julilili42/papers huggingface dataset:
Age, material source, and formation mechanism of bedding-parallel calcite beef veins: Case from the mature Eocene lacustrine shales in the Biyang Sag, Nanxiang Basin, China
2021-11-08

The mechanisms leading to the formation of bedding-parallel calcite beef veins have been widely debated, with discussions centered on timing or burial depth of vein generation, source of the vein material, driving forces for vein initiation and widening, and growth direction and mechanism. To address these issues, a comprehensive study of drill core samples containing beef veins in the mature Eocene lacustrine Hetaoyuan Formation in the Biyang Sag, Nanxiang Basin, China was undertaken through a combination of microstructural observation, isotopic geochronological, geochemical, and fluid inclusion analyses, as well as basin modeling. X-ray diffraction and total organic carbon content analyses indicate that most of the beef veins accumulated in calcite-rich laminated shales with high organic matter contents. These beef veins yielded an absolute laser ablation−multi-collector−inductively coupled plasma−mass spectrometry U-Pb age of ca. 41.02 ± 0.44 Ma, which corresponds to a burial depth of 500−800 m. Such a shallow burial depth suggests that the full compaction and consolidation of sediments would not yet have been achieved, which is compatible with the following observations: (1) plastic deformation of shale laminae adjacent to the veins, and (2) a beef vein formation temperature of ∼59 °C derived from fluid-inclusion microthermometry. The radio-isotopic age of the beef veins is ∼1−3 m.y. younger than the stratigraphic age of the host rock (ca. 43.1 Ma) but earlier than the model-derived timing of oil generation (ca. 35.8 Ma) and tectonic extrusion (ca. 23.0−13.0 Ma). The beef vein formation predated bacterial sulfate reduction, as evidenced by crosscutting relationships with carbonate concretions, pyrite framboids, and apatite pellets. A two-stage formation model for these beef veins is proposed. When burial depth of laminated shales rich in organic matter and calcite reaches the methanogenic zone, overpressure triggered by biogenetic gas generation results in horizontal hydrofracturing, initiating cracks that act as gas expulsion pathways. Once all the generated gas has migrated, the opened fractures close again due to overburden load. The materials fed by pressure solution of host-rock calcite fractions then mobilized into the unhealed horizontal fractures by diffusion. Subsequently, by a force of crystallization, antitaxial, displacive growth of calcite fibers commenced, contemporaneous with fracture dilation, eventually leading to the formation of bedding-parallel beef veins.
Mineral characterization and composition of Fe-rich flocs from wetlands of Iceland: Implications for Fe, C and trace element export
2021-11-08

In freshwater wetlands, redox interfaces characterized by circumneutral pH, steep gradients in O<sub>2</sub>, and a continual supply of Fe(II) form ecological niches favorable to microaerophilic iron(II) oxidizing bacteria (FeOB) and the formation of flocs; associations of (a)biotic mineral phases, microorganisms, and (microbially-derived) organic matter. On the volcanic island of Iceland, wetlands are replenished with Fe-rich surface-, ground- and springwater. Combined with extensive drainage of lowland wetlands, which forms artificial redox gradients, accumulations of bright orange (a)biotically-derived Fe-rich flocs are common features of Icelandic wetlands. These loosely consolidated flocs are easily mobilized, and, considering the proximity of Iceland's lowland wetlands to the coast, are likely to contribute to the suspended sediment load transported to coastal waters. To date, however, little is known regarding (Fe) mineral and elemental composition of the flocs. In this study, flocs from wetlands (n = 16) across Iceland were analyzed using X-ray diffraction and spectroscopic techniques (X-ray absorption and <sup>57</sup>Fe Mössbauer) combined with chemical extractions and (electron) microscopy to comprehensively characterize floc mineral, elemental, and structural composition. All flocs were rich in Fe (229-414 mg/g), and floc Fe minerals comprised primarily ferrihydrite and nano-crystalline lepidocrocite, with a single floc sample containing nano-crystalline goethite. Floc mineralogy also included Fe in clay minerals and appreciable poorly-crystalline aluminosilicates, most likely allophane and/or imogolite. Microscopy images revealed that floc (bio)organics largely comprised mineral encrusted microbially-derived components (i.e. sheaths, stalks, and EPS) indicative of common FeOB Leptothrix spp. and Gallionella spp. Trace element contents in the flocs were in the low μg/g range, however nearly all trace elements were extracted with hydroxylamine hydrochloride. This finding suggests that the (a)biotic reductive dissolution of floc Fe minerals, plausibly driven by exposure to the varied geochemical conditions of coastal waters following floc mobilization, could lead to the release of associated trace elements. Thus, the flocs should be considered vectors for transport of Fe, organic carbon, and trace elements from Icelandic wetlands to coastal waters.
Quality Requirements for gynecological ultrasound examinations of DEGUM level II – Recommendations of the Sections/Working Groups Gynecology and Obstetrics of DEGUM, ÖGUM and SGUM
2021-11-08

Abstract Gynecological sonography is the central and most frequently used technical examination method used by gynecologists. Its focus is on the clarification of masses of the uterus and the adnexa, fertility diagnosis, clarification of bleeding disorders and chronic and acute pelvic problems, pelvic floor and incontinence diagnosis as well as the differential diagnosis of disturbed early pregnancy. The indication for diagnostic and therapeutic interventions, preoperative planning and postoperative controls are largely based on the findings of gynecological sonography. These examinations are particularly dependent on the experience of the examiner. Based on the proven multi-stage concept of obstetric diagnostics, gynecological sonography should primarily be performed by an experienced and specialized examiner in patients for whom the initial gynecological examinations have not yet led to a sufficient assessment of the findings. So that the expert status required for this has an objective basis, the Gynecology and Obstetrics Section of DEGUM in cooperation with ÖGUM and SGUM implemented the option of acquiring DEGUM Level II for gynecological sonography. The effectiveness of the care in the multi-level concept depends on the quality of the ultrasound examination at level I. Quality requirements for the basic examination and the differentiation between the basic and further examination have therefore already been defined by DEGUM/ÖGUM. The present work is intended to set out quality requirements for gynecological sonography of DEGUM level II and for the correspondingly certified gynecologists. Common pathologies from gynecological sonography and requirements for imaging and documentation are described.
Impact of Keratoconus Stage on Outcome After Corneal Crosslinking
2021-11-08

Abstract Background: This study aimed to analyze if the outcome after corneal crosslinking (CXL) in progressive keratoconus patients depends on the stage in which the procedure is performed. This knowledge would help to improve success of CXL and facilitate defining surgery indications in those patients. Methods: In this retrospective study, 124 consecutive eyes of 100 patients with progressive keratoconus undergoing corneal CXL at the University Eye Hospital Tübingen were included. The eyes were graded according to modified Krumeich stages depending on induced myopia or astigmatism, corneal radii, minimum corneal thickness, and morphological changes. The observation period took place from November 2008 to September 2018. Preoperatively, 12 and 24 months after CXL, the best corrected visual acuity (BCVA) was determined and astigmatism as well as keratometric parameters (Kmax, Kmin, central corneal thickness (CCT), minimum corneal thickness (MCT)) were measured by means of a Scheimpflug camera system. Results: BCVA results showed significant differences between the modified Krumeich stages 12 months (p=0.014) and 24 months postoperatively (p=0.032). Also, astigmatism differed significantly among the stages 24 months after CXL (p=0.023); however, after 12 months, no significant differences between the groups were detectable. In terms of Kmax, Kmin, CCT, and MCT, no significant differences between the Krumeich stages were observed. Conclusions: BCVA showed a significantly higher improvement after CXL in the early stage of keratoconus compared to a higher stage. However, the postinterventional keratometric values did not differ significantly between the different modified Krumeich stages. The significantly higher improvement in BCVA after CXL in the early stage might indicate that earlier intervention provides a higher subjective benefit to the individual. Further studies with larger sample sizes are needed to confirm these findings.
Arabidopsis PII Proteins Form Characteristic Foci in Chloroplasts Indicating Novel Properties in Protein Interaction and Degradation
2021-11-08

The PII protein is an evolutionary highly conserved regulatory protein from bacteria to higher plants. In bacteria it modulates the activity of several enzymes, transporters and regulatory factors by interacting with them and thereby regulating important metabolic hubs like carbon/nitrogen homeostasis. More than two decades ago the PII protein was characterized for the first time in plants, but its physiological role is still not sufficiently resolved. To gain more insights into the function of this protein, we investigated the interaction behaviour of AtPII with candidate proteins by BiFC and FRET/FLIM in planta and with GFP/RFP traps in vitro. In the course of these studies we found that AtPII interacts in chloroplasts with itself as well as with known interactors like NAGK in dot-like aggregates, which we named PII foci. In these novel protein aggregates AtPII interacts also with yet unknown partners, which are known to be involved in plastidic protein degradation. Further studies revealed that the C-terminal part of AtPII is crucial for the formation of PII foci. Altogether, the presented results indicate a novel mode of interaction for PII proteins with other proteins in plants, which may be a new starting point for the elucidation of physiological functions of PII proteins in plants.
Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies.
2021-11-09

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like <i>Escherichia coli</i> colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during <i>E. coli</i> colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine <i>via</i> the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, <i>via</i> the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent,Treponema pallidum
2021-11-09

Abstract The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
Zinc Ameliorates the Osteogenic Effects of High Glucose in Vascular Smooth Muscle Cells
2021-11-09

In diabetic patients, medial vascular calcification is common and associated with increased cardiovascular mortality. Excessive glucose concentrations can activate the nuclear factor kappa-light-chain-enhancer of activated B-cells (NF-kB) and trigger pro-calcific effects in vascular smooth muscle cells (VSMCs), which may actively augment vascular calcification. Zinc is able to mitigate phosphate-induced VSMC calcification. Reduced serum zinc levels have been reported in diabetes mellitus. Therefore, in this study the effects of zinc supplementation were investigated in primary human aortic VSMCs exposed to excessive glucose concentrations. Zinc treatment was found to abrogate the stimulating effects of high glucose on VSMC calcification. Furthermore, zinc was found to blunt the increased expression of osteogenic and chondrogenic markers in high glucose-treated VSMCs. High glucose exposure was shown to activate NF-kB in VSMCs, an effect that was blunted by additional zinc treatment. Zinc was further found to increase the expression of TNFα-induced protein 3 (TNFAIP3) in high glucose-treated VSMCs. The silencing of TNFAIP3 was shown to abolish the protective effects of zinc on high glucose-induced NF-kB-dependent transcriptional activation, osteogenic marker expression, and the calcification of VSMCs. Silencing of the zinc-sensing receptor G protein-coupled receptor 39 (GPR39) was shown to abolish zinc-induced TNFAIP3 expression and the effects of zinc on high glucose-induced osteogenic marker expression. These observations indicate that zinc may be a protective factor during vascular calcification in hyperglycemic conditions.
Immobilization of Recombinant Fluorescent Biosensors Permits Imaging of Extracellular Ion Signals
2021-11-09

Given the importance of ion gradients and fluxes in biology, monitoring ions locally at the exterior of the plasma membrane of intact cells in a noninvasive manner is highly desirable but challenging. Classical targeting of genetically encoded biosensors at the exterior of cell surfaces would be a suitable approach; however, it often leads to intracellular accumulation of the tools in vesicular structures and adverse modifications, possibly impairing sensor functionality. To tackle these issues, we generated recombinant fluorescent ion biosensors fused to traptavidin (TAv) specifically coupled to a biotinylated AviTag expressed on the outer cell surface of cells. We show that purified chimeras of TAv and pH-Lemon or GEPII 1.0, Förster resonance energy transfer-based pH and K<sup>+</sup> biosensors, can be immobilized directly and specifically on biotinylated surfaces including glass platelets and intact cells, thereby remaining fully functional for imaging of ion dynamics. The immobilization of recombinant TAv-GEPII 1.0 on the extracellular cell surface of primary cortical rat neurons allowed imaging of excitotoxic glutamate-induced K<sup>+</sup> efflux in vitro. We also performed micropatterning of purified TAv biosensors using a microperfusion system to generate spatially separated TAv-pH-Lemon and TAv-GEPII 1.0 spots for simultaneous pH and K<sup>+</sup> measurements on cell surfaces. Our results suggest that the approach can be greatly expanded by immobilizing various biosensors on extracellular surfaces to quantitatively visualize microenvironmental transport and signaling processes in different cell culture models and other experimental settings.
Citrullinated Epitopes Identified on Tumour MHC Class II by Peptide Elution Stimulate Both Regulatory and Th1 Responses and Require Careful Selection for Optimal Anti-Tumour Responses
2021-11-09

Background Somatic mutations or post-translational modifications of proteins result in changes that enable immune recognition. One such post-translational modification is citrullination, the conversion of arginine residues to citrulline. Citrullinated peptides are presented on MHC class II (MHCII) via autophagy which is upregulated by cellular stresses such as tumourigenesis. Methods Peptides were eluted from B16 melanoma expressing HLA-DP4 and analysed by mass spectrometry to profile the presented citrullinated repertoire. Initially, seven of the identified citrullinated peptides were used in combination to vaccinate HLA-DP4 transgenic mice. Immune responses were characterised from the combination and individual vaccines by ex vivo cytokine ELISpot assay and assessed for tumour therapy. Results The combination vaccine induced only weak anti-tumour therapy in the B16cDP4 melanoma model. Immune phenotyping revealed a dominant IFNγ response to citrullinated matrix metalloproteinase-21 peptide (citMMP21) and an IL-10 response to cytochrome p450 peptide (citCp450). Exclusion of the IL-10 inducing citCp450 peptide from the combined vaccine failed to recover a strong anti-tumour response. Single peptide immunisation confirmed the IFNγ response from citMMP21 and the IL-10 response from citCp450 but also showed that citrullinated Glutamate receptor ionotropic (citGRI) peptide stimulated a low avidity IFNγ response. Interestingly, both citMMP21 and citGRI peptides individually, stimulated strong anti-tumour responses that were significantly better than the combined vaccine. In line with the citGRI T cell avidity, it required high dose immunisation to induce an anti-tumour response. This suggests that as the peptides within the combined vaccine had similar binding affinities to MHC-II the combination vaccine may have resulted in lower presentation of each epitope and weak anti-tumour immunity. Conclusion We demonstrate that tumours present citrullinated peptides that can stimulate Th1 and regulatory responses and that competition likely exists between similar affinity peptides. Characterisation of responses from epitopes identified by peptide elution are necessary to optimise selection for tumour therapy.
Non-invasive vagus nerve stimulation normalizes food liking and improves liking ratings in depression
2021-11-09

Introduction: The vagus nerve plays a prominent role in the regulation of food reward and energy metabolism. However, previous studies using vagus nerve stimulation yielded conflicting results regarding changes in food reward in healthy participants and participants with major depressive disorder (MDD), for which vagal nerve stimulation is an effective treatment. Methods: We investigated the acute effects of right transcutaneous auricular vagus nerve stimulation (taVNS) on ratings of liking and wanting of food and non-food items in 63 participants, including 31 patients with MDD. To test for taVNS-induced changes and interactions with between-subject variables group (MDD vs. healthy controls) and questionnaire scores as well as within-subject variables, we performed linear mixed-effects analysis. In addition, we assessed whether individual taVNS-induced changes in food reward ratings were dependent on average ratings.Results: taVNS increased liking of food cues in participants with MDD (p= 0.023), but not in healthy participants (p= 0.657). Specifically, taVNS induced larger improvements in liking ratings with increasing scores of anhedonia (p= 0.029). Notably, across all participants, taVNS reduced the variance of food liking compared to sham, suggesting that taVNS normalizes extreme liking ratings towards moderate levels (p = 0.039).Discussion: Our results show that taVNS acutely ameliorates hedonic responses in MDD suggesting that it could provide an effective treatment of anhedonia. Since anhedonia is difficult to treat with conventional therapies, taVNS may provide a powerful adjuvant to rapidly improve motivational deficiencies.
Gene-corrected p.A30P SNCA patient-derived isogenic neurons rescue neuronal branching and function
2021-11-09

Abstract Parkinson’s disease (PD) is characterised by the degeneration of A9 dopaminergic neurons and the pathological accumulation of alpha-synuclein. The p.A30P SNCA mutation generates the pathogenic form of the alpha-synuclein protein causing an autosomal-dominant form of PD. There are limited studies assessing pathogenic SNCA mutations in patient-derived isogenic cell models. Here we provide a functional assessment of dopaminergic neurons derived from a patient harbouring the p.A30P SNCA mutation. Using two clonal gene-corrected isogenic cell lines we identified image-based phenotypes showing impaired neuritic processes. The pathological neurons displayed impaired neuronal activity, reduced mitochondrial respiration, an energy deficit, vulnerability to rotenone, and transcriptional alterations in lipid metabolism. Our data describes for the first time the mutation-only effect of the p.A30P SNCA mutation on neuronal function, supporting the use of isogenic cell lines in identifying image-based pathological phenotypes that can serve as an entry point for future disease-modifying compound screenings and drug discovery strategies.