Miracle-dz/UniFAR-FTUs huggingface dataset:
SW-UNet: a U-Net fusing sliding window transformer block with CNN for segmentation of lung nodules

Medical images are information carriers that visually reflect and record the anatomical structure of the human body, and play an important role in clinical diagnosis, teaching and research, etc. Modern medicine has become increasingly inseparable from the intelligent processing of medical images. In recent years, there have been more and more attempts to apply deep learning theory to medical image segmentation tasks, and it is imperative to explore a simple and efficient deep learning algorithm for medical image segmentation. In this paper, we investigate the segmentation of lung nodule images. We address the above-mentioned problems of medical image segmentation algorithms and conduct research on medical image fusion algorithms based on a hybrid channel-space attention mechanism and medical image segmentation algorithms with a hybrid architecture of Convolutional Neural Networks (CNN) and Visual Transformer. To the problem that medical image segmentation algorithms are difficult to capture long-range feature dependencies, this paper proposes a medical image segmentation model SW-UNet based on a hybrid CNN and Vision Transformer (ViT) framework. Self-attention mechanism and sliding window design of Visual Transformer are used to capture global feature associations and break the perceptual field limitation of convolutional operations due to inductive bias. At the same time, a widened self-attentive vector is used to streamline the number of modules and compress the model size so as to fit the characteristics of a small amount of medical data, which makes the model easy to be overfitted. Experiments on the LUNA16 lung nodule image dataset validate the algorithm and show that the proposed network can achieve efficient medical image segmentation on a lightweight scale. In addition, to validate the migratability of the model, we performed additional validation on other tumor datasets with desirable results. Our research addresses the crucial need for improved medical image segmentation algorithms. By introducing the SW-UNet model, which combines CNN and ViT, we successfully capture long-range feature dependencies and break the perceptual field limitations of traditional convolutional operations. This approach not only enhances the efficiency of medical image segmentation but also maintains model scalability and adaptability to small medical datasets. The positive outcomes on various tumor datasets emphasize the potential migratability and broad applicability of our proposed model in the field of medical image analysis.
Assessing estimation techniques for missing plot observations in the U.S. forest inventory

The U.S. Forest Service, Forest Inventory and Analysis Program made a transition from state-by-state periodic forest inventories--with reporting standards largely tailored to regional requirements--to a nationally consistent, annual inventory tailored to large-scale strategic requirements. Lack of measurements on all forest land during the periodic inventory, along with access issues and misidentification of forest plots as nonforest, have resulted in plot-level data gaps spread in the FIA database. In this study, we examined several approaches that compensate for missing observations with respect to the deviation and precision of stratified estimates of carbon stocks per unit area using data from the FIA database. Preliminary estimates of live tree carbon stocks per unit area calculated using all missing data approaches were well within one standard error of the baseline estimates for the Lake States study region.
A Virtual Reality application for the exploration of a modern shipwreck: the case study of the Christoforos wreck

The paper presents the development of a Virtual Reality (VR) application to perform dives in the Christoforos Shipwreck. The huge wreck lies in the Panormos Bay of Skopelos island (Greece) at a depth of 45 meters. Based on a well-known methodology designed for ancient shipwrecks, the 3D reconstruction of the underwater site has been carried out by adjusting the workflow to survey modern shipwrecks. In particular, the methodology, based on photogrammetry, is capable to provide a highly detailed 3D reconstruction of the shipwreck in a few dives, considering issues like working depth, elevations, and thin elements modelling. Moreover, the paper describes the optimization of the 3D model and the software to be executed in low-performance Head Mounted Display (HMD) devices. The resulting VR application, realized for touristic purposes, recreates the exact ambient conditions inside and outside the water simulating the flora and fauna of the place, the coastline, allowing users to live a recreational and educational experience by virtual diving in the underwater site.
Biogeochemical gradients and energetics in geothermal systems of Yellowstone National Park

The fate and behavior of redox-active chemical species in geothermal systems is linked with the metabolic processes of chemotrophic thermophilic microorganisms. The major goal of the current work was to perform a thorough geochemical analysis of redox active species in geothermal outflow channels, and utilize these measurements to quantify the Gibbs free energy (∆Grxn) values for numerous oxidation-reduction reactions that represent potential chemolithotrophic metabolisms. Insights gained from energetic analyses can be used to structure hypotheses regarding novel microbial metabolisms and to guide cultivation strategies for isolating relevant microorganisms. A comprehensive suite of geochemical parameters, including major ions, trace elements, redox-active species and dissolved gases, were analyzed and monitored in vertical transects of 11 geothermal outflow channels in Yellowstone National Park from 20032005. The geothermal springs chosen for this study contained strikingly different aqueous and solid-phase geochemistry. These systems exhibited a wide range of conditions, including ranges in pH (2.7 to 7.0), temperature (60 C to 92 C), Cl (0.01 to 23 mM)), SO4 (0.4 to 7.5 mM), NH4 (0.02 to 5.7 mM), CO2 (aq) (0.1 to 4.5 mM), Fe (0.2 to 230 μM), and As (0.03 to 130 μM). The predominant changes in geochemistry occurring within geothermal outflow channels were consistently related to the dynamics of air-water gas exchange. In all springs studied, dissolved gases including H2, CO2, CH4 and H2S decreased down gradient of geothermal discharge, while O2 ingassing resulted in increases in dissolved O2. Calculated free energy (∆Grxn) values for balanced oxidation-reduction reactions suggest that numerous electron donor/acceptor combinations are exergonic in these systems. Reactions where H2, CH4, H2S, S, As, Fe and or NH4 serve as electron donors were all significantly exergonic (< -30 kJ mole electron at all sites) when O2 was the electron acceptor, even when O2 levels were at the detection limit (3 μM). The geothermal systems included in this study all exhibited significant changes in microbial population distribution from near source-water conditions to sediments lining the outflow channels, consistent with the hypothesis that geochemical gradients and temperature correlate with microbial population distribution.
A Bayesian extreme value analysis of debris flows

Debris flows carry a tremendous potential for physical destruction as well as a threat to human lives. Quantitative analysis of their frequency and magnitude relation is key to the development of mitigation measures to reduce hazard and risk. Yet, the data available for such analysis are typically very sparse, leading to point estimates for return levels that are too imprecise to be of practical value. The aim of the paper is to demonstrate how additional sources of information, in particular, expert judgment which uses physical causes and the size of the active area producing loose sediments, can be incorporated to produce more precise estimates with a smaller upper endpoint of interval estimates of extreme return levels. A Bayesian framework for extreme value analysis is used. We provide a rationale for the prior choice and discuss how its parameters can be elicited from the expert's knowledge. A case study of debris flows at Capricorn Creek in Western Canada is used to illustrate our methodology.
Pipeline Supported on a Nonuniform Winkler Soil Model

After a buried bell-and-spigot pipeline was installed at a site, an interior survey showed that some of the pipe sections were as much as 450 mm above the intended grade. One proposed explanation for this phenomenon was that the pipe sections were acting like teeter-totters, with one end settling and the other heaving, due to the variable foundation conditions. Later, when a similar pipeline was planned for the same vicinity, analyses were made utilizing a nonuniform Winkler soil model with randomized spring constants. The analyses showed that the calculated settlements were negligibly small; and there was no predicted teeter-totter behavior. Subsequent measurements confirmed the analyses.
Economic Valuation of Water Resources Conservation Area in Surakarta City

This study aims to: (1) assess the types of sustainable conservation of water resources that can be done by the community; (2) determine the willingness to pay (WTP) community for the improvement of water resources conservation management; (3) determine the determinants that significantly affect the value of willingness to pay for additional benefits due to increased conservation of water resources management; and (4) development of economic instruments that include the community’s role in the mechanism of raising funds for conservation management of water resources. This study uses a sampling method with proportional stratified random sampling (random sampling proportional stratified). The target population of 42,000 so that the sample size of 350 respondents. The model used is a multiple regression model with double the natural log. The analysis shows that the types of activities that significantly influence the conservation of water resources are the infiltration wells, infiltration holes biopori (LRB), environmental awareness, water quality, ficus benjamina, and caesalpinia pulcherrima. The results of calculations willingness to pay for conservation of water resources in the household customers Surakarta are as follows: WTP for categories R2 at 5,000; R3 at 5,100; R4 at 5,200; and N1 of 21,000. Log regression results obtained the conclusion that the WTP for the conservation of water resources was tested with partial regression coefficients (t test) shows the six variables that affect the WTP conservation, namely, awareness of environmental functions, biopori, tough water quality, infiltration wells, ficus benjamina, and caesalpinia pulcherrima. Another variable are family income, family head education, age of marriage, home ownership, family size, sources of water used, length of stay, filter, filicium decipiens tree and pterocarpus indicus tree does not significantly affect the conservation of water resources.
Cretaceous-Palaeogene ocean and climate change in the subtropical North Atlantic

Abstract Ocean Drilling Program (ODP) Leg 171B recovered continuous sequences that yield evidence for a suite of ‘critical’ events in the Earth’s history. The main events include the late Eocene radiolarian extinction, the late Palaeocene benthic foraminiferal extinction associated with the Late Palaeocene Thermal Maximum (LPTM), the Cretaceous-Palaeogene (K-P) extinction, the mid-Maastrichtian event, and several episodes of sapropel deposition documenting the late Cenomanian, late Albian and early Albian warm periods. A compilation of stable isotope results for foraminifera from Leg 171B sites and previously published records shows a series of large-scale cycles in temperature and δ13C trends from Albian to late Eocene time. Evolution of δ18O gradients between planktic and benthic foraminifera suggests that the North Atlantic evolved from a circulation system similar to the modern Mediterranean during early Albian time to a more open ocean circulation by late Albian-early Cenomanian time. Sea surface temperatures peaked during the mid-Cretaceous climatic optimum from the Albian-Cenomanian boundary to Coniacian time and then show a tendency to fall off toward the cool climates of the mid-Maastrichtian. The Albian-Coniacian period is characterized by light benthic oxygen isotope values showing generally warm deep waters. Lightest benthic oxygen isotopes occurred around the Cenomanian-Turonian boundary, and suggest middle bathyal waters with temperatures up to 20 °C in the North Atlantic. The disappearance of widespread sapropel deposition in Turonian time suggests that sills separating the North Atlantic from the rest of the global ocean were finally breached to sufficient depth to permit ventilation by deep waters flowing in from elsewhere. The Maastrichtian and Palaeogene records show two intervals of large-scale carbon burial and exhumation in the late Maastrichtian-Danian and late Palaeocene-early Eocene. Carbon burial peaked in early Danian time, perhaps in response to the withdrawal of large epicontinental seas from Europe and North America. Much of the succeeding Danian period was spent unroofing previously deposited carbon and repairing the damage to carbon export systems in the deep ocean caused by the K-P mass extinction. The youngest episode of carbon exhumation coincided with the onset of the early Eocene Warm Period and the LPTM, and has been attributed to the tectonic closure of the eastern Tethys and initiation of the Himalayan Orogeny.
Measurement of the normal/tangential fracture compliance ratio (ZN/ZT) during hydraulic fracture stimulation using S‐wave splitting data

We develop a method to invert S‐wave splitting (SWS) observations, measured on microseismic event data, for the ratio of normal to tangential compliance (ZN/ZT) of sets of aligned fractures. We demonstrate this method by inverting for ZN/ZT using SWS measurements made during hydraulic fracture stimulation of the Cotton Valley tight gas reservoir, Texas. When the full SWS data set is inverted, we find that ZN/ZT= 0.74 ± 0.04. Windowing the data by time, we were able to observe variations in ZN/ZT as the fracture stimulation progresses. Most notably, we observe an increase in ZN/ZT contemporaneous with proppant injection. Rock physics models and laboratory observations have shown that ZN/ZT can be sensitive to (1) the stiffness of the fluid filling the fracture, (2) the extent to which this fluid can flow in and out of the fracture during the passage of a seismic wave and (3) the internal architecture of the fracture, including the roughness of the fracture surfaces, the number and size of any asperities and the presence of material filling the fracture. These factors have direct implications for modelling the fluid‐flow properties of fractures. Consequently, the ability to image ZN/ZT using SWS will provide useful information about fractured rocks and allow additional constraints to be placed on reservoir behaviour.
Inter-comparison of predicted population exposure distributions during four selected episodes in Helsinki and evaluation against measured data

Air pollution causes significant excess mortality and health effects. Action plans required by the EU legislation should optimally account for the complex interactions of population distributions, time-activity and the sources of air pollution. This paper presents FUMAPEX study results on probabilistic exposure modelling for evaluation of population exposure distributions during selected episodes in Helsinki. The air quality model characterised best the episodes of local origin, while highest exposures occurred during a long-range transported episode (average annual exposures exceeded three-fold). Fixed monitoring data represented different population exposure percentiles (from 65th to 95th) depending on the episode type and monitoring station.
Reassessing the Effects of Dietary Fat on Cardiovascular Disease in China: A Review of the Last Three Decades

Cardiovascular disease (CVD) is a leading cause of global mortality, and is considered one of diseases with the most rapid growth rate in China. Numerous studies have indicated a closed relationship between an increased incidence of CVD and dietary factors. Dietary fat is one of the three primary nutrients of consumption; however, high fat dietary in causing CVD has been neglected in some official dietary guidelines. Our present review has analyzed the relationship between dietary fat consumption and CVD in China over the past 30 years (from 1990 to 2019). There is a significant correlation between CVD incidence and mortality for consumption of both vegetable oils and animal fats, per capita consumption, and the relative weight of dietary fat exceeding that of other food ingredients (e.g., salt, fruit, and marine food). For fatty acid species, the proportion of ω6 fatty acid consumption increased, causing a significant increase in the ratios of ω6/ω3 fatty acids, whereas the proportion of monounsaturated fatty acid consumption decreased. Such changes have been considered a characteristic of dietary fat consumption in Chinese residents over the past 30 years, and are closely related to the incidence of CVD. Therefore, we suggest that the government should spread awareness regarding the consumption of dietary fat intake to prevent CVD and related health disorders. The public should be educated to avoid high fat diet and increase the intake of monounsaturated fatty acids and ω3 fatty acids.
Genome-wide identification of DUF506 gene family in Oryza sativa and expression profiling under abiotic stresses

The domain of unknown function 560 (DUF560), also known as the PDDEXK_6 family, is a ubiquitous plant protein that has been confirmed to play critical roles in Arabidopsis root development as well as ABA and abiotic responses. However, genome-wide identification and expression pattern analysis in rice (Oryza sativa) still need to be improved. Based on the phylogenetic relationship, 10 OsDUF506 genes were identified and classified into four subfamilies. Segmental duplication was essential to the expansion of OsDUF506s, which were subjected to purifying selective pressure. Except for OsDUF50609 and OsDUF50610, the OsDUF506s shared colinear gene pairs with five monocot species, showing that they were conserved in evolution. Furthermore, the conserved domains, gene structures, SNPs distribution, and targeting miRNAs were systematically investigated. Massive cis-regulatory elements were discovered in promoter regions, implying that OsDUF506s may be important in hormone regulation and abiotic stress response. Therefore, we analyzed plant hormone-induced transcriptome data and performed qRT-PCR on eight OsDUF506s under drought, cold, and phosphorus-deficient stresses. The results revealed that most OsDUF506s respond to ABA and JA treatment, as well as drought and cold conditions. In conclusion, our findings provided insights into the evolution and function of OsDUF506s, which could benefit crop breeding in the future.
Light-Dependent and Aeration-Independent Gram-Scale Hydroxylation of Cyclohexane to Cyclohexanol by CYP450 Harboring Synechocystis sp. PCC 6803.

Oxygenase-containing cyanobacteria constitute promising whole-cell biocatalysts for oxyfunctionalization reactions. Photosynthetic water oxidation thereby delivers the required cosubstrates, that is activated reduction equivalents and O2 , sustainably. A recombinant Synechocystis sp. PCC 6803 strain showing unprecedentedly high photosynthesis-driven oxyfunctionalization activities is developed, and its technical applicability is evaluated. The cells functionally synthesize a heterologous cytochrome P450 monooxygenase enabling cyclohexane hydroxylation. The biocatalyst-specific reaction rate is found to be light-dependent, reaching 26.3 ± 0.6 U gCDW -1 (U = μmol min-1 and cell dry weight [CDW]) at a light intensity of 150 µmolphotons m-2 s-1 . In situ substrate supply via a two-liquid phase system increases the initial specific activity to 39.2 ± 0.7 U gCDW -1 and stabilizes the biotransformation by preventing cell toxification. This results in a tenfold increased specific product yield of 4.5 gcyclohexanol gCDW -1 as compared to the single aqueous phase system. Subsequently, the biotransformation is scaled from a shake flask to a 3 L stirred-tank photobioreactor setup. In situ O2 generation via photosynthetic water oxidation allows a nonaerated process operation, thus circumventing substrate evaporation as the most critical factor limiting the process performance and stability. This study for the first time exemplifies the technical applicability of cyanobacteria for aeration-independent light-driven oxyfunctionalization reactions involving highly toxic and volatile substrates.
Remote geochemical analysis : elemental and mineralogical composition

Remote geochemical analysis offers a powerful tool to study the elemental and mineralogical composition of our planet from its interior through to its atmosphere and to explore our solar system. Such studies have become possible because of major advances in sensor technology. Remote Geochemical Analysis fully covers both techniques and key applications. Chapters have been contributed by experts in their respective fields and describe a variety of remote sensing tools and their use in gaining an understanding of compositional properties. This book offers students as well as researchers a unique single source of information about the acquisition of compositional information using advanced sensors.
Consumption of nuts and seeds and pancreatic ductal adenocarcinoma risk in the European Prospective Investigation into Cancer and Nutrition

Four epidemiologic studies have assessed the association between nut intake and pancreatic cancer risk with contradictory results. The present study aims to investigate the relation between nut intake (including seeds) and pancreatic ductal adenocarcinoma (PDAC) risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Cox proportional hazards models were used to estimate hazards ratio (HR) and 95% confidence intervals (95% CI) for nut intake and PDAC risk. Information on intake of nuts was obtained from the EPIC country‐specific dietary questionnaires. After a mean follow‐up of 14 years, 476,160 participants were eligible for the present study and included 1,283 PDAC cases. No association was observed between consumption of nuts and PDAC risk (highest intake vs nonconsumers: HR, 0.89; 95% CI, 0.72–1.10; p‐trend = 0.70). Furthermore, no evidence for effect‐measure modification was observed when different subgroups were analyzed. Overall, in EPIC, the highest intake of nuts was not statistically significantly associated with PDAC risk.