Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi‐year predictability of the tropical Atlantic atmosphere driven by the high latitude North Atlantic Ocean

Using idealised model experiments we show that the tropical Atlantic main hurricane development region (MDR) is potentially one of the most predictable regions for atmospheric variables such as precipitation and wind shear on multi‐year timescales. Similarly we also find predictability for the number of tropical storms and the position of the inter‐tropical convergence zone. Further experiments that withhold data in different parts of the ocean identify the North Atlantic sub‐polar gyre as the key region for driving the skill in the model MDR. This further highlights the importance of observing the high‐latitude North Atlantic Ocean for initialising future decadal predictions.
Transient, spatially varied groundwater recharge modeling

The objective of this work is to integrate field data and modeling tools in producing temporally and spatially varying groundwater recharge in a pilot watershed in North Okanagan, Canada. The recharge modeling is undertaken by using the Richards equation based finite element code (HYDRUS‐1D), ArcGIS™, ROSETTA, in situ observations of soil temperature and soil moisture, and a long‐term gridded climate data. The public version of HYDUS‐1D and another version with detailed freezing and thawing module are first used to simulate soil temperature, snow pack, and soil moisture over a one year experimental period. Statistical analysis of the results show both versions of HYDRUS‐1D reproduce observed variables to the same degree. After evaluating model performance using field data and ROSETTA derived soil hydraulic parameters, the HYDRUS‐1D code is coupled with ArcGIS™ to produce spatially and temporally varying recharge maps throughout the Deep Creek watershed. Temporal and spatial analysis of 25 years daily recharge results at various representative points across the study watershed reveal significant temporal and spatial variations; average recharge estimated at 77.8 ± 50.8 mm/year. Previous studies in the Okanagan Basin used Hydrologic Evaluation of Landfill Performance without any attempt of model performance evaluation, notwithstanding its inherent limitations. Thus, climate change impact results from this previous study and similar others, such as Jyrkama and Sykes (2007), need to be interpreted with caution.
CT-based classification systems for intra-articular calcaneal fractures: 1 the inter- and intra-observer variations as well as integrality

24 Background: Several primary fracture classification systems (FCSs) have been 25 widely used for intra-articular calcaneal fractures. The purpose of this study was to 26 measure the inter- and intra-observer variations as well as integrality of the Zwipp, 27 Crosby-Fitzgibbons, Sanders, and Eastwood-Atkins classification systems based on 28 more accurate CT scans. 29 Methods: 549 patients with intra-articular calcaneal fractures taken from a database 30 in our level-I trauma centre (3 affiliated hospitals) were included from January 2018 31 to December 2019. For each case, normative CT (1 mm slices) scans were available. 32 Four different observers reviewed all CT scans two times according to these 4 most 33 prevalent FCSs within a 2-month interval. For these four FCSs, the kappa [κ] 34 coefficient was used to evaluate interobserver reliability and intraobserver 35 reproducibility, and the percentage that can be classified was used to indicate 36 integrality. 37 Results: The κ values were measured for Zwipp (κ= 0.38 interobserver, κ= 0.61 38 intraobserver), Crosby-Fitzgibbons (κ= 0.48 interobserver, κ= 0.79 intraobserver), 39 Sanders (κ= 0.40 interobserver, κ= 0.57 intraobserver), and Eastwood-Atkins (κ= 0.44 40 interobserver, κ= 0.72 intraobserver). Furthermore, the integrality were calculated for 41 Zwipp (100 %), Crosby-Fitzgibbons (100 %), Sanders (92 %) as well as 42 Eastwood-Atkins (89.6 %). 43 Conclusion: Compared with previous literatures, CT scanning with higher accuracy can significantly improve intraobserver reproducibility of Zwipp and 45 Eastwood-Atkins FCSs, but it has no positive effect on variability of Sanders FCS and 46 interobserver reliability of Crosby-Fitzgibbons FCS. While in terms of integrality, 47 Zwipp and Crosby-Fitzgibbons FCSs appear to be superior to the other two FCSs. 48
Effects of baroclinicity on storm divergence and stratiform rain in a precipitating subtropical region

Effects of Baroclinicity on Storm Divergence and Stratiform Rain in a Precipitating Subtropical Region. (May 2008) Larry John Hopper, Jr., B.S., University of Oklahoma Chair of Advisory Committee: Dr. Courtney Schumacher Divergence structures associated with the spectrum of precipitating systems in the subtropics and midlatitudes are not well documented. A mesoscale model (MM5) is employed to quantify the relative importance different baroclinic environments have on divergence profiles for common storm types in southeast Texas, a subtropical region. Divergence profiles averaged over a 100 x 100 nested grid with 3-km grid spacing are calculated from the model-derived wind fields for each storm. The divergence profiles simulated for selected storms are consistent with those calculated from an S-band radar using the velocity-azimuth display (VAD) technique. Divergence profiles from well-modeled storms vary in magnitude and structure across the spectrum of baroclinicities and storm types common in southeast Texas. Barotropic storms more characteristic of the Tropics generate the most elevated divergence (and thus diabatic heating) structures with the largest magnitudes. As the degree of baroclinicity increases, stratiform area fractions increase while the levels of non-divergence (LNDs) decrease. However, some weakly baroclinic storms contain stratiform area fractions and divergence profiles with magnitudes and LNDs that are
Snow-ice accretion and snow-cover depletion on Antarctic first-year sea-ice floes

Abstract Between austral late winter 1993 and austral autumn 1998, during five cruises aboard the research vessel Nathaniel B. Palmer, almost 300 m of core was obtained from first-year ice floes in the Ross, Amundsen and Bellingshausen Seas. Analysis of the texture, stratigraphy and stable-isotopic composition of the ice was used to assess the magnitude of the role of flooding and snow-ice formation at the base of the snowpack in the thickening of the ice cover and the thinning of the snow cover. Snow ice occurred in all ice-thickness categories and made a significant contribution to the total ice mass (12−36%) in both autumn and winter. Although the amount of snow ice was often exceeded by the amount of frazil ice and congelation ice, the thickness of individual layers of each ice type indicated that snow ice often made a greater contribution to the thermodynamic thickening of the ice cover than the other ice types. The larger quantities of frazil ice and congelation ice were primarily the result of dynamic thickening. Flooding and snow-ice formation reduced the snow cover to 42−70% of the total snow accumulation depending on time and location. On the basis of this information, ship-based snow-depth estimates were adjusted to estimate the total snow accumulation on different ice-thickness categories.
Transverse and Longitudinal Eigenfunction Analysis of a Navigation Channel Subject to Regular Dredgings: The Adour River Mouth, France

Abstract The Adour river mouth is located in Anglet, on the southwest coast of France, and it provides access to the commercial harbour of Bayonne. The navigation channel suffers from a recurring problem of silting and needs regular dredging. The construction of breakwaters and jetties has not solved the silting problem. Recently, a preventive trench was dug south of the channel to decrease the rate of siltation in the navigation channel. Bathymetric data of the river mouth were monitored for 26 mo, and 40 bathymetric sets of data were analysed. During the investigation period, four dredging campaigns were carried out. The surveys provide a very unusual bathymetric record because the sampling in time is extremely dense for such data. Eigenfunction analysis was performed along transects perpendicular and parallel to the direction of the river flow. These analyses are usually used to explain natural bathymetric or topographic evolutions. Here, there are also used to describe anthropogenic influences. The first spatial eigenfunction corresponds approximately to the mean bathy-metry over the study period. It does not show the preventive trench. This demonstrates that the trench is an ephemeral feature of the bathymetric record. The subsequent eigenfunctions represent the variations about the mean. The second eigenfunction explains the majority of the seabed evolution and reaches a maximum amplitude at the location of the preventive trench. The corresponding temporal eigenfunction presents important discontinuities during the dredging campaigns; its maximum amplitudes correspond to the maximum siltation, and its minimum amplitudes correspond to the dredging periods. A two dimensional empirical eigenfunction analysis confirmed that there was little evidence for any directional bias in the seabed evolution. In conclusion, this study shows that empirical eigenfunction analysis methods can be a helpful tool for analysing the impact of dredging activities and could have a useful role in estuarine management planning.
Tea Consumption and All-Cause and Cause-Specific Mortality in the UK Biobank

BACKGROUND Tea is frequently consumed worldwide, but the association of tea drinking with mortality risk remains inconclusive in populations where black tea is the main type consumed. OBJECTIVE To evaluate the associations of tea consumption with all-cause and cause-specific mortality and potential effect modification by genetic variation in caffeine metabolism. DESIGN Prospective cohort study. SETTING The UK Biobank. PARTICIPANTS 498 043 men and women aged 40 to 69 years who completed the baseline touchscreen questionnaire from 2006 to 2010. MEASUREMENTS Self-reported tea intake and mortality from all causes and leading causes of death, including cancer, all cardiovascular disease (CVD), ischemic heart disease, stroke, and respiratory disease. RESULTS During a median follow-up of 11.2 years, higher tea intake was modestly associated with lower all-cause mortality risk among those who drank 2 or more cups per day. Relative to no tea drinking, the hazard ratios (95% CIs) for participants drinking 1 or fewer, 2 to 3, 4 to 5, 6 to 7, 8 to 9, and 10 or more cups per day were 0.95 (95% CI, 0.91 to 1.00), 0.87 (CI, 0.84 to 0.91), 0.88 (CI, 0.84 to 0.91), 0.88 (CI, 0.84 to 0.92), 0.91 (CI, 0.86 to 0.97), and 0.89 (CI, 0.84 to 0.95), respectively. Inverse associations were seen for mortality from all CVD, ischemic heart disease, and stroke. Findings were similar regardless of whether participants also drank coffee or not or of genetic score for caffeine metabolism. LIMITATION Potentially important aspects of tea intake (for example, portion size and tea strength) were not assessed. CONCLUSION Higher tea intake was associated with lower mortality risk among those drinking 2 or more cups per day, regardless of genetic variation in caffeine metabolism. These findings suggest that tea, even at higher levels of intake, can be part of a healthy diet. PRIMARY FUNDING SOURCE National Cancer Institute Intramural Research Program.
DPP9 deficiency: An inflammasomopathy that can be rescued by lowering NLRP1/IL-1 signaling

Dipeptidyl peptidase 9 (DPP9) is a direct inhibitor of NLRP1, but how it affects inflammasome regulation in vivo is not yet established. Here, we report three families with immune-associated defects, poor growth, pancytopenia, and skin pigmentation abnormalities that segregate with biallelic DPP9 rare variants. Using patient-derived primary cells and biochemical assays, these variants were shown to behave as hypomorphic or knockout alleles that failed to repress NLRP1. The removal of a single copy of Nlrp1a/b/c, Asc, Gsdmd, or Il-1r, but not Il-18, was sufficient to rescue the lethality of Dpp9 mutant neonates in mice. Similarly, dpp9 deficiency was partially rescued by the inactivation of asc, an obligate downstream adapter of the NLRP1 inflammasome, in zebrafish. These experiments suggest that the deleterious consequences of DPP9 deficiency were mostly driven by the aberrant activation of the canonical NLRP1 inflammasome and IL-1β signaling. Collectively, our results delineate a Mendelian disorder of DPP9 deficiency driven by increased NLRP1 activity as demonstrated in patient cells and in two animal models of the disease. Description Loss of DPP9 activity in humans, mice and zebrafish results in pathogenic NLRP1 overactivation. NLRP1 knockout to the rescue The NLRP1 inflammasome is a protein complex crucial for various immune responses; thus, dysregulation of it can lead to severe immune disorders. Here, Harapas et al. looked at four children with dipeptidyl peptidase 9 (DPP9) loss-of-function mutations, showing that these patients had various immune disorders and spontaneous activation of the NLRP1 inflammasome in their isolated keratinocytes. Modeling these patients with a mouse model with a catalytically inactive DPP9 mutation, they found that neonate lethality could be rescued by also knocking out NLRP1. In a zebrafish model, knockout of asc, a molecule involved in NLRP1 inflammasome formation, also rescued the survival of dpp9 knockout zebrafish. Thus, DPP9 mutations seem to result in immune disorders due to NLRP1 inflammasome overactivation.
Integration of SNP genotyping confidence scores in IBD inference

MOTIVATION High-throughput single nucleotide polymorphism (SNP) arrays have become the standard platform for linkage and association analyses. The high SNP density of these platforms allows high-resolution identification of ancestral recombination events even for distant relatives many generations apart. However, such inference is sensitive to marker mistyping and current error detection methods rely on the genotyping of additional close relatives. Genotyping algorithms provide a confidence score for each marker call that is currently not integrated in existing methods. There is a need for a model that incorporates this prior information within the standard identical by descent (IBD) and association analyses. RESULTS We propose a novel model that incorporates marker confidence scores within IBD methods based on the Lander-Green Hidden Markov Model. The novel parameter of this model is the joint distribution of confidence scores and error status per array. We estimate this probability distribution by applying a modified expectation-maximization (EM) procedure on data from nuclear families genotyped with Affymetrix 250K SNP arrays. The converged tables from two different genotyping algorithms are shown for a wide range of error rates. We demonstrate the efficacy of our method in refining the detection of IBD signals using nuclear pedigrees and distant relatives. AVAILABILITY Plinke, a new version of Plink with an extended pairwise IBD inference model allowing per marker error probabilities is freely available at: http://bioinfo.bgu.ac.il/bsu/software/plinke. CONTACT obirk@bgu.ac.il; markusb@bgu.ac.il SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production

Significance Long-range organ-to-organ communications are important for the coordination of development and environmental adaptation in multicellular organisms, particularly plants that continuously produce postembryonic lateral organs in various environmental conditions. The substance of homeostatic regulation of organ development via long-distance signals has not yet been identified, however. Legumes use an autoregulatory negative-feedback system involving root–shoot communication to maintain optimal numbers of nodules by systemically suppressing nodulation. We show that a transcription factor, NODULE INCEPTION (NIN), an essential inducer for nodule primordium formation, directly activates genes encoding small peptides that act as root-derived long-distance mobile signals, leading to repression of endogenous NIN though the root–shoot communication and resulting in systemic suppression of nodulation. We demonstrate that an autoregulatory negative-feedback loop homeostatically regulates nodule production via this long-range signaling. Autoregulatory negative-feedback loops play important roles in fine-balancing tissue and organ development. Such loops are composed of short-range intercellular signaling pathways via cell–cell communications. On the other hand, leguminous plants use a long-distance negative-feedback system involving root–shoot communication to control the number of root nodules, root lateral organs that harbor symbiotic nitrogen-fixing bacteria known as rhizobia. This feedback system, known as autoregulation of nodulation (AON), consists of two long-distance mobile signals: root-derived and shoot-derived signals. Two Lotus japonicus CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE)-related small peptides, CLE ROOT SIGNAL1 (CLE-RS1) and CLE-RS2, function as root-derived signals and are perceived by a shoot-acting AON factor, the HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) receptor protein, an ortholog of Arabidopsis CLAVATA1, which is responsible for shoot apical meristem homeostasis. This peptide–receptor interaction is necessary for systemic suppression of nodulation. How the onset of nodulation activates AON and how optimal nodule numbers are maintained remain unknown, however. Here we show that an RWP-RK–containing transcription factor, NODULE INCEPTION (NIN), which induces nodule-like structures without rhizobial infection when expressed ectopically, directly targets CLE-RS1 and CLE-RS2. Roots constitutively expressing NIN systemically repress activation of endogenous NIN expression in untransformed roots of the same plant in a HAR1-dependent manner, leading to systemic suppression of nodulation and down-regulation of CLE expression. Our findings provide, to our knowledge, the first molecular evidence of a long-distance autoregulatory negative-feedback loop that homeostatically regulates nodule organ formation.
Interannual Variability of Cloud Forcing and Meridional Energy Transport for the Northern Hemisphere Winter from 1984 to 1990

Abstract Broadband radiative flux data from the Earth Radiation Budget Experiment (ERBE) are used to document the interannual variability of net cloud forcing over the lifetime of the ERBE scanner instruments. The study focuses on the high variability observed in the Pacific basin during the Northern Hemisphere winter from 1984 to 1990. This period captures the El Nino season of 1986/87 and the La Nina season of 1988/89, with an average state biased toward La Nina–type conditions. Clouds are found to cool the Pacific basin by approximately 23 W m−2 over the study period. Interannual variations of net cloud forcing vary by less than 5%, with a decrease of cloud cooling during the El Nino and an increase during the La Nina. A key aspect of this study is the concurrent analysis of cloud type and amount information from the International Satellite Cloud Climatology Project (ISCCP). It demonstrates that the variability of middle-thick and high-thin clouds is integral to the observed changes in net cloud forcin.
Subjective cognitive decline predicts lower cingulo-opercular network functional connectivity in individuals with lower neurite density in the forceps minor

Cognitive complaints of attention/concentration problems are highly frequent in older adults with subjective cognitive decline (SCD). Functional connectivity in the cingulo-opercular network (CON-FC) supports cognitive control, tonic alertness, and visual processing speed. Thus, those complaints in SCD may reflect a decrease in CON-FC. Frontal white-matter tracts such as the forceps minor exhibit age- and SCD-related alterations and, therefore, might influence the CON-FC decrease in SCD. Here, we aimed to determine whether SCD predicts an impairment in CON-FC and whether neurite density in the forceps minor modulates that effect. To do so, we integrated cross-sectional and longitudinal analyses of multimodal data in a latent growth curve modeling approach. Sixty-nine healthy older adults (13 males; 68.33 ± 7.95 years old) underwent resting-state functional and diffusion-weighted magnetic resonance imaging, and the degree of SCD was assessed at baseline with the memory functioning questionnaire (greater score indicating more SCD). Forty-nine of the participants were further enrolled in two follow-ups, each about 18 months apart. Baseline SCD did not predict CON-FC after three years or its rate of change (p-values > 0.092). Notably, however, the forceps minor neurite density did modulate the relation between SCD and CON-FC (intercept; b = 0.21, 95% confidence interval, CI, [0.03, 0.39], p = 0.021), so that SCD predicted a greater CON-FC decrease in older adults with relatively lower neurite density in the forceps minor. The neurite density of the forceps minor, in turn, negatively correlated with age. These results suggest that CON-FC alterations in SCD are dependent upon the forceps minor neurite density. Accordingly, these results imply modifiable age-related factors that could help delay or mitigate both age and SCD-related effects on brain connectivity.
Study of the Fabric of Fine-Grained Sediments with the Scanning Electron Microscope

ABSTRACT The mutual disposition of mineral particles and voids in the micron and sub-micron size ranges is generally inaccessible to observation by light microscopy. This instrumental limitation can be overcome by the use of an electron optical system. The scanning electron microscope is an ideal tool for this kind of work, for it produces good resolution at high magnifications with relatively enormous depth of focus. Micrographs obtained with a scanning electron microscope are used to illustrate the fabrics of some fine-grained limestones and clay soils which have properties of special engineering interest. Fine structure is revealed with unusual clarity. Of particular interest are: the nature of contacts of fine-grained crystals with one another and with coarser crystals, particularly dolomi es; the disposition of non-carbonates and (or) cementitious material along grain boundaries; and the orientation of mica-type minerals in shales, mudstones, and clay soils. The relative merit of several methods of sample preparation is discussed.
Rietveld Refinement, Morphology, and Optical and Photoluminescence Properties of a β-Ag1.94Cu0.06MoO4 Solid Solution.

Corner-truncated cubic β-Ag1.94Cu0. 06MoO4 microcrystals were synthesized using the hydrothermal method. These were investigated by X-ray diffraction, confirming obtention of the spinel structure Fd3̅m. Through Raman spectroscopy are confirmed all modes for the point group of Oh7. The Egap shows a decrease of the band gap from 3.20 to 3.07 eV, with reduction of the conduction band occurring from -0.20 eV (β-Ag2MoO4) to -0.13 eV (β-Ag1.94Cu0.06MoO4), suggesting a p-type behavior for the Cu2+ ion. The field-emission scanning electron microscopy images confirm the morphological changes for β-Ag2MoO4, where potato-like microcrystals were found. Meanwhile, corner-truncated cubic microcrystals for β-Ag1.94Cu0. 06MoO4. The photoluminescence (PL) spectrum confirms the increase in the PL emission for β-Ag1.94Cu0. 06MoO4, with suppression of the deep defects occurring in the structure caused by oxygen and silver atoms. In contrast, the green region is intensified because of distortions of the Ag-O and Mo-O bonds. Therefore, the β-Ag1.94Cu0. 06MoO4 solid solution has PL emission with CCT (4510 K) and CIE coordinates (x = 0.372 and y = 0.433), which could be interesting properties for applications as light-emitting diodes.