Miracle-dz/UniFAR-FTUs huggingface dataset:
Curing Rates in the Grass Sward of the Highland Sourveld in the Natal Drakensberg

SYNOPSIS Data on the curing rates of one, two and three-year-old grassland are presented. Curing is initiated at the end of April and progresses rapidly up to the middle of May. By June the grasses are 95 % cured, increasing the fire hazard in winter. A simple model was developed to estimate fuel moisture from easily measured atmospheric variables. This model will enable managers to predict the process of curing more accurately and so aid prescribed burning.
Diet‐related factors strongly shaped the gut microbiota of Japanese macaques

Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large‐scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet‐related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
Immunohistochemistry for MSH2 and MHL1: a method for identifying mismatch repair deficient colorectal cancer

Colorectal cancers with DNA mismatch repair (MMR) gene mutations characteristically display a high rate of replication errors in simple repetitive sequences detectable as microsatellite instability (MSI). Most are the result of somatic MMR dysfunction; however, a subset are caused by germline mutations. The availability of commercial antibodies for MSH1 and MLH2 offers an alternative strategy to molecular methods for identifying MMR deficient cancers. To evaluate immunohistochemistry, MLH1 and MSH2 expression was studied using monoclonal antibodies in formalin fixed, paraffin wax embedded cancers. The immunohistochemical staining patterns of 23 cancers displaying MSI, including four cases with germline mutations, were compared with 23 microsatellite stable (MSS) cancers. All MSS cancers exhibited staining with both antibodies. Twenty two of the MSI cases showed absent MMR expression with either anti-MSH1 or anti-MLH2. The high sensitivity and predictive value of immunohistochemistry in detecting MMR deficiency offers a method of discriminating between MSI and MSS cancers caused by MSH1 and MLH2 dysfunction. The application and suitability of immunohistochemistry for the detection of MSI and as a strategy for prioritising the mutational analysis of MMR genes in routine clinical practice is discussed.
Event-based approach for probabilistic flood risk assessment

ABSTRACT An event-based approach for probabilistic flood risk assessment for financial and civil protection applications is proposed. The risk parameters are evaluated in an event-based probabilistic framework for a set of hazard events and then all these results are probabilistically integrated, including, in a formal way, all uncertainties related to each and every part of the process. The hazard is defined as a stochastic or historic set of events, collectively exhaustive and mutually exclusive, that describes the spatial distribution, the annual frequency, and the randomness of the hazard intensity. The risk is expressed in different economic terms: the average annual loss, the pure risk premium, and the loss exceedance curve. As an illustrative example, this approach is applied to Acapulco city located on the Pacific coast of Mexico. These metrics are of particular importance for risk retention (financing) schemes or risk transfer instruments, and, therefore, they will be a particularly valuable contribution to further studies in defining strategies for financial protection against disasters. With these results, further results may be obtained for civil protection and land use applications.
A comparison of mineral magnetic, geochemical and mineralogical techniques for compositional studies of glacial diamictons

Data from heavy mineral analysis, X-ray fluorescence spectrometry (XRF) and X-ray diffractrometry (XRD) are compared with those obtained from mineral magnetic analysis for a range of glacial diamicton samples taken from the Quaternary sequence in the Isle of Man. These data show that the mineral magnetic approach offers a useful means of characterizing glacial sediments for purposes of lithostratigraphic correlation and provenance indication and that the magnetic data are of a comparable quality to those obtained from standard applications of the more traditional techniques. The heavy mineral and XRD data indicate that little post-depositional chemical alteration of the detrital composition of the sediments has taken place. The mineral magnetic, heavy mineral and XRF analysis suggests both similar lithostratigraphic relationships between the various diamicton units and consistent indications of their likely provenance. These are consistent with published, field-based, stratigraphic relationships of the same sediments and ice-flow directions in the Irish Sea Basin during the Devensian.
Elevation modelling from satellite visible and infrared (VIR) data

Since the early emergence of Earth observation satellites, researchers have investigated different methods of extracting three-dimensional information using satellite data. Apart from a few early stereo images by hand-held photographs acquired during the Gemini and Apollo missions, the first experiments to extract three-dimensional data using stereo viewing from space began with the Earth Terrain Camera flown onboard SkyLab in 1973/74. Since this time, various analogue or digital sensors in the visible spectrum have flown to provide researchers and geoscientists with spatial data to extract and interpret three-dimensional information of the Earth's surface. Although clinometry techniques can be applied with the optical sensor images, stereo viewing of images was and still is the most common method used by the mapping, photogrammetry and remote sensing communities for elevation modelling. The paper will review clinometry and stereoscopy and their applicability to the different satellite sensors (space photographs and scanners). Their performances to extract absolute or relative elevation from various research and commercial organizations are addressed. The respective advantages, difficulties and constraints of the sensors are discussed, as well as the methods and the technologies used for extracting elevation data in an operational context.
Effects of vertical integration on the healthcare system in China: a systematic review and meta-analysis

Abstract Vertical integration is one possible way to improve the performance of a healthcare system; however, its effects are inconsistent, and there is a lack of evidence from undeveloped nations. This study aims to systematically review the evidence regarding effects of vertical integration on healthcare systems in China. We searched PubMed, Embase, Cochrane Library, Web of Science, ProQuest Health & Medicine Collection, China Knowledge Resource Integrated Database and Wanfang databases from April 2009 (initiation of new healthcare reform) to May 2021 for randomized controlled trials (RCTs), controlled before and after (CBA) trials, cohort studies and interrupted time series (ITS) trials. Vertical integration in the included studies must involve both primary health institutions and secondary or tertiary hospitals. After screening 3109 records, we ultimately analysed 47 studies, including 27 CBA trials, 18 RCTs and 2 ITS trials. The narrative synthesis shows that all but three studies indicated that vertical integration improved efficiency (utilization and cost of health services), quality of public health services and medical services, health provider-centred outcomes (knowledge and skill) and patient-centred outcomes (patients’ clinical outcomes, behaviour and satisfaction). Despite the heterogeneity of vertical integration interventions across different studies, the meta-analysis reveals that it lowered diastolic blood pressure (mean difference (MD) −8.41, 95% confidence interval (CI) −15.18 to −1.65) and systolic blood pressure (MD-5.83, 95% CI −9.25 to −2.40) among hypertension patients, and it lowered HbA1c levels (MD −1.95, 95% CI −2.69 to −1.21), fasting blood glucose levels (MD −1.02, 95% CI −1.53 to −0.50) and 2-hour postprandial blood glucose levels (MD −1.78, 95% CI −2.67 to −0.89). The treatment compliance behaviour was improved for hypertension participants (risk ratio (RR) 1.08, 95% CI 1.04–1.13) and for diabetes patients (RR 1.32, 95% CI 1.08–1.61). Vertical integration in China can improve efficiency, quality of care, health provider-centred outcomes and patient-centred outcomes, but high-quality original studies are highly needed.
Phenological response of plants to temperature varies at the same latitude: case study of dog violet and horse chestnut in England and Poland

We analysed phenological observations of first flowering of early dog violet Viola reichenbachiana and horse chestnut Aesculus hippocastanum at similar latitudes (and hence photo- period) in the UK and Poland during the 26 years 1970-1995. Temperatures in Poland were signifi- cantly colder than in the UK for February and March and significantly warmer in May. Mean first flowering dates of both species were not significantly different between the 2 countries. However, records in the UK were significantly more variable. Both species in both locations showed significant temperature responsiveness although plants in the UK were more responsive than those in Poland. We conclude that locally adapted species may differ in their projected change under future climate warming.
TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa

Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell–derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition–like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
In silico identification of novel SARS-COV-2 2′-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches

Abstract The novel coronavirus disease COVID-19, caused by the virus SARS CoV-2, has exerted a significant unprecedented economic and medical crisis, in addition to its impact on the daily life and health care systems all over the world. Regrettably, no vaccines or drugs are currently available for this new critical emerging human disease. Joining the global fight against COVID-19, in this study we aim at identifying a potential novel inhibitor for SARS COV-2 2′-O-methyltransferase (nsp16) which is one of the most attractive targets in the virus life cycle, responsible for the viral RNA protection via a cap formation process. Firstly, nsp16 enzyme bound to Sinefungin was retrieved from the protein data bank (PDB ID: 6WKQ), then, a 3D pharmacophore model was constructed to be applied to screen 48 Million drug-like compounds of the Zinc database. This resulted in only 24 compounds which were subsequently docked into the enzyme. The best four score-ordered hits from the docking outcome exhibited better scores compared to Sinefungin. Finally, three molecular dynamics (MD) simulation experiments for 150 ns were carried out as a refinement step for our proposed approach. The MD and MM-PBSA outputs revealed compound 11 as the best potential nsp16 inhibitor herein identified, as it displayed a better stability and average binding free energy for the ligand-enzyme complex compared to Sinefungin.
Seismic attenuation tomography of the Tonga‐Fiji region using phase pair methods

The anelastic structure of the region surrounding the Tonga slab and Lau back arc spreading center in the southwest Pacific is studied using data from 12 broadband island stations and 30 ocean bottom seismographs. Two differential attenuation methods determine δt* over the frequency band 0.1 to 3.5 Hz for earthquakes in the Tonga slab. The S-P method measures the difference in spectral decay between P and S waves arriving at the same station. The P-P method measures the difference in spectral decay for P waves with different paths through the upper mantle. Eight hundred sixty phase pairs are used to invert for two-dimensional 1/Qα structure using a nonnegative least squares algorithm. A grid search method determines the Qα/Qβ ratio most compatible with both the S-P and P-P differential measurements. The highest attenuation (Qα = 90) is found within the upper 100 km beneath the active portions of the Lau Basin extending westward to the Lau Ridge. These regions probably delineate the source region for the back arc spreading center magmas, expected to be within the upper 100 km based on petrological considerations. The high attenuation regions also correlate well with zones of low P wave velocity determined by regional velocity tomography. Somewhat lower attenuation is found beneath the Fiji Plateau than beneath the Lau Basin. The entire back arc is characterized by a gradual decrease in attenuation to a depth of 300 to 400 km. The slab is imaged as a region of low attenuation (Qα > 900) material. A Qα/Qβ ratio of 1.75 provides the best fit between the S-P and P-P data sets upon inversion. Spectral stacking shows no frequency dependence within the frequency band analyzed.
Artificial intelligence versus radiologist in the accuracy of fracture detection based on computed tomography images: a multi-dimensional, multi-region analysis

Background Extremities fractures are a leading cause of death and disability, especially in the elderly. Avulsion fracture are also the most commonly missed diagnosis, and delayed diagnosis leads to higher litigation rates. Therefore, this study evaluates the diagnostic efficiency of the artificial intelligence (AI) model before and after optimization based on computed tomography (CT) images and then compares it with that of radiologists, especially for avulsion fractures. Methods The digital X-ray photography [digital radiography (DR)] and CT images of adult limb trauma in our hospital from 2017 to 2020 were retrospectively collected, with or without 1 or more fractures of the shoulder, elbow, wrist, hand, hip, knee, ankle, and foot. Labeling of the fracture referred to the visualization of the fracture on the corresponding CT images. After training the pre-optimized AI model, the diagnostic performance of the pre-optimized AI, optimized AI model, and the initial radiological reports were evaluated. For the lesion level, the detection rate of avulsion and non-avulsion fractures was analyzed, whereas for the case level, the accuracy, sensitivity, and specificity were compared among them. Results The total datasets (1,035 cases) were divided into a training set (n=675), a validation set (n=169), and a test set (n=191) in a balanced joint distribution. At the lesion level, the detection rates of avulsion fracture (57.89% vs. 35.09%, P=0.004) and non-avulsion fracture (85.64% vs. 71.29%, P<0.001) by the optimized AI were significantly higher than that by pre-optimized AI. The average precision (AP) of the optimized AI model for all lesions was higher than that of pre-optimized AI model (0.582 vs. 0.425). The detection rate of avulsion fracture by the optimized AI model was significantly higher than that by radiologists (57.89% vs. 29.82%, P=0.002). For the non-avulsion fracture, there was no significant difference of detection rate between the optimized AI model and radiologists (P=0.853). At the case level, the accuracy (86.40% vs. 71.93%, P<0.001) and sensitivity (87.29% vs. 73.48%, P<0.001) of the optimized AI were significantly higher than those of the pre-optimized AI model. There was no statistical difference in accuracy, sensitivity, and specificity between the optimized AI model and the radiologists (P>0.05). Conclusions The optimized AI model improves the diagnostic efficacy in detecting extremity fractures on radiographs, and the optimized AI model is significantly better than radiologists in detecting avulsion fractures, which may be helpful in the clinical practice of orthopedic emergency.
Salt extrusion at Kuh-e-Jahani, Iran, from June 1994 to November 1997

Abstract Kuh-e-Jahani is one of the largest extrusions of salt currently active in the Zagros mountains. Salt rises from about 4 km below sea level to nearly 1.5 km, above, where, unable to support its own weight, it spreads over the surrounding scenery in a process responsible for present and past allochthonous salt sheets elsewhere. We report vertical movements and apparent horizontal displacements of 43 markers dispersed over this mountain of salt for 4.5 years in three consecutive intervals, the first of 18 months and two others of 12 months. The geometry and inferred flow rate of the salt changed between surveys emphasizing that the gravity spreading is not steady. Our field readings of the dimensions and velocities of the salt at Kuh-e-Jahani are used to tune a simple numerical model and constrain the viscosity of the salt to between 1016 and 1017 Pa s−1, its rate of surface dissolution to 2–3 cm a−1, and its rate of rise out of its orifice at 2–3 m a−1 for c. 55 ka. These results imply that vigorous extrusion of salt at Kuh-e-Jahani is probably close to evacuating its deep source and that this mountain will soon begin to waste as salt dissolution overtakes extrusion. This progress report is warranted because our results have significant implications for sophisticated engineering in salt.
Sea ice‐derived dissolved iron and its potential influence on the spring algal bloom in the Bering Sea

Observational and modeling studies in the Bering Sea indicate that changes in the seasonal ice cover and time of ice retreat influence open‐water productivity. In particular, the timing of the spring bloom and its phytoplankton community composition are affected. Dissolved iron (DFe) data in the water column and ice cores collected during the 2007‐ Bering Ecosystem Study (BEST) cruise indicate that the melting ice provided substantial DFe to the water column. The additional DFe input from melting sea ice could be biologically important along the outer shelf and shelf break where in ice‐free areas insufficient DFe (<1 nM) existed for the complete assimilation of available nitrate (>20 μM). Variability in sea ice dynamics are likely to result in a varying supply of DFe to the outer shelf and shelf break in early spring, and to contribute to the observed changes in the timing and community composition of the spring phytoplankton bloom.
Leakage-Aware Energy-Efficient Beamforming for Heterogeneous Multicell Multiuser Systems

Energy-efficient communications has attracted much interest in the research of 5G cellular systems. In this paper, we study energy-efficient coordinated beamforming design for heterogeneous multicell multiuser downlink systems. The considered problem is formulated as maximizing the weighted sum per-cell energy efficiencies (WSPEEMax) subject to predefined per-user target rate demands, maximum leakage interference power constraints, and per-BS transmit power constraints. This formulation is more general than the conventional EE optimization problem and provides a unified way to consider the EE of heterogeneous networks. However, it is hard to tackle due to the weighted sum-of-ratios form of the objective function and the non-convex nature of per-user target rate constraints. To address it, we propose to first transform the original problem into a polynomial form optimization by introducing some auxiliary variables and then further reveal their equivalence in finding the solution. Then, an efficient block coordinate ascent optimization algorithm is developed to solve the equivalent problem by exploiting the concave nature of the considered problem with respect to each optimization variable. To further improve the network EE, we also develop an energy-efficient transmission method for each small-cell network. Finally, extensive numerical results are provided to verify the effectiveness of the proposed schemes and show that both the EE and spectral efficiency (SE) of heterogeneous network can be significantly improved by energy-efficient coordinated multiple-input multiple-output (MIMO) transmission.
Population pharmacokinetics of recombinant factor VIII Fc fusion protein

Population pharmacokinetics (PK) of FVIII activity‐time profiles following recombinant factor VIII Fc fusion protein (rFVIIIFc) and recombinant factor VIII (rFVIII) dosing were evaluated in previously treated patients with severe hemophilia A (from two clinical trials). Potential covariates that may be determinants of variability in FVIII activity were identified. A 2‐compartment model adequately described the PK of both compounds. von Willebrand Factor (VWF) concentration was the major covariate for rFVIIIFc clearance, reflecting its protective role in FVIII activity clearance. The effect of body weight and hematocrit on the central volume of distribution of rFVIIIFc was minor. The results of these analyses confirmed that rFVIIIFc clearance (1.65 dL/h) is much lower than that of rFVIII (2.53 dL/h), while the steady state volumes of distribution were similar. The strong positive correlations between the PK parameters of rFVIIIFc and rFVIII suggest that individuals who have high time‐related PK characteristics with rFVIII are likely to have comparable characteristics with rFVIIIFc. Steady‐state activity‐time profiles for selected rFVIIIFc dosing regimens were simulated accounting for uncertainty in model parameters. These population PK analyses and simulations provide a comprehensive characterization of the PK of rFVIIIFc and rFVIII and may be useful for designing dosing regimens.