Miracle-dz/UniFAR-FTUs huggingface dataset:
A retrospective cohort study predicting and validating impact of the COVID-19 pandemic in individuals with chronic kidney disease

Chronic kidney disease (CKD) is associated with increased risk of baseline mortality and severe COVID-19, but analyses across CKD stages, and comorbidities are lacking. In prevalent and incident CKD, we investigated comorbidities, baseline risk, COVID-19 incidence, and predicted versus observed one-year excess death. In a national dataset (NHS Digital Trusted Research Environment [NHSD TRE]) for England encompassing 56 million individuals), we conducted a retrospective cohort study (March 2020 to March 2021) for prevalence of comorbidities by incident and prevalent CKD, SARS-CoV-2 infection and mortality. Baseline mortality risk, incidence and outcome of infection by comorbidities, controlling for age, sex and vaccination were assessed. Observed versus predicted one-year mortality at varying population infection rates and pandemic-related relative risks using our published model in pre-pandemic CKD cohorts (NHSD TRE and Clinical Practice Research Datalink [CPRD]) were compared. Among individuals with CKD (prevalent:1,934,585, incident:144,969), comorbidities were common (73.5% and 71.2% with one or more condition[s] in respective data sets, and 13.2% and 11.2% with three or more conditions, in prevalent and incident CKD), and associated with SARS-CoV-2 infection, particularly dialysis/ transplantation (odds ratio 2.08, 95% con ﬁ dence interval 2.04-2.13) and heart failure (1.73, 1.71-1.76), but not cancer (1.01, 1.01-1.04). One-year all-cause mortality varied by age, sex, multi-morbidity and CKD stage. Compared with 34,265 observed excess deaths, in the NHSD-TRE and CPRD databases respectively, we predicted 28,746 and 24,546 deaths (infection rates 10% and relative risks 3.0), and 23,754 and 20,283 deaths (observed infection rates 6.7% and relative risks 3.7). Thus, in this largest, national-level study, individuals with CKD have a high burden of comorbidities and multi-morbidity, and high risk of pre-pandemic and pandemic mortality. Hence, treatment of comorbidities, non-pharmaceutical measures, and vaccination are priorities for people with CKD and management of long-term conditions is important during and beyond the pandemic. our risk estimates and applying 1-year population IR of 10%, and overall RR of mortality (set at 3) based on previous reports. 15,26 We predicted total excess deaths by: (i) age groups and number of underlying conditions and (ii) underlying conditions, using assumed and observed IR and RR. The analysis was performed according to a prespeci ﬁ ed analysis plan published on GitHub (https://github.com/BHFDSC/CCU003_01), including implementations and phenotypes.
Micromechanics of pressure-induced grain crushing in porous rocks

The hydrostatic compaction behavior of a suite of porous sandstones was investigated at confining pressures up to 600 MPa and constant pore pressures ranging up to 50 MPa. These five sandstones (Boise, Kayenta, St. Peter, Berea, and Weber) were selected because of their wide range of porosity (5–35%) and grain size (60–460 μm). We tested the law of effective stress for the porosity change as a function of pressure. Except for Weber sandstone (which has the lowest porosity and smallest grain size), the hydrostat of each sandstone shows an inflection point corresponding to a critical effective pressure beyond which an accelerated, irrecoverable compaction occurs. Our microstructural observations show that brittle grain crushing initiates at this critical pressure. We also observed distributed cleavage cracking in calcite and intensive kinking in mica. The critical pressures for grain crushing in our sandstones range from 75 to 380 MPa. In general, a sandstone with higher porosity and larger grain size has a critical pressure which is lower than that of a sandstone with lower porosity and smaller grain size. We formulate a Hertzian fracture model to analyze the micromechanics of grain crushing. Assuming that the solid grains have preexisting microcracks with dimensions which scale with grain size, we derive an expression for the critical pressure which depends on the porosity, grain size, and fracture toughness of the solid matrix. The theoretical prediction is in reasonable agreement with our experimental data as well as other data from soil and rock mechanics studies for which the critical pressures range over 3 orders of magnitude.
Crossing Networks: Competition and Design

In the past two decades, Alternative Trading Systems (ATSs) started to compete with traditional exchanges. Our paper focuses on one such system: a Crossing Network (CN). First, we discuss the distinct institutional aspects a CN offers compared to traditional markets. Next, we present an overview of the theoretical and empirical literature analyzing their success in competing with traditional markets. Finally, we offer some prospects on the potential outcome of this competition, taking into account market design issues such as the optimal degree of transparency of CNs. We also provide a market practioner's view on the market design of CNs.
Nutrient utilization ratios in the Polar Frontal Zone in the Australian sector of the Southern Ocean: A model

To investigate the non‐Redfield N/P depletion ratio in the Polar Frontal Zone (PFZ) of the Southern Ocean, we simulated the seasonal nitrate, phosphate, and silicate cycle in the upper ocean with a biophysical model. Total phytoplankton biomass was prescribed from the Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS) estimates, and we included two phytoplankton types, diatoms and nondiatoms. We set the nondiatoms N/P uptake ratio to 16 while the diatoms N/P and N/Si ratios were determined by fitting the observed seasonal nitrate, phosphate, and silicate cycle in the mixed layer. The best model fit to the observations required an annual N/P utilization ratio of 13.2, but this low N/P ratio still overestimated the nitrate utilization during the summer. We considered three mechanisms for improving the simulated nitrate cycle: (1) seasonal variation in the N/P ratio of the horizontal nutrient supply to the PFZ, (2) different remineralization length scales for particulate organic nitrogen (PON) and particulate organic phosphorus (POP), and (3) seasonal accumulation and decomposition of labile dissolved and suspended organic matter (OM). Model simulations showed that the seasonal variability in the N/P ratio of horizontal supply failed to reduce the simulated excess nitrate utilization in summer. Preferential recycling of PON compared to POP below the mixed layer degrades the simulation and cannot produce results that satisfy both the observed seasonal nitrate and phosphate cycle in the mixed layer. The most realistic model simulation was obtained with preferential recycling of POP over PON, but this mechanism alone was incapable of satisfying the summer nitrate and phosphate data. With the inclusion of an OM pool in our model we were able to reproduce the observed seasonal mixed layer nitrate and phosphate cycles. Satisfactory results can be achieved through various combinations of the N/P ratio of OM and the lifetime of the OM. Seasonal observations of dissolved and suspended organic phosphorus, nitrogen and carbon are needed to confirm their role. The important conclusion of our model study is that in the PFZ the annual nutrient utilization ratio of nitrate to phosphate is considerably less than the classical Redfield value of 16.
Historical oceanographic events reflected in13C/12C ratio of total organic carbon in laminated Santa

An 1844-1987 time series of carbon stable isotope ratios from dated sedimentary total organic carbon (TOC) from the center of the Santa Barbara Basin (SBB) is compared with historical climate and oceanographic records. Four isotopically distinct biogeochemical sources of TOC are important: phytoplankton-derived marine biomass, macroalgal biomass from kelp forests, terrigenous biomass (mainly flushed into the SBB via river discharge), and redeposited fossil organic carbon. The significance of the latter two sources is largely limited to a few unusual flood and oil spill events, whereas the combination of 13C-depleted phytoplankton and 13C-enriched macroalgal biomass appears to be responsible for most of the isotopic variance of the marine coastal biomass as recorded in sedimentary TOC. The isotopic response of marine organic carbon in sediments records strong El Nino-Southern Oscillation (ENSO) and the frequently associated severe storm and wave events in SBB varved sediments. The plausible major isotopic mechanisms are (1) increased physical liberation of 13C-enriched kelp carbon from locally abundant giant kelp (Macrocystis spp.) forests during times of physical and environmental stress, and (2) decreased productivity of 13C-depleted phytoplankton during ENSO events.
Particle Size Variations Between Bed Load and Bed Material in Natural Gravel Bed Channels

Particle sizes of bed load and bed material that represent materials transported and stored over a period of years are used to investigate selective transport in 13 previously sampled, natural gravel bed channels. The ratio (D*) of median particle size of bed material to the transport- and frequency-weighted mean of median bed load size decreases to unity with increasing drainage area, bank-full discharge, dimensionless stream power, and bed material sorting. In channels with high values of D*, significant volumes of fine bed load are transported during discharges that are less than bank-full, which is commonly associated with general entrainment of the coarse pavement in many gravel bed channels. This indicates transport of fine bed load over a more stable substrate of coarser bed material. The apparent breakdown in equal mobility of the bed as a whole may be caused by areal segregation of poorly sorted bed material into superiorly sorted patches of varying mean size. Likely sources of selectively transported fine bed load include fine patches that have low entrainment thresholds and high virtual particle velocities. A simple sediment budget applied to measurements from three channels indicates that velocities of material from fine patches in pools relative to velocities of average bed material are high in low-order channels and decrease distally as more bed material that represents the bed as a whole is accessed for bed load by deeper annual scour.
Experiences with Integrated-Conservation Development Projects in Asia

Integrated Conservation-Development Projects (ICDPs) link the conservation of biodiversity in protected areas with the socio-economic development of adjoining communities. Chapter 1 defines what ICDPs are, when to use this approach, and the necessary conditions for appropriate sites. Chapter 2 outlines issues that need to be adequately addressed once it is decided to go forward with an ICDP. Chapter 3 identifies issues for consideration when designing the monitoring and evaluating component of an ICDP. The annexes contain the preparation and implementation cycle recommended by an ICDP workshop (Annex 1), case study focus at another ICDP workshop (Annex 2), and a list of selected organizations engaged in analytical ICDP work (Annex 4).
Nitrogen availability links forest productivity, soil nitrous oxide and nitric oxide fluxes of a tropical montane forest in southern Ecuador

Tropical forests are important sources of the greenhouse gas nitrous oxide (N2O) and of nitric oxide (NO), a precursor of ozone. In tropical montane forests nitrogen limitation is common which affects both soil N2O and NO fluxes and forest productivity. Here we present evidence that forest productivity and N‐oxide (N2O + NO) fluxes are linked through N availability along elevation and topographic gradients in tropical montane forests. We measured N‐oxide fluxes, several indices of N availability, and forest productivity along an elevation gradient from 1000 m to 3000 m and along topographic gradients. Organic layer thickness of the soils increased and N availability decreased with increasing elevation and along the topographic gradient from the lower slope position to the ridges. Annual N2O fluxes ranged from −0.53 μg(N)m−2h−1 to 14.54 μg(N)m−2h−1 while NO fluxes ranged from −0.02 μg(N)m−2h−1 to 1.13 μg(N)m−2h−1. Both N‐oxide fluxes and forest productivity increased with increasing N availability and showed close positive correlations with indices of N availability (C/N ratio andδ 15N signature of litterfall). We interpret the close correlations of N‐oxide fluxes with total litterfall and tree basal area increment as evidence that N availability links N‐oxide fluxes and forest productivity. This opens the possibility to include forest productivity as co‐variable in predictions of N‐oxide fluxes in nitrogen limited tropical montane forests. Especially increment of tree basal area was a promising proxy to predict soil N‐oxide fluxes in these N limited ecosystems, possibly because it better reflects long‐term forest productivity than total litterfall.
Real time GPS data processing for regional atmospheric delay derivation

We have developed a GPS data processing software and demonstrate that by using receivers in an area of approximately 800 × 400 km we can produce estimates of the atmospheric zenith total delay (ZTD) with a latency of a few seconds. It is based on a Kalman filter which simultaneously estimates clock offsets and satellite coordinates. The ZTD quality is typically 15 mm in terms of rms difference to post‐processed ZTD time series. This level of uncertainty is useful in many navigation applications and if an additional reduction in the uncertainty can be obtained the usefulness for short term weather forecasting could be significant.
Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding

G-quadruplexes (G4s) are unusual DNA structures and can stall DNA replication, causing genomic instability for the cell. Although the solved crystal structure of the DHX36 helicase demonstrated that G4 was specifically targeted by a DHX36-specific motif (DSM), lack of complete structural details for general G4-resolving helicases without specific target motifs remains a barrier to the complete understanding of the molecular basis underlying the recognition and unfolding of G4s. Herein, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif) complexed with a G4, thereby mimicking the physiological G4 formed during DNA replication. Strictly different from the previous determined G4-helicase structure of DHX36, our structure revealed that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B constituting a G4-Recognizing Surface (GRS). The overall topology of the G4 structure solved in this work maintains its three-layered propeller-type G4 topology, with no significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 were differentially recognized by GRS residues mainly through electrostatic, ionic interactions and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Our structure explains how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.
Temporal Moment‐Generating Equations: Modeling Transport and Mass Transfer in Heterogeneous Aquifers

We present an efficient method for determining temporal moments of concentration for a solute subject to first-order and diffusive mass transfer in steady velocity fields. The differential equations for the moments of all orders have the same form as the steady state nonreactive transport equation. Thus temporal moments can be calculated by a solute transport code that was written to simulate nonreactive steady state transport, even though the actual transport system is reactive and transient. Higher-order moments are found recursively from lower-order moments. For many cases a small number of moments sufficiently describe the movement of a solute plume. The first four moments describe the accumulated mass, mean, spread, and skewness of the concentration histories at all locations. Actual concentration histories at any location can be approximated from the moments by applying the principle of maximum entropy, a constraint consistent with the physical process of dispersion. The forms of the moment-generating equations for different mass transfer models provide insight into reactive transport through heterogeneous aquifers. For the mass transfer models we considered, the zeroth moment in a heterogeneous aquifer is independent of the mass transfer coefficients. Thus, if the velocity field is known, the mass transported past any point, or out any boundary, can be calculated without knowledge of the spatial pattern of mass transfer coefficients and, in fact, without knowledge of whether mass transfer is occurring. Also, for both first-order and diffusive mass transfer models, the mean arrival time depends on the distribution coefficient but is independent of the values of the rate coefficients, regardless of the spatial variability of groundwater velocity and mass transfer coefficients.
Thermospheric neutral winds at southern mid‐latitudes: A comparison of optical and ionosonde hmF2 methods

During the first 6 days of March 1995, measurements of the ionospheric electron density were made with a digisonde, and thermospheric winds were measured with a Fabry-Perot interferometer. This was a period of low solar activity and moderate to high magnetic activity. The ionograms have been scaled and the traces inverted to obtain the electron density profile and the peak height of the F2 layer (hmF2). Modeling has been employed to derive equivalent thermospheric neutral winds at hmF2. The derived neutral winds are in very good agreement with the measured optical winds most of the time. The winds follow a strong diurnal pattern with poleward winds during the day, weak winds near dawn and dusk, and strong equatorward winds peaking near local midnight. On most nights the peak equatorward wind speed was around 200 m s−1, but on March 1 it did not exceed 110 m s−1. For these magnetic and solar activity conditions the wind at the F2 peak altitude (∼350 km) from the HWM93 empirical wind model[Hedin et al., 1996] did not exceed 90 m s−1 at any time but was in generally good agreement with the hmF2 wind during the day and with both measured winds on the nights of March 1 and 2. The good agreement between the optical and hmF2 winds was obtained by using the recommended Burnside factor of 1.7 to multiply the O+-O collision frequency, but better agreement was obtained either by using a Burnside factor of 2.0 or by increasing the atomic oxygen density by 20%. Recent suggestions of much lower Burnside factors could be tolerated only if there were large systematic errors in the measurements or large electric fields.
Lung Abnormalities Depicted with Hyperpolarized Xenon MRI in Patients with Long COVID

Background Post-Covid-19 condition describes symptoms following COVID-19 infection after four weeks. Symptoms are wide-ranging but breathlessness is common. Purpose The purpose of this study was to determine whether the previously described lung abnormalities on Hp-XeMRI in post-hospitalised COVID-19 participants are also present in non-hospitalised participants with Post-Covid-19 condition. Methods In this prospective study, non-hospitalised Post-Covid-19 condition (NHLC) and post-hospitalised COVID-19 (PHC) participants were enrolled from 06/2020 to 08/2021. Participants had chest CT, hyperpolarized pulmonary 129 Xenon MRI (Hp-XeMRI), pulmonary function tests, 1-minute sit-to-stand test and breathlessness questionnaires. Control subjects underwent HP-XeMRI only. CT scans were analysed for post COVID interstitial lung disease severity using a previously published scoring system, and Full-scale Airway Network (FAN) modelling. Analysis used group and pair-wise comparisons between participants and controls, and correlations between participant clinical and imaging data.
Geoid height‐age relation from SEASAT altimeter profiles across the Mendocino Fracture Zone

Twenty-eight SEASAT altimeter profiles crossing the Mendocino Fracture Zone are used together with seafloor ages determined from magnetic lineations to estimate the change in oceanic geoid height with age, between ages of 15 and 135 m.y. An unbiased estimate of the overall geoid offset along each profile is determined from a least-squares fit of the along-track derivative of the geoid to the geoid slope predicted from a simple two-layer gravitational edge effect model. Uncertainties based upon the statistical properties of each profile are also determined. A geoid slope-age relation is constructed by normalizing the geoid offsets and uncertainties by the age offsets. The results are in agreement with geoid slope-age relations determined from symmetrically spreading ridges (Sandwell and Schubert, 1980). However, the fracture zone estimates have smaller uncertainties and show less scatter. A comparison of these results with the geoid slope-age prediction of the boundary layer cooling model shows that the thermal structure begins to deviate from this model at an early age (20–40 m.y.). A plate cooling model with a thickness of 125 km is most compatible with the geoid slope-age estimates, although significant deviations occur; these may indicate that the lithospheric thermal structure is not entirely age dependent.
Dual methylation and hydroxymethylation study of alcohol use disorder

Using an integrative, multi‐tissue design, we sought to characterize methylation and hydroxymethylation changes in blood and brain associated with alcohol use disorder (AUD). First, we used epigenomic deconvolution to perform cell‐type‐specific methylome‐wide association studies within subpopulations of granulocytes/T‐cells/B‐cells/monocytes in 1132 blood samples. Blood findings were then examined for overlap with AUD‐related associations with methylation and hydroxymethylation in 50 human post‐mortem brain samples. Follow‐up analyses investigated if overlapping findings mediated AUD‐associated transcription changes in the same brain samples. Lastly, we replicated our blood findings in an independent sample of 412 individuals and aimed to replicate published alcohol methylation findings using our results. Cell‐type‐specific analyses in blood identified methylome‐wide significant associations in monocytes and T‐cells. The monocyte findings were significantly enriched for AUD‐related methylation and hydroxymethylation in brain. Hydroxymethylation in specific sites mediated AUD‐associated transcription in the same brain samples. As part of the most comprehensive methylation study of AUD to date, this work involved the first cell‐type‐specific methylation study of AUD conducted in blood, identifying and replicating a finding in DLGAP1 that may be a blood‐based biomarker of AUD. In this first study to consider the role of hydroxymethylation in AUD, we found evidence for a novel mechanism for cognitive deficits associated with AUD. Our results suggest promising new avenues for AUD research.