An Interpretation of Cloud Overlap Statistics

Abstract Observational studies have shown that the vertical overlap of cloudy layers separated by clear sky can exceed that of the random overlap assumption, suggesting a tendency toward minimum overlap. In addition, the rate of decorrelation of vertically continuous clouds with increasing layer separation is sensitive to the horizontal scale of the cloud scenes used. The authors give a heuristic argument that these phenomena result from data truncation, where overcast or single cloud layers are removed from the analysis. This occurs more frequently as the cloud sampling scale falls progressively below the typical cloud system scale. The postulate is supported by sampling artificial cyclic and subsequently more realistic fractal cloud scenes at various length scales. The fractal clouds indicate that the degree of minimal overlap diagnosed in previous studies for discontinuous clouds could result from sampling randomly overlapped clouds at spatial scales that are 30%–80% of the cloud system scale. Removing scenes with cloud cover exceeding 50% from the analysis reduces the impact of data truncation, with discontinuous clouds not minimally overlapped and the decorrelation of continuous clouds less sensitive to the sampling scale. Using CloudSat–CALIPSO data, a decorrelation length scale of approximately 4.0 km is found. In light of these results, the previously documented dependence of overlap decorrelation length scale on latitude is not entirely a physical phenomenon but can be reinterpreted as resulting from sampling cloud systems that increase significantly in size from the tropics to midlatitudes using a fixed sampling scale

Generalizing Cloud Overlap Treatment to Include the Effect of Wind Shear

Abstract Six months of CloudSat and CALIPSO observations have been divided into over 8 million cloud scenes and collocated with ECMWF wind analyses to identify an empirical relationship between cloud overlap and wind shear for use in atmospheric models. For vertically continuous cloudy layers, cloud decorrelates from maximum toward random overlap as the layer separation distance increases, and the authors demonstrate a systematic impact of wind shear on the resulting decorrelation length scale. As expected, cloud decorrelates over smaller distances as wind shear increases. A simple, empirical linear fit parameterization is suggested that is straightforward to add to existing radiation schemes, although it is shown that the parameters are quite sensitive to the processing details of the cloud mask data and also to the fitting method used. The wind shear–overlap dependency is implemented in the radiation scheme of the ECMWF Integrated Forecast System. It has a similar-magnitude impact on the radiative budget as that of switching from a fixed decorrelation length scale to the latitude-dependent length scale presently used in the operational model, altering the zonal-mean, top-of-atmosphere, equator-to-midlatitude gradient of shortwave radiation by approximately 2 W m−2

Forced Alignment for Understudied Language Varieties: Testing Prosodylab-Aligner with Tongan Data

Automated alignment of transcriptions to audio files expedites the process of preparing data for acoustic analysis. Unfortunately, the benefits of auto-alignment have generally been available only to researchers studying majority languages, for which large corpora exist and for which acoustic models have been created by large-scale research projects. Prosodylab-Aligner (PL-A), from McGill University, facilitates automated alignment and segmentation for understudied languages. It allows researchers to train acoustic models using the same audio files for which alignments will be created. Those models can then be used to create time-aligned Praat TextGrids with word and phone boundaries marked. For the benefit of others who wish to use PL-A for research projects, this paper reports on our use of PL-A on Tongan field recordings, reviewing the software, outlining required steps, and providing tips. Since field recordings often contain more background noise than the laboratory recordings for which PL-A was designed, the paper also discusses the relative benefits of removing background noise for both training and alignment purposes. Finally, it compares acoustic measures based on various alignments and compares boundary placements with those of human aligners, demonstrating that automated alignment is both feasible and less time-consuming than manual alignment.National Foreign Language Resource Cente

Template-dependent multiple displacement amplification for profiling human circulating RNA

Multiple displacement amplification (MDA) is widely used in whole-genome/transcriptome amplification. However, template-independent amplification (TIA) in MDA is a commonly observed phenomenon, particularly when using high concentrations of random hexamer primers and extended incubation times. Here, we demonstrate that the use of random pentamer primers with 5´ ends blocked by a C18 spacer results in MDA solely in a template-dependent manner, a technique we have named tdMDA. Together with an optimized procedure for the removal of residual genomic DNA during RNA extraction, tdMDA was used to profile circulating RNA from 0.2 mL of patient sera. In comparison to regular MDA, tdMDA demonstrated a lack of quantifiable DNA amplification in the negative control, a remarkable reduction of unmapped reads from Illumina sequencing (7 ± 10.9% versus 58.6 ± 39%, P = 0.006), and increased mapping rates of the serum transcriptome (26.9 ± 7.9% versus 5.8 ± 8.2%, P = 3.8 × 10-4). Transcriptome profiles could be used to separate patients with chronic hepatitis C virus (HCV) infection from those with HCV-associated hepatocellular carcinoma (HCC). We conclude that tdMDA should facilitate RNA-based liquid biopsy, as well as other genome studies with biological specimens having ultralow amounts of genetic material. </jats:p

High-resolution quantification of hepatitis C virus genome-wide mutation load and its correlation with the outcome of peginterferon-alpha2a and ribavirin combination therapy

Hepatitis C virus (HCV) is a highly mutable RNA virus and circulates as a heterogeneous population in individual patients. The magnitude of such population heterogeneity has long been proposed to be linked with diverse clinical phenotypes, including antiviral therapy. Yet data accumulated thus far are fairly inconclusive. By the integration of long RT-PCR with 454 sequencing, we have built a pipeline optimized for the quantification of HCV genome-wide mutation load at 1% resolution of mutation frequency, followed by a retrospective study to examine the role of HCV mutation load in peginterferon-alpha2a and ribavirin combination antiviral therapy. Genome-wide HCV mutation load varied widely with a range from 92 to 1639 mutations and presented a Poisson distribution among 56 patients (Kolmogorov-Smirnov statistic  = 0.078, p = 0.25). Patients achieving sustained virological response (n = 26) had significantly lower mutation loads than that in null responders (n = 30) (mean and standard derivation: 524±279 vs. 805±271, p = 0.00035). All 36,818 mutations detected in 56 patients displayed a power-law distribution in terms of mutation frequency in viral population. The low-frequency mutation load, but not the high-frequency load, was proportional firmly to the total mutation load. In-depth analyses revealed that intra-patient HCV population structure was shaped by multiple factors, including immune pressure, strain difference and genetic drift. These findings explain previous conflicting reports using low-resolution methods and highlight a dominant role of natural selection in response to therapeutic intervention. By attaining its signatures from complex interaction between host and virus, the high-resolution quantification of HCV mutation load predicts outcomes from interferon-based antiviral therapy and could also be a potential biomarker in other clinical settings

Potential Predictability of Malaria in Africa Using ECMWF Monthly and Seasonal Climate Forecasts

AbstractIdealized model experiments investigate the advance warning for malaria that may be presently possible using temperature and rainfall predictions from state-of-the-art operational monthly and seasonal weather-prediction systems. The climate forecasts drive a dynamical malaria model for all of Africa, and the predictions are evaluated using reanalysis data. The regions and months for which climate is responsible for significant interannual malaria transmission variability are first identified. In addition to epidemic-prone zones these also include hyperendemic regions subject to high variability during specific months of the year, often associated with the monsoon onset. In many of these areas, temperature anomalies are predictable from 1 to 2 months ahead, and reliable precipitation forecasts are available in eastern and southern Africa 1 month ahead. The inherent lag between the rainy seasons and malaria transmission results in potential predictability in malaria transmission 3–4 months in advance, extending the early warning available from environmental monitoring by 1–2 months, although the realizable forecast skill will be less than this because of an imperfect malaria model. A preliminary examination of the forecasts for the highlands of Uganda and Kenya shows that the system is able to predict the years during the last two decades in which documented highland outbreaks occurred, in particular the major event of 1998, but that the timing of outbreaks was often imprecise and inconsistent across lead times. In addition to country-level evaluation with district health data, issues that need addressing to integrate such a climate-based prediction system into health-decision processes are briefly discussed

Prospects for personalizing antiviral therapy for hepatitis C virus with pharmacogenetics

Chronic hepatitis C virus (HCV) infection is a major cause of liver disease worldwide. HCV infection is currently treated with IFNα plus ribavirin for 24 to 48 weeks. This demanding therapy fails in up to 50% of patients, so the use of pharmacogenetic biomarkers to predict the outcome of treatment would reduce futile treatment of non-responders and help identify patients in whom therapy would be justified. Both IFNα and ribavirin primarily act by modulating the immune system of the patient, and HCV uses multiple mechanisms to counteract the antiviral effects stimulated by therapy. Therefore, response to therapy is influenced by variations in human genes governing the immune system and by differences in HCV genes that blunt antiviral immune responses. This article summarizes recent advances in understanding how host and viral genetic variation affect outcome of therapy. The most notable human associations are polymorphisms within the IL28B gene, but variations in human leukocyte antigen and cytokine genes have also been associated with treatment outcome. The most prominent viral genetic association with outcome of therapy is that HCV genotype 1 is much less sensitive to treatment than genotypes 2 and 3, but genetic differences below the genotype level also influence outcome of therapy, presumably by modulating the ability of viral genes to blunt antiviral immune responses. Pharmacogenetic prediction of the outcome of IFN-based therapy for HCV will require integrating the efficacies of the immunosuppressive mechanisms of a viral isolate, and then interpreting the viral resistance potential in context of the genetic profile of the patient at loci associated with outcome of therapy. Direct-acting inhibitors of HCV that will be used in combination with IFNα are nearing approval, so genetic prediction for anti-HCV therapy will soon need to incorporate viral genetic markers of viral resistance to the new drugs

Distribution, comportement migratoire et conservation du Synallaxe de Hudson Asthenes hudsoni (Furnariidae): un spécialiste des prairies de la pampa humide

Hudson’s Canastero, Asthenes hudsoni (Furnariidae) is a secretive passerine from the Rio de la Plata grasslands of South America. It is considered near threatened, but little is known about its distribution and seasonal movements. We performed a thorough revision of historical and recent records of the species and estimated its original and current geographic distribution using niche modeling based on climatic and land cover information. We found that A. hudsoni is not widespread across the Río de la Plata grasslands but mostly restricted to the humid pampas in Argentina, with isolated populations in central Argentina and SE Brazil. Most records north of the humid pampas in Argentina and Uruguay correspond to wintering individuals, revealing that the species is a partial seasonal migrant. Our distribution models indicate that its original area of occupancy may have been reduced by 65% to a current ~50,000 km², with a stronghold in the flooding Pampas in eastern Buenos Aires province. However, because of the specific microhabitat requirements of the species, we suspect that this figure underestimates the extent of appropriate habitat available, and that A. hudsoni could be very close to the threshold of area of occupancy for vulnerable species under IUCN criteria. Further research on habitat requirements, distribution, and population trends are urgently needed.Le Synallaxe de Hudson, Asthenes hudsoni (Furnariidae) est un passereau discret des prairies du Rio de la Plata en Amérique du Sud. Il est considéré comme quasi menacé, mais on sait peu de choses sur sa répartition et ses mouvements saisonniers. Nous avons effectué une révision complète des enregistrements historiques et récents de l'espèce et estimé sa distribution géographique originale et actuelle en utilisant un modèle de niche basé sur des informations climatiques et de couverture terrestre. Nous avons constaté que A. hudsoni n'est pas répandu dans les prairies du Río de la Plata, mais qu'il est surtout limité à la pampa humide en Argentine, avec des populations isolées dans le centre de l'Argentine et le sud-est du Brésil. La plupart des enregistrements au nord de la pampa humide en Argentine et en Uruguay correspondent à des individus hivernants, ce qui révèle que l'espèce est un migrateur saisonnier partiel. Nos modèles de distribution indiquent que sa zone d'occupation initiale pourrait avoir été réduite de 65% pour atteindre actuellement ~50 000 km², avec un bastion dans les pampas inondées de l'est de la province de Buenos Aires. Cependant, en raison des exigences spécifiques de l'espèce en matière de microhabitat, nous soupçonnons que ce chiffre sous-estime l'étendue de l'habitat approprié disponible et que A. hudsoni pourrait être très proche du seuil de la zone d'occupation des espèces vulnérables selon les critères de l'UICN. Il est urgent de poursuivre les recherches sur les exigences en matière d'habitat, la distribution et les tendances de la population.Fil: Claramunt, Santiago. University of Toronto; Canadá. Royal Ontario Museum; CanadáFil: Aldabe, Joaquín. Manomet Center For Conservation Sciences; Uruguay. Universidad de la Republica; UruguayFil: Etchevers, Ismael. Universidad de la Republica; UruguayFil: Di Giacomo, Adrian Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; ArgentinaFil: Kopuchian, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; ArgentinaFil: Milensky, Christopher M.. National Museum of Natural History; Estados Unido

Diffusion tensor imaging and white matter abnormalities in patients with disorders of consciousness.

Progress in neuroimaging has yielded new powerful tools which, potentially, can be applied to clinical populations, improve the diagnosis of neurological disorders and predict outcome. At present, the diagnosis of consciousness disorders is limited to subjective assessment and objective measurements of behavior, with an emerging role for neuroimaging techniques. In this review we focus on white matter alterations measured using Diffusion Tensor Imaging on patients with consciousness disorders, examining the most common diffusion imaging acquisition protocols and considering the main issues related to diffusion imaging analyses. We conclude by considering some of the remaining challenges to overcome, the existing knowledge gaps and the potential role of neuroimaging in understanding the pathogenesis and clinical features of disorders of consciousness

Treatment of hepatocellular carcinoma

Fifty-one patients with unresectable hepatocellular carcinoma were treated by embolization of the hepatic artery with Gelfoam powder, contrast material and three chemotherapeutic agents (doxorubicin, mitomycin, cisplatin). Twelve patients (24%) had a partial response with a decrease in the tumor diameter by at least 50%, 13 patients (26%) had only minor responses, 12 (24%) had stabilization of disease and the remainder had progressive disease. Tumor liquefaction was noted on computed tomographic scanning in 70% of patients, and 23 of 34 patients with elevations in serum alphafetoprotein values had a greater than 50% reduction following treatment. The median patient survival time from treatment was 207 days. Most patients experienced transient pain, fever, nausea and elevations in serum aminotransferase activities as a result of therapy. Ascites developed in 14 patients. There were two treatment-related deaths: one from tumor hemorrhage and one from liver failure. Chemoembolization therefore appears to have significant activity in patients with hepatocellular carcinoma and is relatively well tolerated. This study reports the results of resection in 72 cirrhotic patients with hepatocellular carcinoma from Europe. One and 3 year survival rates were 68% and 51% respectively. Survival was significantly higher in Child's class A than in class B or C patients. Patients with a thickly encapsulated tumor lived longer than those with an infiltrating tumor and also had a significantly lower recurrence rate. There was no relationship between the size of the tumor or the presence of symptoms and survival. These data suggest that good results can be achieved by resection of hepatocellular carcinoma in European cirrhotic patients. A thickly encapsulated tumor and good liver function are the main determinants of low cancer recurrence and high survival.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38355/1/1840130431_ftp.pd