Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of multi-functional lactic acid bacteria strains in a pilot scale feta cheese production

Feta cheese is the most recognized Greek Protected Designation of Origin (PDO) product in the world. The addition of selected autochthonous lactic acid bacteria (LAB) strains to cheese milk as adjunct cultures is gaining more attention, since they can impact the nutritional, technological and sensory properties of cheeses, as well as improve the safety of the product. The aim of this study was to produce Feta cheese with enhanced quality and safety, and distinctive organoleptic characteristics by applying autochthonous lactic acid bacteria (LAB) with multi-functional properties as adjunct cultures. Feta cheeses were produced with the commercial lactococcal starter culture and the addition of 9 LAB strains (Lactococcus lactis SMX2 and SMX16, Levilactobacillus brevis SRX20, Lacticaseibacillus paracasei SRX10, Lactiplantibacillus plantarum FRX20 and FB1, Leuconostoc mesenteroides FMX3, FMX11, and FRX4, isolated from artisanal Greek cheeses) in different combinations to produce 13 cheese trials (12 Feta trials with the adjunct LAB isolates and the control trial). In addition, Feta cheese manufactured with FMX3 and SMX2 and control Feta cheese were artificially inoculated (4 log CFU/g) with Listeria monocytogenes (a cocktail of 4 acid or non-acid adapted strains). Cheese samples were monitored by microbiological and physicochemical analyses during ripening, and microbiological, physicochemical, molecular and sensory analyses during storage at 4°C. The results showed that after manufacture, the LAB population was ca. 9.0 log CFU/g at all samples, whereas during storage, their population declined to 6.5–7.0 log CFU/g. In the Listeria inoculated samples, Listeria was absent after 60 days (end of ripening) and after 90 days in the adjunct culture, and in the control trials, respectively. Moreover, the addition of selected strains, especially Lcb. paracasei SRX10, led to cheeses with desirable and distinctive organoleptic characteristics. Furthermore, randomly amplified polymorphic PCR (RAPD-PCR) molecular analysis confirmed that the multi-functional LAB strains were viable by the end of storage. Overall, the results of this study are promising for the use of autochthonous strains in various combinations with the commercial starter culture to satisfy industry requirements and consumer demands for traditional and high added value fermented products.
Kinematics of the Chugach metamorphic complex, southern Alaska: Plate geometry in the north Pacific margin during the Late Cretaceous to Eocene

The Paleogene plate geometry of the north Pacific margin is poorly constrained because all of the plates involved, except the trailing Pacific plate, have been subducted. However, the kinematic history of the Chugach metamorphic complex in southern Alaska constrains plate configurations because of its link to ridge‐subduction. We synthesize recent regional mapping of the complex, finite strain data, and geochronology to show that progressive deformation records the Paleogene triple junction interaction occurred over a period of less than 2 m.y. across ∼350 km of the margin. We document that 140–190 km of distributed dextral shear occurred across the complex during the latest phase of deformation in the complex. This analysis suggests dextral motion of at least 70–95 mm/yr which can account for most, or all, of the margin parallel plate motion during a brief period of the Eocene. We use these results to compare and evaluate possible plate configurations based on older and newer plate motion models. Using modern plate motion models it is difficult to reconcile a Kula‐Farallon ridge‐subduction model with the available data, but our preferred plate geometry model involving a Kula‐Resurrection ridge provides a reasonable explanation for our observations.
Evaluating the impact of testing strategies for the detection of nosocomial COVID-19 in English hospitals through data-driven modeling

Introduction During the first wave of the COVID-19 pandemic 293,204 inpatients in England tested positive for SARS-CoV-2. It is estimated that 1% of these cases were hospital-associated using European centre for disease prevention and control (ECDC) and Public Health England (PHE) definitions. Guidelines for preventing the spread of SARS-CoV-2 in hospitals have developed over time but the effectiveness and efficiency of testing strategies for preventing nosocomial transmission has not been explored. Methods Using an individual-based model, parameterised using multiple datasets, we simulated the transmission of SARS-CoV-2 to patients and healthcare workers between March and August 2020 and evaluated the efficacy of different testing strategies. These strategies were: 0) Testing only symptomatic patients on admission; 1) Testing all patients on admission; 2) Testing all patients on admission and again between days 5 and 7, and 3) Testing all patients on admission, and again at days 3, and 5-7. In addition to admissions testing, patients that develop a symptomatic infection while in hospital were tested under all strategies. We evaluated the impact of testing strategy, test characteristics and hospital-related factors on the number of nosocomial patient infections. Results Modelling suggests that 84.6% (95% CI: 84.3, 84.7) of community-acquired and 40.8% (40.3, 41.3) of hospital-associated SARS-CoV-2 infections are detectable before a patient is discharged from hospital. Testing all patients on admission and retesting after 3 or 5 days increases the proportion of nosocomial cases detected by 9.2%. Adding discharge testing increases detection by a further 1.5% (relative increase). Increasing occupancy rates, number of beds per bay, or the proportion of admissions wrongly suspected of having COVID-19 on admission and therefore incorrectly cohorted with COVID-19 patients, increases the rate of nosocomial transmission. Over 30,000 patients in England could have been discharged while incubating a non-detected SARS-CoV-2 infection during the first wave of the COVID-19 pandemic, of which 3.3% could have been identified by discharge screening. There was no significant difference in the rates of nosocomial transmission between testing strategies or when the turnaround time of the test was increased. Discussion This study provides insight into the efficacy of testing strategies in a period unbiased by vaccines and variants. The findings are relevant as testing programs for SARS-CoV-2 are scaled back, and possibly if a new vaccine escaping variant emerges.
A comparison of volcanic edifices at the Reykjanes Ridge and the Mid‐Atlantic Ridge at 24°–30°N

A detailed analysis of high-resolution side-scan sonar data shows that the volcanic edifices built within the axial zones of the slow spreading (20 mm/yr) Reykjanes Ridge and the slow spreading (25 mm/yr) Mid-Atlantic Ridge are remarkably similar. In fact, individual seamounts, hummocks (rounded mounds), and hummocky ridges at the Reykjanes Ridge have nearly identical morphological counterparts at the Mid-Atlantic Ridge (MAR), arguing that commonly eruptive conditions are similar at the two ridges. The construction of these volcanic edifices, typical of slow spreading ridges, occurs at the Reykjanes Ridge despite its proximity to the Iceland hot spot and the influence of the hot spot on other characteristics of the ridge axis, such as its overall shape (an axial high north of about 59°N), its shallow axial depths, and its thicker crustal section. The volume of magma that goes into constructing volcanic edifices at each of 12 segments of the MAR and four regions of the Reykjanes Ridge is calculated using multibeam bathymetry data. Our results indicate that edifice volume per unit seafloor area, equivalent to a uniform thickness over the area of interest, is larger at the MAR than at the Reykjanes Ridge, on average. Taking into account spreading rate, we then estimate B, the average building rate per unit length along the axis, which is also larger at the MAR. We conclude that the same volcanic edifices build the crust at the Reykjanes Ridge and MAR, but that their emplacement is more frequent at the MAR. To explain our results and reconcile them with those of Magde and Smith (1995) who documented that seamounts are taller and more abundant at the Reykjanes Ridge than at the MAR, we consider the controls on diking and eruption within the axial zones of the two ridges. We suggest that the combination of slower spreading rate and the oblique geometry of spreading at the Reykjanes Ridge leads to fewer eruptions which are more widely dispersed across the axial zone than at the MAR. If this hypothesis is correct, the proportion of seamounts modified by subsequent eruptions will be less. This might also explain the taller heights of the seamounts if there is less overlap and infilling between edifices.
Soil-to-crop Transfer Factors of Radium in Japanese Agricultural Fields

Radium-226 (Ra), an α emitter with a half-life of about 1600 y, is a natural decay product of U. Radium-226 is of special interest because it is an important radionuclide for the assessment of radioactive waste disposal. This radionuclide can reach humans through several transfer paths in the environment. Once Ra is taken into the human body by ingestion of food and water or inhalation, it can distribute into bone where it has a long biological half-life; exposure to Ra can cause cancers and other body disorders. Therefore, its longterm management is required and understanding of Ra behavior in the environment is important. In mathematical models that are used for long-term radiological assessment, environmental transfer parameters are needed. Among them, the soil-to-crop transfer factor (TF) is a key parameter that directly affects the internal radiation dose assessment for the ingestion pathway. TF is defined as the ratio of radioactivity concentration in plant to radioactivity concentration in soil. Although Ra is present in the environment, due to its low concentration in crops, TFs that have been obtained from agricultural fields are limited. In many cases, therefore, TFs used in such models were from the Technical Report Series 364 (TRS-364) compiled by IAEA. These data were obtained in temperate zones mainly from Europe and North America, and thus, the numbers of TFs for rice and crops native to Japan were limited. Yunoki et al. measured TF-Ra for spinach and Chinese cabbage, but they collected their samples from only two fields. Recently, Sasaki et al. tried to measure crop TF-Ra, however, most sample concentrations were under the detection limit, and only two hulled rice sample data were available from their study. Thus, it is necessary to collect TFs of Ra nationwide. In this study, we determined the concentrations of Ra in upland field crops (leafy vegetables, onion, potato, and so on) and associated soils collected from 45 locations throughout Japan in order to obtain TFs. We also measured alkaline earth metal concentrations to compare their behavior with Ra, which is the last member of this group and whose lighter members, Mg and Ca, are plant nutrients. 2. Experimental
TrackAnalyzer: A Fiji/ImageJ toolbox for a holistic analysis of tracks

Abstract Current live-cell imaging techniques make possible the observation of live events and the acquisition of large datasets to characterize the different parameters of the visualized events. They provide new insights into the dynamics of biological processes with unprecedented spatial and temporal resolutions. Here we describe the implementation and application of a new tool called TrackAnalyzer, accessible from Fiji and ImageJ. Our tool allows running semi-automated single-particle tracking (SPT) and subsequent motion classification, as well as quantitative analysis of diffusion and intensity for selected tracks relying on the graphical user interface (GUI) for large sets of temporal images (X–Y–T or X–Y–C–T dimensions). TrackAnalyzer also allows 3D visualization of the results as overlays of either spots, cells or end-tracks over time, along with corresponding feature extraction and further classification according to user criteria. Our analysis workflow automates the following steps: (1) spot or cell detection and filtering, (2) construction of tracks, (3) track classification and analysis (diffusion and chemotaxis), and (4) detailed analysis and visualization of all the outputs along the pipeline. All these analyses are automated and can be run in batch mode for a set of similar acquisitions.
Use of heat as tracer to quantify vertical streambed flow in a two‐dimensional flow field

Analytical solutions to the heat transport equation in porous media have been developed in the past to estimate surface water‐groundwater interactions. These solutions, however, are based upon simplifying assumptions that are frequently violated in natural systems. A nonvertical flow field, inherent to most field settings, can violate the one‐dimensional (1‐D) flow assumption and lead to erroneous velocity estimates. In this study, we have developed a 2‐D heat and mass transport finite element‐based numerical model for a stream aquifer cross section experiencing flow‐through. Synthetic multilevel streambed temperature time series were generated with the model using a sinusoidal temperature boundary. The temperature data was used to quantify the vertical flow velocity with a 1‐D analytical solution based on the amplitude decay and phase shift of temperature with depth. Results demonstrate that erroneous vertical components of fluid velocity can be obtained by the 1‐D analytical solution when the true vertical velocity approaches zero and the flow regime becomes almost horizontal. The results also illustrate that the amplitude ratio method performs quite poorly on the gaining side of the stream where the only reliable method is phase shift. On the losing side of the stream, both methods can be employed but a better estimation is obtained from the amplitude ratio method. In general, amplitude ratio and phase shift data should be used in conjunction to maximize the information of the system.
Hydraulic constraints on habitat suitability for benthic invertebrates in gravel‐bed rivers

The primary components of the physical habitat in a stream are water depth, velocity and substrate size, and these appear to be the best predictors of benthic invertebrate distribution within a stream. Substrate stability and fine sediment deposition also influence benthic invertebrate abundance, with reduced abundance where substrates are frequently disturbed or where fine sediment accumulates. Substrate stability and deposition of fine sediment provide hydraulic constraints on habitat suitability and their limits can be predicted by hydraulic formulae. Hydraulic conditions near or at the surface of the stream bed may have a more direct influence on benthic invertebrates than either water depth or mean velocity in the water column above them. If benthic invertebrates have ‘preferred’ near‐bed conditions, hydraulic considerations suggest that optimum mean water velocities for benthic invertebrates should increase with average stream depth and substrate size. Examination of three sets of field data from rivers of varying size showed that benthic invertebrate abundance was strongly related to mean velocity and substrate size, with large differences in habitat use between species. However, although there were large differences in preferred mean velocities between rivers of different size and depth, there was little evidence that this occurred within rivers of similar size and hence little support for the hypothesis that near‐bed hydraulics can provide a generalized method of predicting invertebrate habitat suitability between rivers of different size. Copyright © 2003 John Wiley & Sons, Ltd.
The effects of post‐orogenic extension on different scales: an example from the Apennine–Maghrebide fold‐and‐thrust belt, SW Sicily

ABSTRACT Many structures produced under one single deformation regime, namely extensional, contractional or strike‐slip, exhibit remarkable geometrical analogies when analysed at different scales. By contrast, field examples that illustrate the scale effects on structures resulting from superimposed deformations, which were produced under different tectonic regimes, are rare. Yet the change from contraction to extension is known to occur often in the most thickened portions of the continental crust. The Apennine–Maghrebide fold‐and‐thrust belt of Sicily shows many examples of post‐orogenic extensional deformations. Composite structures, resulting from late normal faults that offset folds and thrusts, are observed at four different scales, from regional to mesoscopic, in the south‐western portion of Sicily and in the adjacent Isle of Favignana. The recognized analogies in the geometry of these composite structures may provide a key for the interpretation of the features of regional structures, whose deep geometry is often poorly constrained. Moreover, comparison of normalized displacements accommodated by contractional and extensional faults of different scales indicates that self‐similarity is not unique to structures produced under single tectonic regimes.
S wave velocity structure of the Northern Cascadia Subduction Zone

Teleseismic receiver functions from an array of portable broadband seismograph stations located in southwestern British Columbia are interpreted to estimate the S wave velocity structure to upper mantle depths across the northern Cascadia subduction zone. At our westernmost station on central Vancouver Island, a prominent low-velocity zone (ΔVs = −1 km s−1) with a high Poisson's ratio is estimated at 36–41 km depth. This feature correlates with the reflective “E” zone observed in LITHOPROBE reflection data, a region that also exhibits high electrical conductivity and has recently been interpreted as a fluid-saturated shear zone above the subducting Juan de Fuca (JdF) plate. Analysis of data at our stations to the NE permits this zone to be mapped into the upper mantle, 54 km beneath the British Columbia mainland, and approximately 250 km from the locus of subduction. The subducting oceanic crust is imaged at 47–53 km depth dipping 15°± 5° in the direction N30°E ± 20° beneath central Vancouver Island. The dip angle increases to 22° ± 5° at a depth of 60–65 km beneath the Strait of Georgia. The results of this analysis provide the first definitive evidence for the location of the subducting plate in this region and indicate that the seismicity at depth occurs within the oceanic crust. The dip direction of N30°E at each station provides new evidence that the JdF plate is arched upward as it subducts in this region. A low-velocity zone that coincides with the “C” reflectors beneath Vancouver Island is interpreted to extend east to the British Columbia mainland near the base of the North American crust. The top of this zone, near 20–26 km depth, lies near the lower limit of shallow seismicity. The continental Moho is estimated to be 36 km below the Strait of Georgia.
EXTRACTION AND UTILIZATION OF BANANA PSEUDOSTEM SAP AS ORGANIC LIQUID BIO-FERTILIZER ON ONION (ALLIUM CEPA L)

The high input cost of onion production through the application of chemical fertilizers is a significant concern for small farmers. Every year, Banana harvesting generates a large amount of banana pseudostem waste, which is generally burnt or thrown away despite containing many nutrients after harvest. Utilizing the banana's pseudo-stem sap as liquid fertilizer for increasing onion productivity through sustainable agricultural practices, a greenhouse trial was conducted to determine the optimum banana pseudostem sap (BPS) to be applied by foliar spray. There were five treatments designed in CRD with four replicates. The reduced mineral fertilizer was given to test the impact of the pseuodstem sap on the seedlings. The results indicated that sap application showed a positive and significant effect on all parameters of onion seedlings. The onion plant height increased to 48.96 cm, the number of leaves was 14.50, and the shoot length of 8.67 cm was recorded best. The onion bulb diameter ranged from 3 to 6 cm bulb weight from 54 to 92.75 g comparing the control. The best rate found was 80% RDF, along with 20% BSP in all parameters. It can be concluded that application of 80% RDF + Foliar spray of 20% banana pseudostem sap was found to be the most viable option for getting higher growth and yield in onion. This will reduce 20% chemical fertilizer and about 25% increase in the yield. This will be an eco-friendly practice and sustainable ergonomically, economically and environmentally.
Dolomite Growth in Coralline Algae

ABSTRACT Thin-section study of dolomitized limestone of Eocene age from the subsurface of Eniwetok reveals the localization of dolomite crystals within segments of articulate coralline algae. Corals and large Foraminifera are little affected. The writer suggests, in view of recent work by others on the crystal chemistry and occurrence of high-magnesian calcite, that the dolomitized algae are the end product of the crystallographic ordering of the Ca-Mg solid solution that made up the original high-magnesian algal calcite. This ordering is thought to take place on scattered dolomite nuclei inherent in the original algal precipitate, these nuclei being the result of local concentrations of Mg ions within the algal calcite.
Craters as an Indicator of Martian Regolith Thickness

Two craters (D approx.900 m) found in MOC images of Xanthe Terra have concentric terraced morphologies, where one crater lies within a second, larger crater. This type of morphology has been documented on the Moon and attributed to an impact into fragmental material overlying a more competent substrate. These craters offer a mechanism by which to estimate thickness of unconsolidated surface material over large areas on Mars. Such measurements may constrain deflation rates and volume estimates of hydrologic reservoirs on Mars and yield information on the strength of the local bedrock. Additional information is contained in the original extended abstract.
Ostracod palaeoecology and environmental change in the Laptev and Kara seas (Siberian Arctic) during the last 18 000 years

Fossil ostracod assemblages were investigated in five AMS 14 C‐dated cores from various water depths of the Laptev and Kara seas ranging from the upper continental slope (270 m) to the present‐day shelf depth (40 m). Six fossil assemblages were distinguished. These represent the varying environmental conditions at the North Siberian continental margin since about 18 ka. In the cores from the shelf the ostracod assemblages reflect the gradual transition from an estuarine brackish‐water environment to modern marine conditions since 12.3 ka, as induced by the regional early Holocene transgression. The core from the upper continental slope dates back to c. 17.6 ka and contains assemblages that are absent in the shelf cores. The assemblage older than 10 ka stands out as a specific community dominated by relatively deep‐water Arctic and North Atlantic species that also contains euryhaline species. Such an assemblage provides evidence for past inflows of Atlantic‐derived waters from as early as c. 17.2 ka, probably facilitated by upwelling in coastal polynyas, and a considerable riverine freshwater influence with enhanced surface water stratification owing to the proximity of the palaeocoastline until early Holocene times. In all studied cores, relative increases in euryhaline species dominant in the inner‐shelf regions are recorded in the mid–late Holocene sediments (<7 ka), which otherwise already contain modern‐like ostracod assemblages with relatively deep‐water species. This observation suggests euryhaline species to be largely sea‐ice‐ and/or iceberg‐rafted and therefore may provide evidence for a climate cooling trend.