Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Soil-Structure Interaction of a Gravity Quay Wall and the Effect of Densification in Liquefiable Sites

AbstractThe lateral spreading of backfill soil caused by displacement of gravity-type quay walls is a major concern for geotechnical engineers. This paper evaluates the efficiency of a technique for mitigation of damage to quay walls, which involves densification of loose sand around the toe. The beneficial and unfavorable effects of densification of sand of different locations of the gravity-type quay walls are also answered. For these purposes, numerical simulations (using a finite-element code) and shake table tests were conducted. From numerical simulations and model tests, it was observed that the displacement of a gravity-type quay wall occurred mainly because of shear strain in the foundation. It was also found that the densification of soil at the toe could mitigate the quay wall damage significantly.
GM agricultural technologies for Africa: A state of affairs

The African Development Bank (AfDB), in commissioning this report to be prepared by the International Food Policy Research Institute (IFPRI), highlighted the need for a comprehensive, evidenced-based review of agricultural biotechnology in order to better understand its current status, issues, constraints, and opportunities for Africa. Agricultural biotechnology comprises several scientific techniques (genetic engineering, molecular marker-assisted breeding, the use of molecular diagnostics and vaccines, and tissue culÂ­ture) that are used to improve plants, animals, and microorganisms. However, in preparÂ­ing this desktop analysis, IFPRI has focused on genetic modification (GM) technologies in particular and on the agricultural context in which they are being applied, because GM technologies are at the center of the controversy about biotechnologyâ€™s role in Africa. In addition, because we have attempted to focus our review on peer-reviewed evidence and documented examples, the preponderance of data presented in the report is focused on genetically modified (also abbreviated GM) crops in use and under development, although we recognize the potential of the technology for livestock, fisheries, and forestry.
A Candidate Gene Study of Canine Joint Diseases

Canine osteoarthritis (OA) commonly occurs in association with articular diseases, such as hip dysplasia (HD), elbow dysplasia (ED), or cranial cruciate ligament rupture (CCLR). We hypothesized that a common genomic risk for the development of canine joint disease and canine OA would be identified by evaluating the allele frequencies of candidate gene single nucleotide polymorphisms (SNPs) in dogs with OA associated with different articular diseases when compared with a general population of breed-matched dogs. DNA was extracted from blood samples obtained from Labrador Retrievers and Golden Retrievers surgically treated for ED, HD, and CCLR and confirmed to have radiographic evidence of OA. One hundred and thirteen SNPs in 20 candidate genes were genotyped. No significant associations were identified for SNPs or haplotypes in the candidate genes for the diseases evaluated. The candidate gene approach for the study of genetic association is unlikely to be successful for complex canine diseases such as OA without prior trait mapping evaluation.
Cathodoluminescence (CL) behaviour and crystal chemistry of apatite from rare-metal deposits

Abstract Apatite samples from rare-metal mineralization were investigated by a combination of cathodoluminescence (CL) microscopy and spectroscopy, microchemical analysis and trace element analysis. Internal structures revealed by CL can be related to variations in the crystal chemistry and may sometimes reflect changes in the composition of the mineralizing fluids. Apatite from mineralization related to alkaline rocks and carbonatites (Type 1) typically exhibits relatively homogeneous blue and lilac/violet CL colours due to activation by trace quantities of rare earth element ions (Ce3+, Eu2+, Sm3+, Dy3+ and Nd3+). These results correlate with determined trace element abundances, which show strong light rare earth element (LREE) enrichment for this type of apatite. However, a simple quantitative correlation between emission intensities of REE3+/2+ and analysed element concentrations was not found. Apatite from P-rich altered granites, greisens, pegmatites and veins from Sn-W deposits (Type 2) shows strong Mn2+-activated yellow-greenish CL, partially with distinct oscillatory zoning. Variations in the intensity of the Mn2+-activated CL emission can be related either to varying Mn/Fe ratios (quenching of Mn activated CL by Fe) or to self-quenching effects in zones with high Mn contents (>2.0 wt.%). The REE distribution patterns of apatite reflect the specific geological position of each sample and may serve as a "tracer" for the REE behaviour within the ore system. Although the REE contents are sometimes as high as several hundred parts per million, the spectral CL measurements do not exhibit typical REE emission lines because of dominance of the Mn emission. In these samples, REE-activated luminescence is only detectable by time-resolved laser-induced luminescence spectroscopy. Both types of apatite (Type 1 in the core and Type 2 in the rim) were found in single crystals from the Be deposit Ermakovka (Transbaikalia). This finding proves the existence of two stages of mineralization within this deposit.
Seismic modelling for the sub-basalt imaging problem including an analysis and development of the boundary element method

The north-east Atlantic margin (NEAM) is important for hydrocarbon exploration because of the growing evidence of hydrocarbon reserves in the region. However, seismic exploration of the sub-surface is hampered by large deposits of flood basalts, which cover possible hydrocarbon-bearing reservoirs underneath. There are several hypotheses as to why imaging beneath basalt is a problem. These include: the high impedance contrast between the basalt and the layers above; the thin-layering of the basalt due to the many flows which make up a basalt succession; and the rough interfaces on the top-basalt interface caused by weathering and emplacement mechanisms. I perform forward modelling to assess the relative importance of these factors for imaging of sub-basalt reflections. The boundary element method (BEM) is used for the rough-interface modelling. The method was selected because only the interfaces between layers need to be discretized, in contrast to grid methods such as finite difference for which the whole model needs to be discretized, and so should lead to fast generation of shot gathers for models which have only a few homogeneous layers. I have had to develop criteria for accurate modelling with the boundary element method and have considered the following: source near an interface, two interfaces close together, removal of model edge effects and precise modelling of a transparent interface. I have improved efficiency of my code by: resampling the model so that fewer discretization elements are required at low frequencies, and suppressing wrap-around so that the time window length can be reduced. I introduce a new scheme which combines domain decomposition and a far-field approximation to improve the efficiency of the boundary element code further. I compare performance with a standard finite difference code. I show that the BEM is well suited to seismic modelling in an exploration environment when there are v
Sequence of pR3521, an IncB Plasmid from Escherichia coli Encoding ACC-4, SCO-1, and TEM-1 (cid:1) -Lactamases (cid:1)

The sequence of pR3521, a self-transmissible plasmid from Escherichia coli , was determined. pR3521 (110,416 bp) comprised a contiguous IncB sequence (84,034 bp) sharing extensive similarities with IncI replicons and an acquired region (26,382 bp) carrying sequences of diverse origin, containing bla ACC-4 , bla SCO-1 , bla TEM-1b (two copies), strA , strB , sul2 , and aacC2 . Multidrug resistance among enterobacteria is commonly due to acquisition of plasmids carrying various resistance determinants (4). We have previously identiﬁed pR3521, a self-trans-ferable and multiresistant plasmid from an Escherichia coli isolate from a hospitalized patient in Greece (18). Work had been largely focused on the characterization of loci containing bla ACC-4 , an ampC gene encoding ACC-4, an extended-spec-trum variant of the ACC-1 cephalosporinase (19), and bla SCO-1 , a novel gene of unknown origin coding for an RTG-type carbenicillinase (18,
A ] 12 O ct 2 00 4 Three Dimensional Nonlinear Dynamics of Slender Structures : Cosserat Rod Element Approach

In this paper, the modelling strategy of a Cosserat rod eleme nt (CRE) is addressed systematically for 3-dimensional dynamical analysis of slender structures. W e employ the exact nonlinear kinematic relationships in the sense of Cosserat theory, and adopt the Bern oulli hypothesis. For the sake of simplicity, the Kirchoff constitutive relations are adopted to provide an adequate description of elastic properties in terms of a few elastic moduli. A deformed configuration of t he rod is described by the displacement vector of the deformed centroid curves and an orthonormal mo ving frame, rigidly attached to the crosssection of the rod. The position of the moving frame relative o the inertial frame is specified by the rotation matrix, parametrized by a rotational vector. The a pproximate solutions of the nonlinear partial differential equations of motion in quasi-static sens are chosen as the shape functions with up to third order nonlinear terms of generic nodal displacements . Based on the Lagrangian constructed by the Cosserat kinetic energy and strain energy expressions, the principle of virtual work is employed to derive the ordinary differential equations of motion with third or de nonlinear generic nodal displacements. A simple example is presented to illustrate the use of the form ulation developed here to obtain the lower order nonlinear ordinary differential equations of motion of a given structure. The corresponding nonlinear dynamical responses of the structures have been present ed through numerical simulations by Matlab software.
Replication timing maintains the global epigenetic state in human cells

DNA is replicated in a defined temporal order termed the replication timing (RT) program. RT is spatially segregated in the nucleus with early/late replication corresponding to Hi-C A/B chromatin compartments, respectively. Early replication is also associated with active histone modifications and transcriptional permissiveness. However, the mechanistic interplay between RT, chromatin state, and genome compartmentalization is largely unknown. Here we report that RT is central to epigenome maintenance and compartmentalization in both human embryonic stem cells (hESCs) and cancer cell line HCT116. Knockout (KO) of the conserved RT control factor RIF1, rather than causing discrete RT switches as previously suspected, lead to dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1’s enrichment in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike all prior RIF1 KO cells, including HCT116, which show localized alterations. Regions that retain RT, which are prevalent in HCT116 but rare in hESCs, consist of large H3K9me3 domains revealing two independent mechanisms of RT regulation that are used to different extents in different cell types. RIF1 KO results in a striking genome wide downregulation of H3K27ac peaks and enrichment of H3K9me3 at large domains that remain late replicating, while H3K27me3 and H3K4me3 are re-distributed genome wide in a cell type specific manner. These histone modification changes coincided with global reorganization of genome compartments, transcription changes and a genome wide strengthening of TAD structures. Inducible degradation of RIF1 revealed that disruption of RT is upstream of genome compartmentalization changes. Our findings demonstrate that disruption of RT leads to widespread epigenetic mis-regulation, supporting previously speculative models in which the timing of chromatin assembly at the replication fork plays a key role in maintaining the global epigenetic state, which in turn drives genome architecture.
Dating of zircon from Ti-clinohumite–bearing garnet peridotite: Implication for timing of mantle meta-somatism: Comment and Reply COMMENT

[Katayama et al. (2003)][1] dated zircon in some ultramafic rocks dominated by garnet and titanian clinohumite (hereafter Ti-clinohumite rocks) from the Kokchetav ultrahigh-pressure (UHP) metamorphic terrane, and interpreted that the zircon cores formed in the mantle in the Proterozoic and the
A three‐dimensional Eulerian acid deposition model: Physical concepts and formulation

We have developed a three-dimensional Eulerian regional acid deposition model to calculate episodic chemical concentrations and dry and wet deposition of acids in North America. This transport, transformation, and deposition modeling system subdivides the troposphere over the eastern United States, southeastern Canada, and the western Atlantic Ocean into a six-level, 30 by 30 horizontal grid with a horizontal grid size of 80 x 80 km/sup 2/. Transport and vertical diffusion of 24 trace gases and particles are calculated using temporally and spatially varying meteorology, provided by a mesoscale meteorological model. A gas phase chemical reaction mechanism is used to simulate concentrations and chemical conversion rates for 36 species, including 14 stable organics and 11 short-lived radicals. Altitude-, latitude-, and season-dependent photolysis rates for nine reactions in the chemical mechanism are specified using a delta-Eddington radiative transfer model which includes O/sub 2/ and O/sub 3/ absorption, scattering and absorption by clouds and aerosols, Rayleigh scattering, and ground relections.
First Report of Pectobacterium versatile as the Causal Pathogen of Soft Rot in Kimchi Cabbage in Korea

In September 2021, gray-to-brown discoloration and expanding water-soaked lesions were observed on the outer and inner layers and the core of kimchi cabbage (Brassica rapa subsp. pekinensis) in fields located in Samcheok, Gangwondo, Korea. A bacterial strain designated as KNUB-02-21 was isolated from infected cabbage samples. Phylogenetic analysis based on the sequences of the 16S rRNA region and the dnaX, leuS, and recA genes confirmed that the strain was affiliated with Pectobacterium versatile. Additionally, the biochemical and morphological profiles of the isolate were similar to those of P. versatile. Based on these results, the isolate was identified as a novel strain of P. versatile. Healthy kimchi cabbage slices developed soft rot upon inoculation with P. versatile KNUB-02-21 and exhibited symptoms similar to those observed in the diseased plants in fields. The re-isolated strains were similar to those of P. versatile. Prior to our study, P. versatile as the causative pathogen of kimchi cabbage soft rot had not been reported in Korea.
Proteomic profiling reveals novel biomarkers and pathways in type 2 diabetes risk

Recent advances in proteomic technologies have made high throughput profiling of low abundance proteins in large epidemiological cohorts increasingly feasible. We investigated whether aptamer-based proteomic profiling could identify biomarkers associated with future development of type 2 diabetes (T2DM) beyond known risk factors. We identified dozens of markers with highly significant associations with future T2DM across two large longitudinal cohorts (n=2,839) followed for up to 16 years. We leveraged proteomic, metabolomic, genetic and clinical data from humans to nominate one specific candidate to test for potential causal relationships in model systems. Our studies identified functional effects of aminoacylase 1 (ACY1), a top protein association with future T2DM risk, on amino acid metabolism and insulin homeostasis in vitro and in vivo. Further, a loss-of-function variant associated with circulating levels of the biomarker WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 (WFIKKN2) was in turn associated with fasting glucose, hemoglobin A1c and HOMA-IR measurements in humans. In addition to identifying novel disease markers and potential pathways in T2DM, we provide publicly available data to be leveraged for new insights about gene function and disease pathogenesis in the context of human metabolism. Research Endocrinology
The Tasman Front: A Study Using Satellite Infrared Imagery

Abstract Monthly charts of the approximately zonal Tasman Front between the Australian coast, (near 152°E) and 164°E, and between latitudes, 31° to 37°S have been constructed from infrared satellite imagery for 29 months from March 1982 to April 1985. From these it was found that one to three meanders, but usually two, are present between 152° and 164°E, and that the second meander pinches off at times to form a warm-core ring in the same manner as is known to occur for the first meander. Both second meander and ring tend to propagate westwards. The mean zonal widths of the first and second meander are similar and are 3.6° to 3.7° longitude (330–345 km). The average and the most likely (modal) positions of the Tasman Front were determined and the two positions are most different when the Front meanders northward. The zonal length scale of frontal perturbations increases eastward from 140 near 155°E to 300 km near 161°E, and perturbations propagate westward at approximately 0.1 m s−1.
The impact of climate‐vegetation interactions on the onset of the Antarctic ice sheet

A global coupled atmosphere/vegetation model and a dynamic ice sheet model were employed to study the impact of climate‐vegetation interactions on the onset of the Antarctic ice sheet during the Eocene‐Oligocene transition. We found that the CO2 threshold for Antarctic glaciation is highly sensitive to the prevailing vegetation. In our experiments, the CO2 threshold is less than 280 ppm if the Antarctic vegetation is dominated by forests and between 560 and 1120 ppm for tundra and bare ground conditions. The large impact of vegetation on inception is attributed to the ability of canopies to shade the snow‐covered ground, which leads to a weaker snow albedo feedback and higher summer temperatures. However, the overall effect of canopy shading on the Antarctic climate also depends on features like local cloudiness and atmospheric meridional heat transport. Our results suggest that vegetation feedbacks on climate are crucial for the timing of the Antarctic glaciation.
Vertical infiltration in dry soil

An approximate method is proposed to integrate the ordinary differential equations governing the terms in Philip's (1957) series formulation of the water content profile. The method is related to the weighting solution used earlier (Brutsaert, 1976) for the sorption problem, and it is intermediate between the quasi-steady state method and the sharp front method. In a comparison with an available exact solution (Brutsaert, 1968b) it is shown that the derived solution is usually accurate to within less than 1%. The water content profile and the infiltration rate can be expressed concisely in terms of soil physical parameters by making use of suitable expressions for the soil water diffusivity and the capillary conductivity. As an illustration, the infiltration rate is calculated for the Averjanov-Irmay capillary conductivity and the author's three-parameter power function diffusivity. Inspection of two extreme cases in this calculation finally leads to a new infiltration equation in closed form which is valid not only for short but also for large time of infiltration.
Interactions Between Hyphosphere-Associated Bacteria and the Fungus Cladosporium herbarum on Aquatic

We investigated microbial interactions of aquatic bacteria associated with hyphae (the hyphosphere) of freshwater fungi on leaf litter. Bacteria were isolated directly from the hyphae of fungi from sedimented leaves of a small stream in the National Park "Lower Oder," Germany. To investigate interactions, bacteria and fungi were pairwise co-cultivated on leaf-extract medium and in microcosms loaded with leaves. The performance of fungi and bacteria was monitored by measuring growth, enzyme production, and respiration of mono- and co-cultures. Growth inhibition of the fungus Cladosporium herbarum by Ralstonia pickettii was detected on leaf extract agar plates. In microcosms, the presence of Chryseobacterium sp. lowered the exocellulase, endocellulase, and cellobiase
Enhanced and Persistent Inhibition of Organic Cation Transporter 1 Activity by Preincubation of Cyclosporine A

Recent pharmacogenetic evidence indicates that hepatic organic cation transporter (OCT) 1 can serve as the locus of drug-drug interactions (DDIs) with significant pharmacokinetic and pharmacodynamic consequences. We examined the impact of preincubation on the extent of OCT1 inhibition in transfected human embryonic kidney 293 (HEK293) cells. Following 30-minute preincubation with an inhibitor, approximately 50-fold higher inhibition potency was observed for cyclosporine A (CsA) against OCT1-mediated uptake of metformin compared with coincubation, with IC50 values of 0.43 ± 0.12 and 21.6 ± 4.5 µM, respectively. By comparison, only small shifts (≤2-fold) in preincubation IC50 versus coincubation were observed for quinidine, pyrimethamine, ritonavir, and trimethoprim. The shift in CsA OCT1 IC50 was substrate dependent since it ranged from >1.2- to 50.2-fold using different experimental substrates. The inhibition potential of CsA toward OCT1 was confirmed by fenoterol hepatocyte uptake experiment. Furthermore, no shift in CsA IC50 was observed with HEK293 cells transfected with OCT2 and organic anion transporter (OAT) 1 and OAT3. Short exposure (30 minutes) to 10 µM CsA produced long-lasting inhibition (at least 120 minutes) of the OCT1-mediated uptake of metformin in OCT1-HEK293 cells, which was likely attributable to the retention of CsA in the cells, as shown by the fact that inhibitory cellular concentrations of CsA were maintained long after the removal of the compound from the incubation buffer. The potent and persistent inhibitory effect after exposure to CsA warrants careful consideration in the design and interpretation of clinical OCT1 DDI studies. SIGNIFICANCE STATEMENT Preincubation of OATP1B1 and OATP1B3 with their inhibitor may result in the enhancement of the inhibitory potency in a cell-based assay. However, limited data are available on potentiation of OCT1 inhibition by preincubation, which is a clinically relevant drug transporter. For the first time, we observed a 50-fold increase in CsA inhibitory potency against OCT1-mediated transport of metformin following a preincubation step. The CsA preincubation effect on OCT1 inhibition is substrate dependent. Moreover, the inhibition potential of CsA toward OCT1 is confirmed by hepatocyte uptake experiment. This study delivers clear evidences about the potent and persistent inhibitory effect on OCT1 after exposure to CsA. Further studies are needed to assess the effect of CsA on OCT1 drug substrates in vivo.