Miracle-dz/UniFAR-FTUs huggingface dataset:
Impacts of Fire on Hydrology and Erosion in Steep Mountain Big Sagebrush Communities

Wildfire is an important ecological process and management issue on western rangelands. Major unknowns associated with wildfire are its affects on vegetation and soil conditions that influence hydrologic processes including infiltration, surface runoff, erosion, sediment transport, and flooding. Post wildfire hydrologic response was studied in big sagebrush plant communities on steep slopes with coarse-textured soils. Significant rill erosion was observed following both thunderstorm and rapid snowmelt events. Rainfall simulation and controlled overland flow techniques were used to study postfire effects on infiltration, and interrill and rill erosion processes on burned and adjacent unburned areas. Results indicate that burn severity and the development of water repellent soil conditions play significant roles in determining infiltration and interrill erosion rates, particularly on shrub coppice dunes characterized by high surface litter accumulations. The most dramatic and long-lasting affect of fire was on rill erosion processes by reducing ground cover needed to slow and spread water as it moves across the soil surface. Ongoing research efforts are aimed at characterizing the hydrologic impacts of prescribed fire used as a tool to manage vegetation and mitigate the impacts of catastrophic wildfire events.
Highly efficient cellular expression of circular mRNA enables prolonged protein expression

A major problem with mRNA therapeutics is the limited duration of protein expression due to the short half-life of mRNA. New approaches for generating highly stable circular mRNA in vitro have allowed increased duration of protein expression. However, it remains difficult to genetically encode circular mRNAs in mammalian cells, which limits the use of circular mRNA in cell-derived therapeutics. Here we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We identify the promoter and internal ribosomal entry site (IRES) that result in high levels of protein expression in cells. We then show that these circular mRNAs can be packaged into virus-like particles (VLPs) thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can markedly enhance the ability of VLPs to function as a mRNA delivery tool.
Complete Compared With Partial Salpingectomy for Postpartum Sterilization

In the postpartum period, complete salpingectomy is a safe and feasible alternative to partial salpingectomy for permanent contraception, with the additional benefit of ovarian cancer risk reduction. In this narrative review, we describe evidence regarding the associated risks, benefits, and cost effectiveness of postpartum complete salpingectomy compared with partial salpingectomy. Permanent contraception can be performed via several methods, but complete salpingectomy is becoming more common secondary to its coincident benefit of ovarian cancer risk reduction. Small prospective studies and larger retrospective cohort studies have demonstrated the feasibility and safety of complete salpingectomy in the postpartum period. Additionally, multiple cost-effectiveness analyses have demonstrated the cost effectiveness of this method secondary to ovarian cancer reduction over the life span. Although future larger cohort studies will allow for more precise estimates of the effect of complete salpingectomy on ovarian cancer risk and incidence of rare complications, current data suggest that complete salpingectomy should be offered to patients as a method of permanent contraception in the postpartum period.
New Metrics To Differentiate Species of Stenopterygius (Reptilia: Ichthyosauria) from the Lower Jurassic of Southwestern Germany

Abstract Ichthyosaurs represent one of the most highly specialized lineages of marine reptiles, but our understanding of the evolution of this group is based on specimens found at a surprisingly small number of stratigraphic intervals and localities. The Lower Jurassic (Toarcian) Posidonia Shale of southwestern Germany is one of the richest ichthyosaur-bearing formations in the world and has produced thousands of skeletons, including specimens with preserved soft tissue, and fetal remains inside the body cavity. The most abundant ichthyosaur genus in the Posidonia Shale is Stenopterygius. In spite of almost 200 years of research effort, the number of species in this genus is still a point of active disagreement in the literature. Here, bivariate and multivariate analyses are used to classify both articulated and disarticulated skeletons to the level of species, using measurement data from individual cranial and postcranial elements. Unlike previous classification attempts, this technique pinpoints ontogenetically conserved differences in size and proportion between the species, and so can be applied to adult, subadult, and neonatal specimens. Using this method, three species of Stenopterygius, S. quadriscissus, S. triscissus, and S. uniter are differentiated.
Exogenous protease influences protein digestibility, growth performance, and gut microflora in weanling pigs on a limited protein diet

ABSTRACT The study was conducted to evaluate the impact of dietary level of crude protein (CP) and protease supplementation on growth performance, digestibility of nutrients, intestinal morphology, and gut microbiota in weaning pigs. Three hundred cross-bred piglets (Duroc × Landrace × Yorkshire) were allotted to five dietary treatments on the basis of initial body weight (BW) and sex. Pigs were group-housed in pens with each treatment with 10 replicate pens with six pigs per pen. The treatments included a standard diet (STD), STD with 0.6% lower protein (STD0.6), STD with 0.6% lower protein and protease supplementation (Pro0.6), STD with 1.0% lower protein (STD1.0), STD with 1.0% lower protein and protease supplementation (Pro1.0). Results indicated a higher BW (p < 0.05) of piglets in the Pro0.6 group at days 0–42 compared to the STD0.6 and STD1.0 groups. The average daily gain was higher (p < 0.05) in the Pro0.6 treatments at days 0–42 compared to the STD0.6 and STD1.0. The gain to feed ratio was higher (p < 0.05) in the STD, and Pro0.6 groups compared to the STD0.6, Pro1.0 and the STD1.0 groups at days 0–42. Dry matter digestibility was lower (p < 0.05) in the STD1.0 group than the Pro0.6 and Pro1.0 groups. The crude protein digestibility was higher (p < 0.05) in the Pro0.6 group compared to the STD, STD0.6 and STD1.0 treatment groups while crude fat digestibility was higher (p < 0.05) in the STD and Pro0.6 compared with the STD0.6 and STD1.0 groups. Digestibility was higher for histidine (p < 0.05), leucine (p < 0.05) in the protease Pro0.6 and Pro1.0 groups than in the STD0.6 and STD1.0 groups. The digestibility of non-essential AA was higher for alanine (p < 0.05) in the Pro0.6 than the STD1.0 group. For faecal microbial population, Faecalibacterium abundance was higher (p < 0.05) in the Pro0.6 compared to all the other groups while the population of Actinobacteria was greater (p < 0.05) in the STD group and lowest in the Pro1.0 treatment. In the ileum, villus height was greater (p < 0.05) in the protease Pro0.6, and Pro1.0 groups compared to the STD0.6, and STD1.0 groups while the villus height to crypts depth ratio was lower (p < 0.05) in the STD 1.0 group compared to the STD, Pro0.6, and Pro1.0 groups. Based on these results, dietary protease supplementation improved nutrient digestibility and gut histo-morphology translating to improved utilisation of nutrients thus positively impacting growth performance in weaned pigs. Further, reducing the CP content in the diets increased the abundance of Muribaculaceae while protease supplementation increased the population of Faecalibacterium in the gut of the weanling piglets on the STD0.6 diet.
Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these are in turn determined by the multiscale structural features within condensates. However, structural characterizations of condensates are challenging, and hence rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and bespoke coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that mimic nucleolar granular components (GCs). We show that facsimiles of GCs are network fluids featuring spatial inhomogeneities across hierarchies of length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights, extracted from a combination of approaches, suggest that condensates formed by multivalent proteins share features with network fluids formed by associative systems such as patchy or hairy colloids.
Precipitation over Greenland Retrieved by a Dynamic Method and Its Relation to Cyclonic Activity

Abstract In order to calculate the vertical motion over some high mountain regions, such as Greenland, an ω-equation without the quasigeostrophic approximation in σ-coordinates has been developed. A dynamic method for retrieving precipitation over Greenland is based on this ω-equation. The retrieved annual mean precipitation distribution for 1987 and 1988 is in very good agreement with the observed annual accumulation pattern over the Greenland Ice Sheet. The major weather system producing precipitation over Greenland is the frontal cyclone. Based on the precipitation characteristics, Greenland can be divided into five subregions. Precipitation over the north coastal and central interior regions primarily occurs in summer. For the three other subregions, if the composite monthly mean sea level pressure charts for high and low monthly precipitation amounts are constructed, a clear relationship between precipitation and cyclonic activity emerges. If a mean cyclone exists in the Labrador Sea, heavy precipita.
Numerical Representation for Action in Crows Obeys the Weber-Fechner Law

The psychophysical laws governing the judgment of perceived numbers of objects or events, called the number sense, have been studied in detail. However, the behavioral principles of equally important numerical representations for action are largely unexplored in both humans and animals. We trained two male carrion crows (Corvus corone) to judge numerical values of instruction stimuli from one to five and to flexibly perform a matching number of pecks. Our quantitative analysis of the crows’ number production performance shows the same behavioral regularities that have previously been demonstrated for the judgment of sensory numerosity, such as the numerical distance effect, the numerical magnitude effect, and the logarithmical compression of the number line. The presence of these psychophysical phenomena in crows producing number of pecks suggests a unified sensorimotor number representation system underlying the judgment of the number of external stimuli and internally generated actions.
COVID-19 epidemiology and rural healthcare: a survey in a Spanish village

Abstract We used primary care data to retrospectively describe the entry, spread, and impact of COVID-19 in a remote rural community and the associated risk factors and challenges faced by the healthcare team. Generalized linear models were fitted to assess the relationship between age, sex, period, risk group status, symptom duration, post-COVID illness, and disease severity. Social network and cluster analyses were also used. The first six cases, including travel events and a social event in town, contributed to early infection spread. About 351 positive cases were recorded and 6% of patients experienced two COVID-19 episodes in the 2.5-year study period. Five space–time case clusters were identified. One case, linked with the social event, was particularly central in its contact network. The duration of disease symptoms was driven by gender, age, and risk factors. The probability of suffering severe disease increased with symptom duration and decreased over time. About 27% and 23% of individuals presented with residual symptoms and post-COVID illness, respectively. The probability of developing a post-COVID illness increased with age and the duration of COVID-associated symptoms. Carefully registered primary care data may help optimize infection prevention and control efforts and upscale local healthcare capacities in vulnerable rural communities.
CDS-DB, an omnibus for patient-derived gene expression signatures induced by cancer treatment

Abstract Patient-derived gene expression signatures induced by cancer treatment, obtained from paired pre- and post-treatment clinical transcriptomes, can help reveal drug mechanisms of action (MOAs) in cancer patients and understand the molecular response mechanism of tumor sensitivity or resistance. Their integration and reuse may bring new insights. Paired pre- and post-treatment clinical transcriptomic data are rapidly accumulating. However, a lack of systematic collection makes data access, integration, and reuse challenging. We therefore present the Cancer Drug-induced gene expression Signature DataBase (CDS-DB). CDS-DB has collected 78 patient-derived, paired pre- and post-treatment transcriptomic source datasets with uniformly reprocessed expression profiles and manually curated metadata such as drug administration dosage, sampling time and location, and intrinsic drug response status. From these source datasets, 2012 patient-level gene perturbation signatures were obtained, covering 85 therapeutic regimens, 39 cancer subtypes and 3628 patient samples. Besides data browsing, download and search, CDS-DB also supports single signature analysis (including differential gene expression, functional enrichment, tumor microenvironment and correlation analyses), signature comparative analysis and signature connectivity analysis. This provides insights into drug MOA and its heterogeneity in patients, drug resistance mechanisms, drug repositioning and drug (combination) discovery, etc. CDS-DB is available at http://cdsdb.ncpsb. org.cn/.
‘SAXS-osmometer’ method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state

Abstract We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA–DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.
QEVIS: Multi-Grained Visualization of Distributed Query Execution

Distributed query processing systems such as Apache Hive and Spark are widely-used in many organizations for large-scale data analytics. Analyzing and understanding the query execution process of these systems are daily routines for engineers and crucial for identifying performance problems, optimizing system configurations, and rectifying errors. However, existing visualization tools for distributed query execution are insufficient because (i) most of them (if not all) do not provide fine-grained visualization (i.e., the atomic task level), which can be crucial for understanding query performance and reasoning about the underlying execution anomalies, and (ii) they do not support proper linkages between system status and query execution, which makes it difficult to identify the causes of execution problems. To tackle these limitations, we propose QEVIS, which visualizes distributed query execution process with multiple views that focus on different granularities and complement each other. Specifically, we first devise a query logical plan layout algorithm to visualize the overall query execution progress compactly and clearly. We then propose two novel scoring methods to summarize the anomaly degrees of the jobs and machines during query execution, and visualize the anomaly scores intuitively, which allow users to easily identify the components that are worth paying attention to. Moreover, we devise a scatter plot-based task view to show a massive number of atomic tasks, where task distribution patterns are informative for execution problems. We also equip QEVIS with a suite of auxiliary views and interaction methods to support easy and effective cross-view exploration, which makes it convenient to track the causes of execution problems. QEVIS has been used in the production environment of our industry partner, and we present three use cases from real-world applications and user interview to demonstrate its effectiveness. QEVIS is open-source at https://github.com/DBGroup-SUSTech/QEVIS.
Assessment of Surgical Accuracy in Maxillomandibular Advancement Surgery for Obstructive Sleep Apnea: A Preliminary Analysis

This retrospective study aimed to: (1) investigate the surgical accuracy of maxillomandibular advancement (MMA) in obstructive sleep apnea (OSA) patients, with a specific focus on maxillary and mandibular advancement and counter-clockwise rotation and (2) investigate the correlation between the amount of achieved advancement and the reduction in the relative apnea hypopnea index (AHI). Sixteen patients, for whom a three-dimensional virtual surgical plan was generated preoperatively and a computed tomography scan (CT) or cone-beam computer tomography (CBCT) was acquired postoperatively, were included. The postoperative CT or CBCT was compared to the virtual surgical plan, and differences in the mandibular and maxillary advancement and counter-clockwise rotation were assessed. Maxillary and mandibular advancement (median 3.1 mm, p = 0.002 and 2.3 mm, p = 0.03, respectively) and counter-clockwise rotation (median 3.7°, p = 0.006 and 4.7°, p = 0.001, respectively) were notably less than intended. A significant correlation was found between the planned maxillary advancement and the difference between the planned and actual maxillary advancement (p = 0.048; adjusted R2 = 0.1979) and also between the planned counter-clockwise rotation and the difference between the planned and actual counter-clockwise rotation for the mandible (p = 0.012; adjusted R2 = 0.3261). Neither the maxilla-first nor the mandible-first surgical sequence proved to be superior in terms of the ability to achieve the intended movements (p > 0.45). Despite a significant reduction (p = 0.001) in the apnea hypopnea index (AHI) from a median of 62.6 events/h to 19.4 events/h following MMA, no relationship was found between the extent of maxillary or mandibular advancement and AHI improvement in this small cohort (p = 0.389 and p = 0.387, respectively). This study underlines the necessity for surgeons and future research projects to be aware of surgical inaccuracies in MMA procedures for OSA patients. Additionally, further research is required to investigate if sufficient advancement is an important factor associated with MMA treatment outcome.
HumanLectome, an update of UniLectin for the annotation and prediction of human lectins

Abstract The UniLectin portal (https://unilectin.unige.ch/) was designed in 2019 with the goal of centralising curated and predicted data on carbohydrate-binding proteins known as lectins. UniLectin is also intended as a support for the study of lectomes (full lectin set) of organisms or tissues. The present update describes the inclusion of several new modules and details the latest (https://unilectin.unige.ch/humanLectome/), covering our knowledge of the human lectome and comprising 215 unevenly characterised lectins, particularly in terms of structural information. Each HumanLectome entry is protein-centric and compiles evidence of carbohydrate recognition domain(s), specificity, 3D-structure, tissue-based expression and related genomic data. Other recent improvements regarding interoperability and accessibility are outlined.
A comparison of approaches to the prediction of surface wave amplitude

A controlled experiment is performed to investigate how assumptions and simpliﬁcations in the measurement and analysis of surface wave amplitudes affect inferred attenuation variations in the mantle. Synthetic seismograms are generated using a spectral-element method for 42 earthquakes, 134 receiver locations and two earth models, both of which contain 3-D elastic properties and 1-D anelastic properties. Fundamental-mode Rayleigh-wave amplitudes are measured at periods of 50, 75 and 125 s for 4749 paths. The amplitudes are measured with respect to a reference waveform based on 1-D Earth structure, and thus amplitude observations that are not equal to unity can be attributed to differences in the computation of the spectral-element and reference waveforms or to uncertainties in the amplitude measurements themselves. Calculation of earthquake source excitation in the 3-D earth model versus the 1-D earth model has a signiﬁcant effect on the amplitudes, especially at shorter periods, and variations in the average amplitude for each event are well explained by the effect of Earth structure at the event location on the source excitation. The effect of local Earth structure at the receiver location on the amplitude is, for most paths, much smaller than for the source amplitude. After correcting for source and receiver effects on amplitude, the remaining signal is compared to predictions of elastic focusing effects using the great-circle ray approximation, exact ray theory (ERT) and ﬁnite-frequency theory (FFT). We ﬁnd that, for the earth models we have tested, ERT provides the best ﬁt at 50 s, and FFT is most successful at 75 and 125 s, indicating that the broad zone of surface wave sensitivity cannot be neglected for the longer periods in our experiment. The bias introduced into attenuation models by focusing effects, which is assessed by inverting the measured amplitudes for 2-D attenuation maps, is most important at high spherical-harmonic degrees. Unaccounted-for scattering of seismic energy may slightly ( < 5 per cent) raise average global attenuation values at short periods but has no detectable effect at longer periods. The ﬁndings of this study also provide a set of guidelines for handling source, receiver and focusing effects that can be applied to surface wave amplitudes measured for the real Earth.