The utility of the Moderate Resolution Imaging Spectroradiometer (MODIS) snow-cover products is limited by cloud cover which causes gaps in the daily snow-cover map products. We describe a ...cloud-gap-filled (CGF) daily snow-cover map using a simple algorithm to track cloud persistence, to account for the uncertainty created by the age of the snow observation. Developed from the 0.05° resolution climate-modeling grid daily snow-cover product, MOD10C1, each grid cell of the CGF map provides a cloud-persistence count (CPC) that tells whether the current or a prior day was used to make the snow decision. Percentage of grid cells “observable” is shown to increase dramatically when prior days are considered. The effectiveness of the CGF product is evaluated by conducting a suite of data assimilation experiments using the community Noah land surface model in the NASA Land Information System (LIS) framework. The Noah model forecasts of snow conditions, such as snow–water equivalent (SWE), are updated based on the observations of snow cover which are obtained either from the MOD10C1 standard product or the new CGF product. The assimilation integrations using the CGF maps provide domain-averaged bias improvement of ~11%, whereas such improvement using the standard MOD10C1 maps is ~3%. These improvements suggest that the Noah model underestimates SWE and snow depth fields, and that the assimilation integrations contribute to correcting this systematic error. We conclude that the gap-filling strategy is an effective approach for increasing cloud-free observations of snow cover.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Human milk is a complex fluid comprised of myriad substances, with one of the most abundant substances being a group of complex carbohydrates referred to as human milk oligosaccharides (HMOs). There ...has been some evidence that HMO profiles differ in populations, but few studies have rigorously explored this variability.
We tested the hypothesis that HMO profiles differ in diverse populations of healthy women. Next, we examined relations between HMO and maternal anthropometric and reproductive indexes and indirectly examined whether differences were likely related to genetic or environmental variations.
In this cross-sectional, observational study, milk was collected from a total of 410 healthy, breastfeeding women in 11 international cohorts and analyzed for HMOs by using high-performance liquid chromatography.
There was an effect of the cohort (
< 0.05) on concentrations of almost all HMOs. For instance, the mean 3-fucosyllactose concentration was >4 times higher in milk collected in Sweden than in milk collected in rural Gambia (mean ± SEM: 473 ± 55 compared with 103 ± 16 nmol/mL, respectively;
< 0.05), and disialyllacto-
-tetraose (DSLNT) concentrations ranged from 216 ± 14 nmol/mL (in Sweden) to 870 ± 68 nmol/mL (in rural Gambia) (
< 0.05). Maternal age, time postpartum, weight, and body mass index were all correlated with several HMOs, and multiple differences in HMOs e.g., lacto-
-neotetrose and DSLNT were shown between ethnically similar (and likely genetically similar) populations who were living in different locations, which suggests that the environment may play a role in regulating the synthesis of HMOs.
The results of this study support our hypothesis that normal HMO concentrations and profiles vary geographically, even in healthy women. Targeted genomic analyses are required to determine whether these differences are due at least in part to genetic variation. A careful examination of sociocultural, behavioral, and environmental factors is needed to determine their roles in this regard. This study was registered at clinicaltrials.gov as NCT02670278.
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CMK, GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In the central nervous system, serotonergic signaling modulates sleep, mood, and cognitive control. During serotonergic transmission, the synaptic concentration of serotonin is tightly controlled in ...a spatial and temporal manner by the serotonin transporter (SERT). Dysregulation of this process is implicated in the pathogenesis of major-depressive, obsessive-compulsive, and autism-spectrum disorders, which makes SERT a primary target for prescription therapeutics, most notably selective serotonin reuptake inhibitors (SSRIs). S-Palmitoylation, the reversible addition of a 16-carbon fatty acid to proteins, is an increasingly recognized dynamic post-translational modification responsible for modulating protein kinetics, trafficking, and localization patterns in response to physiologic/cellular stimuli. In this study, we reveal that human SERTs are a target for palmitoylation, and using the irreversible palmitoyl acyltransferase inhibitor 2-bromopalmitate (2BP), we have identified several associated functions. Using a lower dose of 2BP in shorter time frames, inhibition of palmitoylation was associated with reductions in SERT V max, without changes in K m or surface expression. With higher doses of 2BP for longer time intervals, inhibition of palmitoylation was consistent with the loss of cell surface and total SERT protein, suggesting palmitoylation is an important mechanism in regulating SERT trafficking and maintenance of SERT protein through biogenic or anti-degradative processes. Additionally, we have identified that treatment with the SSRI escitalopram decreases SERT palmitoylation analogous to 2BP, reducing SERT surface expression and transport capacity. Ultimately, these results reveal that palmitoylation is a major regulatory mechanism for SERT kinetics and trafficking and may be the mechanism responsible for escitalopram-induced internalization and ultimately decreased cellular SERT protein levels.
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Clearcut is an open source implementation for the relaxed neighbor joining (RNJ) algorithm. While traditional neighbor joining (NJ) remains a popular method for distance-based phylogenetic tree ...reconstruction, it suffers from a O(N3) time complexity, where N represents the number of taxa in the input. Due to this steep asymptotic time complexity, NJ cannot reasonably handle very large datasets. In contrast, RNJ realizes a typical-case time complexity on the order of N2logN without any significant qualitative difference in output. RNJ is particularly useful when inferring a very large tree or a large number of trees. In addition, RNJ retains the desirable property that it will always reconstruct the true tree given a matrix of additive pairwise distances. Clearcut implements RNJ as a C program, which takes either a set of aligned sequences or a pre-computed distance matrix as input and produces a phylogenetic tree. Alternatively, Clearcut can reconstruct phylogenies using an extremely fast standard NJ implementation. Availability: Clearcut source code is available for download at: Contact:sheneman@hungry.com Supplementary information:
Early detection of sepsis is key to ensure timely clinical intervention. Since very few end-to-end pipelines are publicly available, fair comparisons between methodologies are difficult if not ...impossible. Progress is further limited by discrepancies in the reconstruction of sepsis onset time. This retrospective cohort study highlights the variation in performance of predictive models under three subtly different interpretations of sepsis onset from the sepsis-III definition and compares this against inter-model differences. The models are chosen to cover tree-based, deep learning, and survival analysis methods. Using the MIMIC-III database, between 867 and 2178 intensive care unit admissions with sepsis were identified, depending on the onset definition. We show that model performance can be more sensitive to differences in the definition of sepsis onset than to the model itself. Given a fixed sepsis definition, the best performing method had a gain of 1-5% in the area under the receiver operating characteristic (AUROC). However, the choice of onset time can cause a greater effect, with variation of 0-6% in AUROC. We illustrate that misleading conclusions can be drawn if models are compared without consideration of the sepsis definition used which emphasizes the need for a standardized definition for sepsis onset.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The maintenance of a low pH in the vagina through the microbial production of lactic acid is known to be an important defense against infectious disease in reproductive age women. Previous studies ...have shown that this is largely accomplished through the metabolism of lactic acid bacteria, primarily species of Lactobacillus. Despite the importance of this defense mechanism to women's health, differences in the species composition of vaginal bacterial communities among women have not been well defined, nor is it known if and how these differences might be linked to differences in the risk of infection. In this study, we defined and compared the species composition of vaginal bacterial communities in 144 Caucasian and black women in North America. This was carried out based on the profiles of terminal restriction fragments of 16S rRNA genes, and phylogenetic analysis of 16S rRNA gene sequences of the numerically dominant microbial populations. Among all the women sampled, there were eight major kinds of vaginal communities ('supergroups') that occurred in the general populace at a frequency of at least 0.05 (P=0.99). From the distribution of these supergroups among women, it was possible to draw several conclusions. First, there were striking, statistically significant differences (P=0.0) in the rank abundance of community types among women in these racial groups. Second, the incidence of vaginal communities in which lactobacilli were not dominant was higher in black women (33%) as compared to Caucasian women (7%). Communities not dominated by lactobacilli had Atopobium and a diverse array of phylotypes from the order Clostridiales. Third, communities dominated by roughly equal numbers of more than one species of Lactobacillus were rare in black women, but common in Caucasian women. We postulate that because of these differences in composition, not all vaginal communities are equally resilient, and that differences in the vaginal microbiota of Caucasian and black women may at least partly account for known disparities in the susceptibility of women in these racial groups to bacterial vaginosis and sexually transmitted diseases.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, SBNM, UL, UM, UPUK
The shell disorder models have predicted that SARS-CoV-2 is of a specific but peculiar evolutionary nature. All coronaviruses (CoVs) closely related to SARS-CoV-2 have been found to have the hardest ...outer shells (M protein) among CoVs. This hard shell (low M percentage of intrinsic disorder (PID)) is associated with burrowing animals, for example, pangolins, and is believed to be responsible for the high contagiousness of SARS-CoV-2 because it will be more resistant to antimicrobial enzymes found in saliva/mucus. Incoming clinical and experimental data do support this along with a prediction based on another aspect of the shell (N, inner shell) disorder models that SARS-CoV-1 is more virulent than SARS-CoV-2 because SARS-CoV-2 produces fewer virus copies in vital organs even if large amounts of infections particles are shed orally and nasally. A phylogenetic study using M reveals a closer relationship of SARS-CoV to pangolin-CoVs than the bat-RaTG13 found in Yunnan, China. Previous studies may have been confused by recombinations that were poorly handled. The shell disorder models suggest that a pangolin-CoV strain may have entered the human population in 2017 or before as an attenuated virus, which could explain why SARS-CoV is found to be highly adapted to humans.
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IJS, KILJ, NUK, PNG, UL, UM
Abstract
V503 Her was previously proposed as an eclipsing symbiotic candidate based on photometric behavior and spectroscopic appearance indicating the composite optical spectrum. To investigate its ...nature, we analyzed long-term photometric observations covering 100 yr of its photometric history and new low-resolution optical spectroscopic data, supplemented with the multifrequency measurements collected from several surveys and satellites. Based on the analysis presented in this paper, we claim that V503 Her is not an eclipsing binary star. The optical and infrared wavelengths are dominated by a K-type bright giant with an effective temperature of 4500 K, luminosity of 1900
L
⊙
, and subsolar metallicity on the asymptotic giant branch showing semiregular complex multiperiodic pulsation behavior. V503 Her does not show the characteristics of strongly interacting symbiotic variables, but some pieces of evidence suggest that it could still be one of the “hidden” accreting-only symbiotic systems. However, the currently available data do not allow us to fully confirm or constrain the parameters of a possible companion.
Snow cover over the Northern Hemisphere plays a crucial role in the Earth’s hydrology and surface energy balance, and modulates feedbacks that control variations of global climate. While many of ...these variations are associated with exchanges of energy and mass between the land surface and the atmosphere, other expected changes are likely to propagate downstream and affect oceanic processes in coastal zones. For example, a large component of the freshwater flux into the Arctic Ocean comes from snow melt. The timing and magnitude of this flux affects biological and thermodynamic processes in the Arctic Ocean, and potentially across the globe through their impact on North Atlantic Deep Water formation.
Several recent global remotely sensed products provide information at unprecedented temporal, spatial, and spectral resolutions. In this article we review the theoretical underpinnings and characteristics of three key products. We also demonstrate the seasonal and spatial patterns of agreement and disagreement amongst them, and discuss current and future directions in their application and development. Though there is general agreement amongst these products, there can be disagreement over certain geographic regions and under conditions of ephemeral, patchy and melting snow.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Neonatal sepsis due to intestinal bacterial translocation is a major cause of morbidity and mortality. Understanding microbial colonisation of the gut in prematurity may predict risk of sepsis to ...guide future strategies to manipulate the microbiome.
Prospective longitudinal study of premature infants. Stool samples were obtained weekly. DNA was extracted and the V6 hypervariable region of 16S rRNA was amplified followed by high throughput pyrosequencing, comparing subjects with and without sepsis.
Six neonates were 24-27 weeks gestation at birth and had 18 samples analysed. Two subjects had no sepsis during the study period, two developed late-onset culture-positive sepsis and two had culture-negative systemic inflammation. 324 350 sequences were obtained. The meconium was not sterile and had predominance of Lactobacillus, Staphylococcus and Enterobacteriales. Overall, infants who developed sepsis began life with low microbial diversity, and acquired a predominance of Staphylococcus, while healthy infants had more diversity and predominance of Clostridium, Klebsiella and Veillonella.
In very low birth weight infants, the authors found that meconium is not sterile and is less diverse from birth in infants who will develop late-onset sepsis. Empiric, prolonged antibiotics profoundly decrease microbial diversity and promote a microbiota that is associated not only with neonatal sepsis, but the predominant pathogen previously identified in the microbiome. Our data suggest that there may be a 'healthy microbiome' present in extremely premature neonates that may ameliorate risk of sepsis. More research is needed to determine whether altered antibiotics, probiotics or other novel therapies can re-establish a healthy microbiome in neonates.
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