Miracle-dz/UniFAR-FTUs huggingface dataset:
Stability of additive treatment effects in multiple treatment comparison meta-analysis: a simulation study

Background Many medical interventions are administered in the form of treatment combinations involving two or more individual drugs (eg, drug A + drug B). When the individual drugs and drug combinations have been compared in a number of randomized clinical trials, it is possible to quantify the comparative effectiveness of all drugs simultaneously in a multiple treatment comparison (MTC) meta-analysis. However, current MTC models ignore the dependence between drug combinations (eg, A + B) and the individual drugs that are part of the combination. In particular, current models ignore the possibility that drug effects may be additive, ie, the property that the effect of A and B combined is equal to the sum of the individual effects of A and B. Current MTC models may thus be suboptimal for analyzing data including drug combinations when their effects are additive or approximately additive. However, the extent to which the additivity assumption can be violated before the conventional model becomes the more optimal approach is unknown. The objective of this study was to evaluate the comparative statistical performance of the conventional MTC model and the additive effects MTC model in MTC scenarios where additivity holds true, is mildly violated, or is strongly violated. Methods We simulated MTC scenarios in which additivity held true, was mildly violated, or was strongly violated. For each scenario we simulated 500 MTC data sets and applied the conventional and additive effects MTC models in a Bayesian framework. Under each scenario we estimated the proportion of treatment effect estimates that were 20% larger than ‘the truth’ (ie, % overestimates), the proportion that were 20% smaller than ‘the truth’ (ie, % underestimates), the coverage of the 95% credible intervals, and the statistical power. We did this for all the comparisons under both models. Results Under true additivity, the additive effects model is superior to the conventional model. Under mildly violated additivity, the additive model generally yields more overestimates or underestimates for a subset of treatment comparisons, but comparable coverage and greater power. Under strongly violated additivity, the proportion of overestimates or underestimates and coverage is considerably worse with the additive effects model. Conclusion The additive MTC model is statistically superior when additivity holds true. The two models are comparably advantageous in terms of a bias-precision trade-off when additivity is only mildly violated. When additivity is strongly violated, the additive effects model is statistically inferior.
Trends in the incidence and prevalence of end-stage renal disease with hemodialysis in entire Korean population

Supplemental Digital Content is available in the text Abstract Data on the overall epidemiology and temporal trends of end-stage renal disease (ESRD) requiring hemodialysis in Korea are scarce. We aimed to estimate the prevalence and incidence of ESRD requiring hemodialysis in Korea between 2002 and 2017. Using the National Health Insurance Service database, we analyzed data from the entire Korean population between 2002 and 2017. Hemodialysis patients were identified using rare incurable disease codes (V001) or prescription of medical fee codes of hemodialysis (O7020 and O7021). We only included patients who had been maintained on hemodialysis for more than 90 days from the date of dialysis initiation, to exclude patients who required short-term dialysis for acute kidney injury, conversion to peritoneal dialysis, or kidney transplantation. During the 16-year follow-up, the number of hemodialysis patients in Korea has steadily increased from 11,215 in 2002 to 67,486 in 2017. The mean age of these patients has gradually increased from 55.57 ± 13.31 years in 2002 to 62.13 ± 13.23 years in 2017. In 2017, the crude prevalence rate of hemodialysis was 1303.4 per million population. Overall, the number of men tended to be somewhat higher than that of women, and the proportion of men increased slightly from 55.56% in 2002 to 58.45% in 2017. The proportion of diabetic patients increased rapidly from 23.84% to 47.84%, and the percentage of dyslipidemic patients rose from 18.9% to 86.7%. The number of incident hemodialysis patients increased significantly from 4406 in 2003 to 12,134 in 2014, and then decreased to 8090 in 2017. In the incident cases of hemodialysis, the observed increase in the proportion of male patients and in diabetes and dyslipidemia were similar to that of prevalent patients. The more recent era of hemodialysis initiation, the better 5-year survival rates were observed. The prevalence and incidence of hemodialysis in Korea gradually increased between 2002 and 2017. The proportion of men, and patients with diabetes and dyslipidemia requiring hemodialysis also increased continuously. The survival rate of hemodialysis patients was gradually improving. These findings may serve as a reference for future epidemiological studies on hemodialysis in Korea.
Regional distribution and sources of Au, Pd and Pt in moss and O-,B- and C-horizon podzol samples in the European Arctic

A cost-effective analytical method for analysing various terrestrial sample materials for noble metals at detection limits in the sub-ppb range has been developed. The method has been used to analyse c. 600 samples of moss, O-, B- and C-horizon samples collected from a large area (188,000 km2) in the European Arctic at a sample density of 1 site/300 km2. For the first time reliable analytical data for Au, Pd and Pt for a large, statistically representative number of samples from four different sample materials can be reported. The regional distribution of Au, Pd and Pt in moss and O-horizon samples provides clear evidence that the Russian nickel industry on the Kola Peninsula is emitting Au and platinum group elements (PGEs). However, maps and profiles for moss and the O-horizon also demonstrate that the emissions of one of the very few and largest Pd emission sources on earth cannot be traced further than 200 km on the ground before reaching background values. The predominant natural geochemical characteristics of the study area are visible in the maps of the B- and C-horizon samples even when using such low-density sampling. Furthermore, the data allow estimation of realistic ‘background values’ for these three elements in the four sample materials. By collecting four interrelated sample materials from a large area it is possible to detect unusual processes leading to the enrichment of certain elements in specific compartments of the ecosystem. Most dramatic is a greater than four-fold higher Pt concentration in the B-horizon of arctic podzols compared to all other media. Platinum concentrations are also slightly higher in the O-horizon than in the C-horizon. Palladium shows a tendency to organic binding. Moss is actively enriching Pd and shows even higher Pd concentrations than in the O-horizon. The highest Au values can be found in the deepest soil layers (C-horizon). Natural, geogenic sources influence Au concentrations measured in moss and the O-horizon as much as industrial emissions.
Comparison of Inter Subject Variability and Reproducibility of Whole Brain Proton Spectroscopy

The aim of these studies was to provide reference data on intersubject variability and reproducibility of metabolite ratios for Choline/Creatine (Cho/Cr), N-acetyl aspartate/Choline (NAA/Cho) and N-acetyl aspartate/Creatine (NAA/Cr), and individual signal-intensity normalised metabolite concentrations of NAA, Cho and Cr. Healthy volunteers underwent imaging on two occasions using the same 3T Siemens Verio magnetic resonance scanner. At each session two identical Metabolic Imaging and Data Acquisition Software (MIDAS) sequences were obtained along with standard structural imaging. Metabolite maps were created and regions of interest applied in normalised space. The baseline data from all 32 volunteers were used to calculate the intersubject variability, while within session and between session reproducibility were calculated from all the available data. The reproducibility of measurements were used to calculate the overall and within session 95% prediction interval for zero change. The within and between session reproducibility data were lower than the values for intersubject variability, and were variable across the different brain regions. The within and between session reproducibility measurements were similar for Cho/Cr, NAA/Choline, Cho and Cr (11.8%, 11.4%, 14.3 and 10.6% vs. 11.9%, 11.4%, 13.5% and 10.5% respectively), but for NAA/Creatine and NAA between session reproducibility was lower (9.3% and 9.1% vs. 10.1% and 9.9%; p <0.05). This study provides additional reference data that can be utilised in interventional studies to quantify change within a single imaging session, or to assess the significance of change in longitudinal studies of brain injury and disease.
Modified approach for transcatheter correction of superior sinus venosus atrial septal defect: a case series

Abstract Background Transcatheter correction of superior sinus venosus atrial septal defect (SVASD) with partial anomalous pulmonary venous drainage (PAPVD) of the right upper and/or right middle pulmonary vein (RUPV/RMPV) has recently been described as an alternative to surgical approach in a substantial number of patients. We describe a modified technical approach for transcatheter correction of SVASD using transoesophageal echocardiography (TOE) to confirm adequate stent landing zone and apposition and evaluate its feasibility, safety, and procedural success. Case summary From 2019 to 2021, three consecutive patients received a transcatheter correction of SVASD with PAPVD by redirecting the superior vena cava and RUPV/RMPV to the left atrium by implantation of a custom-made covered Cheatham platinum stent (10-zig, length: 60–80 mm). Prior to stent implantation, a balloon testing was performed in the anticipated landing zone using TOE to confirm complete defect closure and unobstructed pulmonary venous drainage. Stent deployment and flaring of the interior stent portion were performed with TOE guidance to confirm adequate landing zone and apposition and to avoid residual shunt or pulmonary vein obstruction. Conclusion Transcatheter correction of SVASD with PAPVD was performed without any complications. The follow-up period was 7.8, 13.6, and 29.8 months, respectively. During follow-up, no mortality, stent embolization, or obstruction of pulmonary venous drainage occurred. The TOE-guided modified transcatheter approach for correction of SVASD with PAPVD is safe and feasible with excellent post-procedural results and represents an alternative to surgical treatment in a pre-selected patient cohort.
Compaction of Sediments

An attempt is made to explore the theoretical relations between compaction of sediments and depth of burial. On the basis of available data and assumptions that seem to be reasonable, a porosity-depth curve for mud and shale is constructed and overburden pressure is calculated. From these data, other relations of interest in stratigraphy are derived. Mud and shale are compacted in several stages that involve: (1) squeezing out of interstitial water until the sedimentary grains come in contact with each other; (2) rearrangement of grains and development of closer packing; (3) soft clay minerals are forced into the interstices between the more resistant minerals; (4) the latter are deformed until all porosity is eliminated. The colloidal properties of clay are very important in this process whose results appear to be predictable for sediments with different proportions of clay minerals. Much less compaction is possible in sand and sandstone because initial porosity is much lower. Colloidal effects are negligible. Most compaction appears to result from intergranular solution but the results are unpredictable because intergranular cement strengthens structure. No consistent relations exist between porosity and depth of burial. The consolidation of limestone is not understood. The initial porosity of most calcareous sediments is greater than that of sand but most limestones show little evidence of compaction. Their consolidation appears to have been accomplished by the deposition of intergranular cement at an early stage before the sediment was subjected to the pressure of much overburden. The source of the cementing calcium carbonate is not known. Organic material, of which coal is presented as an example, is reduced in volume by (1) compression and elimination of pore space, and (2) the loss of substance resulting from, first, biochemical decay and, later, dynamochemical metamorphism. Coal is essentially non-porous and its volume is reduced also by dehydration and increase in specific density. The degradation of organic matter follows one or the other of two paths: (1) carbonaceous (coal), leading to development of larger and more complex molecules (polymerization), or (2) bituminous (oil and natural gas), leading to the development of smaller and simpler molecules (cracking). The difference probably is related to the type of decay that occurs very soon after organic material is deposited as a sediment. Compaction data probably can be applied to the solution of some stratigraphic and structural problems but serious difficulties will remain until the lithification of limestone is more adequately understood. The study of diagenesis has been greatly neglected and it deserves much increased attention from geologists. End_Page 273------------------------------
The polarity protein Baz forms a platform for the centrosome orientation during asymmetric stem cell division in the Drosophila male germline

Many stem cells divide asymmetrically in order to balance self-renewal with differentiation. The essence of asymmetric cell division (ACD) is the polarization of cells and subsequent division, leading to unequal compartmentalization of cellular/extracellular components that confer distinct cell fates to daughter cells. Because precocious cell division before establishing cell polarity would lead to failure in ACD, these two processes must be tightly coupled; however, the underlying mechanism is poorly understood. In Drosophila male germline stem cells, ACD is prepared by stereotypical centrosome positioning. The centrosome orientation checkpoint (COC) further serves to ensure ACD by preventing mitosis upon centrosome misorientation. In this study, we show that Bazooka (Baz) provides a platform for the correct centrosome orientation and that Baz-centrosome association is the key event that is monitored by the COC. Our work provides a foundation for understanding how the correct cell polarity may be recognized by the cell to ensure productive ACD. DOI: http://dx.doi. org/10.7554/eLife.04960. 001
The design of rainfall networks in time and space

A methodology for the design of precipitation networks is formulated. The network problem is discussed in its general conception, and then focus is made on networks to provide background information for the design of more specific gaging systems. The rainfall process is described in terms of its correlation structure in time and space. A general framework is developed to estimate the variance of the sample long-term mean areal precipitation and mean areal rainfall of a storm event. The variance is expressed as a function of correlation in time, correlation in space, length of operation of the network, and geometry of the gaging array. The trade of time versus space is quantitatively developed, and realistic examples are worked out showing the influence of the network design scheme on the variance of the estimated values.
Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA. DOI: http://dx.doi. org/10.7554/eLife.08193. 001
A fossil record full of holes: The Phanerozoic history of drilling predation

The evolutionary history of drilling predation, despite a long and rich fossil record (Precambrian–Holocene), contains a 120 m.y. gap (Late Triassic–Early Cretaceous). Drilled bivalve and brachiopod shells from Jurassic deposits of Hungary, India, and four localities documented in the literature indicate that drillers may have existed continuously throughout the Mesozoic. They may have been descendants of Paleozoic predators, unknown Mesozoic carnivores, or precursors of modern drillers. A literature database suggests three major phases in the Phanerozoic history of drilling predators: (1) the Paleozoic phase (latest Precambrian–Carboniferous) dominated by rare to moderately frequent drillings in brachiopods and sessile echinoderms; (2) the Mesozoic phase (Permian–Early Cretaceous) with very rare, or even facultative, drillers that had little impact on marine benthic communities, but nevertheless may have been present continuously; and (3) the Cenozoic phase (Late Cretaceous –Holocene) dominated by frequent gastropod drillings in mollusks.
Kinetic isotopic fractionation during air‐water gas transfer of O2, N2, CH4, and H2

The authors present experimental results that show that the kinetic isotopic fractionation during gas exchange is 0.9972 [plus minus] 0.0002 for oxygen, 0.9992 [plus minus] 0.0002 for methane, 0.9987 [plus minus] 0.0001 for nitrogen and 0.982 [plus minus] 0.002 for hydrogen, and that the equilibrium fractionation between water and gas phases is 1.037 for hydrogen. They show that the isotopic fractionation during gas transfer for these gases is not equal to the square root of their reduced mass in water, as would be predicted by an extension of the kinetic theory of ideal gases to dissolved gases. The use of isotopes as tracers of biogeochemical gases requires knowledge of the fractionation factor for air-water gas transfer; there have been few direct measurements of these factors. 31 refs., 11 figs., 1 tab.
Social Exclusion Modifies Climate and Deforestation Impacts on a Vector-Borne Disease

Background The emergence of American Cutaneous Leishmaniasis (ACL) has been associated with changes in the relationship between people and forests, leading to the view that forest ecosystems increase infection risk and subsequent proposal that deforestation could reduce re-emergence of this disease. Methodology/Principal Findings We analyzed county-level incidence rates of ACL in Costa Rica (1996–2000) as a function of social and environmental variables relevant to transmission ecology with statistical models that incorporate breakpoints. Once social marginality was taken into account, the effect of living close to a forest on infection risk was small, and diminished exponentially above a breakpoint. Forest cover was associated with the modulation of temporal effects of El Niño Southern Oscillation (ENSO) at small spatial scales, revealing an additional complex interplay of environmental forces and disease patterns. Conclusions/Significance Social factors, which previously have not been evaluated rigorously together with environmental and climatic factors, appear to play a critical role that may ultimately determine disease risk.
Inversion of multimode Rayleigh waves in the presence of a low‐velocity layer: numerical and laboratory study

SUMMARY The dispersion and the surface displacement as a function of frequency of multiple modes guided waves in stratified media including a low-velocity layer are studied by numerical simulation and experiment. A method is developed to determine the thickness and the shear wave velocity of individual layers. First, the modal analysis of Rayleigh wave is investigated numerically for three layered media. Then, ultrasonic surface measurements are performed for three specimens: Steel half-space, Lucite/Steel half-space and Aluminum/Lucite/Steel half-space. The Characteristics of the dispersion curves are analyzed using the frequency–wavenumber method. The non-dispersive Rayleigh wave is obtained for the first simple specimen. The dispersion curves for two modes are obtained for the second specimen with a low-velocity layer on a fast substrate. The dispersion curves for the third specimen containing a low-velocity layer are apparently discontinuous and correspond to different mode branches. Further analysis demonstrates that the apparent discontinuity is caused by a rapid change of mode excitation with frequency at the surface. While one mode vanishes from the recorded wavefield, the other appears. This indicates that the surface displacements of the modes should be also accounted for in the inverse problem, especially in stratified media with a low-velocity layer. Finally, shear wave velocity profiles are inverted based on the experimental (maybe discontinuous) dispersion curves of fundamental or/and higher modes using a Genetic Algorithm(GA). Besides the dispersion characteristics of each mode, the surface displacement distribution is also taken into account for the case of a low-velocity layer, and as a result, the mode-misidentification is avoided.
Investigating multiple fault rupture at the Salar del Carmen segment of the Atacama Fault System (northern Chile): Fault scarp morphology and knickpoint analysis

This study presents a new geomorphological approach to investigate the past activity and potential seismic hazard of upper crustal faults at the Salar del Carmen segment of the Atacama Fault System in the northern Chile forearc. Our contribution is based on the analysis of a large set of topographic profiles and allows extrapolating fault analysis from a few selected locations to distances of kilometers along strike of the fault. We detected subtle changes in the fault scarp geometry which may represent the number of paleoearthquakes experienced by the structure and extracted the cumulative and last incremental displacement along strike of the investigated scarps. We also tested the potential of knickpoints in channels crossing the fault scarps as markers for repeated fault rupture and proxies for seismic displacement. The number of paleoearthquakes derived from our analysis is 2–3, well in agreement with recent paleoseismological investigations, which suggest 2–3 earthquakes (Mw = 6.5–6.7) at the studied segments. Knickpoints record the number of events for about 55% of the analyzed profile pairs. Only few knickpoints represent the full seismic displacement, while most retain only a fraction of the displacement. The along‐strike displacement distributions suggest fault growth from the center toward the tips and linkage of individual ruptures. Our approach also improves the estimation of paleomagnitudes in case of multiple fault rupture by allowing to quantify the last increment of displacement separately. Paleomagnitudes calculated from total segment length and the last increment of displacement (Mw = 6.5–7.1) are in agreement with paleoseismological results.