determined using negative-binomial modeling. RESULTS: Of 446 censused children who were eligible to participate, 317 presented for the study visit examination and 269 provided stool samples. The median age of children with stool samples was 36 months. Species richness was highest in watery-consistency stool and decreased as stool consistency became firmer (Spearman's r = - 0.45, p = 0.013). The greatest differential abundance comparing loose or watery to formed stool was for norovirus GII (7.64, 95% CI 5.8, 9.5) followed by aichivirus A (5.93, 95% CI 4.0, 7.89) and adeno-associated virus 2 (5.81, 95%CI 3.9, 7.7). CONCLUSIONS: In conclusion, we documented a difference in pediatric enteric viromes according to mBSFS-C stool consistency category, both in species richness and composition.

Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease.

OBJECTIVES: We examined the fecal virome and bacterial community composition of children with Crohn disease (CD), ulcerative colitis (UC), and healthy controls to test the hypothesis that unique patterns of viral organisms and/or presence of bacterial pathogens may be identified that could contribute to the pathogenesis of pediatric inflammatory bowel disease (IBD). METHODS: Fecal samples from 24 children (mean 12.2 years) with CD (n = 7) or UC (n = 5) and similar aged controls (n = 12) were processed to determine individual viromes. Viral sequences were identified through translated protein sequence similarity search. Bacterial microbiota were determined by sequencing of the V4 region of the 16S rRNA gene. RESULTS: Only a few human viruses were detected, so virome analyses focused on bacterial viruses. The relative abundance of Caudovirales was greater than that of Microviridae phages in both IBD and healthy controls. Caudovirales phages were more abundant in CD (mean 80.8%) than UC (48.8%) (P = 0.05) but not controls. The richness of viral strains in Microviridae but not Caudovirales was higher in controls than CD (P = 0.05) but not UC cases. No other measure of phage abundance, richness, or Shannon diversity showed significant difference between the 2 IBD and control groups. Bacterial microbiota analysis revealed that IBD diagnosis, albumin, hemoglobin, erythrocyte sedimentation rate, and probiotic supplementation correlated to the composition of gut bacterial microbiota. CONCLUSIONS: Minor patterns in gut virome and bacterial community composition distinguish pediatric IBD patients from healthy controls. Probiotics are associated with bacterial microbiota composition. These exploratory results need confirmation in larger studies.

Genotoxic damage in end-stage renal disease.

End-stage renal disease (ESRD) patients are at increased risk for cardiovascular events and cancer, possibly due to genomic instability associated with renal disease and/or its therapy. Prognostic biomarkers of genomic instability may prove useful for initiating appropriate intervention strategies. We conducted a case-control study, performing the single-cell gel electrophoresis assay (circulating leukocytes) and the micronucleus cytome assay (buccal epithelial cells). Cases (ESRD patients; n = 55) were on weekly/fortnightly dialysis therapy and controls (n = 39) were healthy adults. The patients had significantly elevated levels of DNA damage and micronucleated cells. DNA damage showed higher validity and sensitivity than did chromosome damage, for discriminating patients from controls. The patient group showed significant increases in cell proliferation, cytokinetic defects, and cell death, and a decrease in repair index. Correlations were seen between genetic damage and both time-on-medication and time-on-dialysis; between condensed chromatin cells and sex; and between pyknotic cells and dietary pattern. Following stratification by age, gender, and dialysis frequency, significantly elevated DNA damage and MN frequency were seen in the fortnightly dialysis patients, perhaps due to accumulated uremic toxicants. DNA and chromosome damage may be useful prognostic biomarkers for initiating timely interventions against co-morbidities in ESRD patients.

Enteric virome of Ethiopian children participating in a clean water intervention trial.

BACKGROUND: The enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial. METHODOLOGY/PRINCIPAL FINDINGS: Fecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1-4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well. CONCLUSIONS: We describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.

Small Circular Rep-Encoding Single-Stranded DNA Genomes in Peruvian Diarrhea Virome.

Metagenomic analysis of diarrhea samples revealed the presence of numerous human enteric viruses and small circular Rep-encoding single-stranded DNA (CRESS-DNA) genomes. One such genome was related to smacoviruses, while eight others were related to genomes reported in the feces of different mammals. The tropism of these CRESS-DNA viruses remains unknown.

Sensitivity and specificity prediction of the buccal micronucleus cytome assay in end-stage renal disease patients on dialysis: A case-control study.

Patients with end-stage renal disease (ESRD) require hemodialysis. However, dialysis therapy may cause genomic damage due to increased oxidative stress. Non-invasive assessment of genotoxicity may be helpful for developing management strategies. We applied the buccal micronucleus cytome (BMCyt) assay to ESRD patients on dialysis. Patients (n=35, age 52±2 year) on dialysis therapy (20.9±0.8months) had low glomerular filtration rates (GFR=5.00±0.36ml/min/1.73m2); controls (n=21, age 51±2 year) were healthy adults with no known recent illnesses or exposures. Patients had significantly increased chromosome damage: clastogenic/aneugenic events (frequency of cells with MN), cellproliferation (basal cells), cytokinesis defects (binucleated cells), and celldeath (pyknotic cells); Repair Index was lower in the patient group. Receiver Operator Characteristic (ROC) curve analysis showed that cells with MN were the best predictor for discriminating between patients and controls. Other predictivebiomarkers were the frequencies of basal, binucleated,and pyknotic.

Rotavirus I in feces of a cat with diarrhea.

A divergent rotavirus I was detected using viral metagenomics in the feces of a cat with diarrhea. The eleven segments of rotavirus I strain Felis catus encoded non-structural and structural proteins with amino acid identities ranging from 25 to 79% to the only two currently sequenced members of that viral species both derived from canine feces. No other eukaryotic viral sequences nor bacterial and protozoan pathogens were detected in this fecal sample suggesting the involvement of rotavirus I in feline diarrhea.

A new protoparvovirus in human fecal samples and cutaneous T cell lymphomas (mycosis fungoides).

We genetically characterized seven nearly complete genomes in the protoparvovirus genus from the feces of children with diarrhea. The viruses, provisionally named cutaviruses (CutaV), varied by 1-6% nucleotides and shared ~76% and ~82% amino acid identity with the NS1 and VP1 of human bufaviruses, their closest relatives. Using PCR, cutavirus DNA was found in 1.6% (4/245) and 1% (1/100) of diarrhea samples from Brazil and Botswana respectively. In silico analysis of pre-existing metagenomics datasets then revealed closely related parvovirus genomes in skin biopsies from patients with epidermotropic cutaneous T-cell lymphoma (CTCL or mycosis fungoides). PCR of skin biopsies yielded cutavirus DNA in 4/17 CTCL, 0/10 skin carcinoma, and 0/21 normal or noncancerous skin biopsies. In situ hybridization of CTCL skin biopsies detected viral genome within rare individual cells in regions of neoplastic infiltrations. The influence of cutavirus infection on human enteric functions and possible oncolytic role in CTCL progression remain to be determined.

New parvovirus in child with unexplained diarrhea, Tunisia.

A divergent parvovirus genome was the only eukaryotic viral sequence detected in feces of a Tunisian child with unexplained diarrhea. Tusavirus 1 shared 44% and 39% identity with the nonstructural protein 1 and viral protein 1, respectively, of the closest genome, Kilham rat parvovirus, indicating presence of a new human viral species in the Protoparvovirus genus.

Discovery of a novel polyomavirus in acute diarrheal samples from children.

Polyomaviruses are small circular DNA viruses associated with chronic infections and tumors in both human and animal hosts. Using an unbiased deep sequencing approach, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. The ∼5.0 kB viral genome exhibits little overall homology (<46% amino acid identity) to known polyomaviruses, and, due to phylogenetic variation among its individual proteins, cannot be placed in any existing taxonomic group. PCR-based screening detected MXPyV in 28 of 834 (3.4%) fecal samples collected from California, Mexico, and Chile, and 1 of 136 (0.74%) of respiratory samples from Mexico, but not in blood or urine samples from immunocompromised patients. By quantitative PCR, the measured titers of MXPyV in human stool at 10% (weight/volume) were as high as 15,075 copies. No association was found between the presence of MXPyV and diarrhea, although girls were more likely to shed MXPyV in the stool than boys (p=0.012). In one child, viral shedding was observed in two stools obtained 91 days apart, raising the possibility of chronic infection by MXPyV. A multiple sequence alignment revealed that MXPyV is a closely related variant of the recently reported MWPyV and HPyV10 polyomaviruses. Further studies will be important to determine the association, if any, of MXPyV with disease in humans.

Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus.

Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.

Genetic diversity of the genus Cosavirus in the family Picornaviridae: a new species, recombination, and 26 new genotypes.

The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses.

A third gyrovirus species in human faeces.

Until 2011 the genus Gyrovirus in the family Circoviridae consisted of a single virus (Chicken anemia virus or CAV) causing a common immunosuppressive disease in chickens when a second gyrovirus (HGyV) was reported on the skin of 4 % of healthy humans. HGyV is very closely related to a recently described chicken gyrovirus, AGV2, suggesting that they belong to the same viral species. During a viral metagenomic analysis of 100 human faeces from children with diarrhoea in Chile we identified multiple known human pathogens (adenoviruses, enteroviruses, astroviruses, sapoviruses, noroviruses, parechoviruses and rotaviruses) and a novel gyrovirus species we named GyV3 sharing <63 % similarity with other gyrovirus proteins with evidence of recombination with CAV in its UTR. Gyroviridae consensus PCR revealed a high prevalence of CAV DNA in diarrhoea and normal faeces from Chilean children and faeces of USA cats and dogs, which may reflect consumption of CAV-infected/vaccinated chickens. Whether GyV3 can infect humans and/or chickens requires further studies.

The fecal viral flora of wild rodents.

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.

Delayed Gadolinium-Enhanced MR Imaging of Cartilage (dGEMRIC) following ACL injury.

OBJECTIVE: Early detection of glycosaminoglycan (GAG) loss may provide insight into mechanisms of cartilage damage in the anterior cruciate ligament (ACL)-injured patient. We hypothesized that tibial and femoral Delayed Gadolinium-Enhanced MR Imaging of Cartilage (dGEMRIC) indices would be lower in the medial compartment of the ACL-injured knee than in the contralateral, uninjured knee, and that scan order (i.e., whether the injured or the uninjured knee was imaged first) would not affect the indices. METHODS: 15 subjects with unilateral ACL injuries received a double dose of gadolinium [Gd(DTPA)(2-)] intravenously. After 90 min, both knees were sequentially imaged. The injured knee was scanned first in the odd-numbered subjects and second in the even-numbered subjects. The dGEMRIC indices of the median slice of the medial compartment were determined using the MRIMapper software. Index comparisons were made between knee status (ACL-injured vs uninjured), scan order (ACL-injured first vs uninjured first), and cartilage location (tibia vs femur) using a mixed model. RESULTS: There was a significant difference in the mean dGEMRIC indices of the medial compartment between injured and uninjured knees (P<0.007). On average, there was a 13% decrease in the dGEMRIC index of the injured knee compared to the uninjured knee. There were no significant effects due to test order (P=0.800) or cartilage location (P=0.439). CONCLUSIONS: The results demonstrate lower GAG concentrations in the medial compartment of the femoral and tibial articular cartilage of the ACL-injured knee when compared to the contralateral uninjured knee. The dGEMRIC indices were not sensitive to scan order; thus, sequential imaging of both knees is possible in this patient population.

Quantitative MR imaging using "LiveWire" to measure tibiofemoral articular cartilage thickness.

OBJECTIVE: To assess the reliability and accuracy of manual and semi-automated segmentation methods for quantifying knee cartilage thickness. This study employed both manual and LiveWire-based semi-automated segmentation methods, ex vivo and in vivo, to measure tibiofemoral (TF) cartilage thickness. METHODS: The articular cartilage of a cadaver knee and a healthy volunteer's knee were segmented manually and with LiveWire from multiple 3T MR images. The cadaver specimen's cartilage thickness was also evaluated with a 3D laser scanner, which was assumed to be the gold standard. Thickness measurements were made within specific cartilage regions. The reliability of each segmentation method was assessed both ex vivo and in vivo, and accuracy was assessed ex vivo by comparing segmentation results to those obtained with laser scanning. RESULTS: The cadaver specimen thickness measurements showed mean coefficients of variation (CVs) of 4.16%, 3.02%, and 1.59%, when evaluated with manual segmentation, LiveWire segmentation, and laser scanning, respectively. The cadaver specimen showed mean absolute errors versus laser scanning of 4.07% and 7.46% for manual and LiveWire segmentation, respectively. In vivo thickness measurements showed mean CVs of 2.71% and 3.65% when segmented manually and with LiveWire, respectively. CONCLUSIONS: Manual segmentation, LiveWire segmentation, and laser scanning are repeatable methods for quantifying knee cartilage thickness; however, the measurements are technique-dependent. Ex vivo, the manual segmentation error was distributed around the laser scanning mean, while LiveWire consistently underestimated laser scanning by 8.9%. Although LiveWire offers repeatability and decreased segmentation time, manual segmentation more closely approximates true cartilage thickness, particularly in cartilage contact regions.

Effects of ACL interference screws on articular cartilage volume and thickness measurements with 1.5 T and 3 T MRI.

OBJECTIVE: To assess the effects of interference screws, which are commonly used to surgically fix an anterior cruciate ligament (ACL) graft in the ACL-deficient knee, and magnetic field strength on cartilage volume and thickness measurements with quantitative magnetic resonance imaging (qMRI). METHODS: Five cadaver knees were imaged using a cartilage-sensitive sequence (T1-weighted water-excitation, three-dimensional (3D) fast low-angle shot) on 1.5T and 3T scanners with and without interference screws implanted. The tibiofemoral articular cartilage was segmented and reconstructed from the magnetic resonance images, and volume and thickness measurements were made on the resulting 3D models. RESULTS: Although several load-bearing regions showed significant differences in volume and thickness between magnet strengths, most showed no significant difference between screw conditions. The medial tibial cartilage showed a mean decrease in volume of 5.9% and 8.0% in the presence of interference screws at 3T and 1.5T, respectively. At 3T and 1.5T, the medial tibial cartilage showed a mean decrease in thickness of 7.0% and 12.0%, respectively, in the presence of interference screws. CONCLUSIONS: Caution should be used when interpreting thickness and volume of cartilage at 3T in the presence of interference screws, particularly in the medial tibial compartment. Additionally, 3T and 1.5T qMRI should not be used interchangeably to assess structural changes in tibiofemoral articular cartilage during longitudinal studies.

Landau-Kleffner syndrome with lateral temporal focal cortical dysplasia and mesial temporal sclerosis: a 30-year follow-up.

A 39-year-old man, who presented at age 312 with Landau-Kleffner syndrome, had persisting oral and written language deficits into adulthood. Seizures were easily controlled in childhood, but reemerged in adulthood as medication-refractory complex partial seizures. Abnormal T2 signal hyperintensity was seen in the left mesial temporal area on brain MRI. Later, left temporal lobectomy revealed focal cortical dysplasia in the lateral temporal neocortex and gliosis plus neuronal loss in the hippocampus. This case suggests that focal cortical microdysgenesis may be a cause of the Landau-Kleffner syndrome. Persistent seizures in this illustrative case may have led to the evolution of dual-temporal-lobe pathology with mesial temporal sclerosis.