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The contemporary crustal stress state is primarily driven by gravitational volume forces and plate tectonics. However, there are various smaller-scale sources such as geological structures and stiffness contrast that perturb stresses and deviate them from the regional pattern. For example, borehole stress analysis in numerous cases has revealed abrupt rotations of horizontal stress orientation of up to 90° when faults are crossed. Herein, we investigate the rotation of principal stress axes at a fault by means of a 2D generic numerical model. We focus on the near field of the fault and the damage zone with a fault parameterized as a rock stiffness contrast. A substantial influence of the far-field stress field in terms of the differential stress and in terms of the stress ratio RS=S1/S_3 is shown. Furthermore, the contrast in material properties is the basis for any stress rotation, and in particular the stiffness is demonstrated to have a significant influence. Eventually, the impact of the angle between the fault strike and the orientation of SHmax is demonstrated. Our results show that the stress rotation is negatively correlated with the ratio of principal far-field stresses. A small angle between the far-field stress orientation and the fault facilitates stress rotation. A high contrast in rock stiffness further increases the stress rotation angle. Faults striking perpendicular to the maximum principal stress orientation experience no rotation at all. However, faults oriented parallel to the maximum principal stress orientation experience either no rotation or a 90° rotation, dependent on the ratio of principal stresses and the rock stiffness contrast. A comparison with observations from various boreholes worldwide shows that in general the findings are in agreement, even though the dip angle proves to have an influence on the stress rotation, in particular for shallow-dipping faults. [ABSTRACT FROM AUTHOR]

Background: The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated. Methods: Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort. Results: Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04–0.28, p < 0.001 and OR 0.11 95% CI 0.02–0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%). Conclusions: This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence. [ABSTRACT FROM AUTHOR]

Even though the crustal stress state is primarily driven by gravitational volume forces and plate tectonics, interpretations of borehole breakout observations show occasionally abrupt rotations of horizontal stress orientation of up to 90° when faults are crossed. This indicates the influence of faults on the local stress state, which parameter control the degree of rotation. Herein, we investigate the phenomenon of principal stress rotation at a fault by means of a 2D generic numerical model. We parametrised the fault as a rock stiffness contrast and investigate systematically the full model parameter space in terms of the ratio of the applied principal stresses, the rock stiffness contrast, as well as the angle between fault strike and orientation of the principal stress axis. General findings are that the stress rotation is negatively correlated with the ratio of principal stresses. A small angle between the far field stress orientation and the fault facilitates stress rotation. A high contrast in rock stiffness further increases the stress rotation angle. Faults striking perpendicular to the maximum principal stress orientation experience no rotation at all. However, faults oriented parallel to the maximum principal stress orientation experience either no rotation or a 90° rotation, dependent on the ratio of principal stresses and the rock stiffness contrast. A comparison with observations from various boreholes worldwide shows that in general, the findings are well in agreement, even though the dip angle proves to have an influence on the stress rotation, in particular for shallow dipping faults. [ABSTRACT FROM AUTHOR]

Background: Mechanical hysteroscopic tissue removal (mHTR) systems are widely used for removing intrauterine pathology. Given the startup and procedural costs for electrically powered mechanical units, disposable manual mHTR systems have been developed. Methods: With little published, we describe its effectiveness for hysteroscopic intrauterine polypectomy. Results: One-hundred fifty-seven infertile women underwent hysteroscopic polypectomy with the manual mHTR device. Complete removal was accomplished in all but three cases, with blood loss being <10 mL and all specimens deemed sufficient for histopathologic diagnosis. Conclusions: These results suggest that the disposable manual mHTR system is effective in removing endometrial polyps. Head-to-head comparisons with other alternative technologies are needed. [ABSTRACT FROM AUTHOR]

Evaluating uncertainties of geological features on fluid temperature and pressure changes in a reservoir plays a crucial role in the safe and sustainable operation of high-temperature aquifer thermal energy storage (HT-ATES). This study introduces a new automated surface fitting function in the Python API (application programming interface) of Gmsh (v4.11) to simulate the impacts of structural barriers and variations of the reservoir geometries on thermohydraulic behaviour in heat storage applications. These structural features cannot always be detected by geophysical exploration but can be present due to geological complexities. A Python workflow is developed to implement an automated mesh generation routine for various geological scenarios. This way, complex geological models and their inherent uncertainties are transferred into reservoir simulations. The developed meshing workflow is applied to two case studies: (1) Greater Geneva Basin with the Upper Jurassic ("Malm") limestone reservoir and (2) the 5° eastward-tilted DeepStor sandstone reservoir in the Upper Rhine Graben with a uniform thickness of 10 m. In the Greater Geneva Basin example, the top and bottom surfaces of the reservoir are randomly varied by ± 10 and ± 15 m , generating a total variation of up to 25 % from the initially assumed 100 m reservoir thickness. The injected heat plume in this limestone reservoir is independent of the reservoir geometry variation, indicating the limited propagation of the induced thermal signal. In the DeepStor reservoir, a vertical sub-seismic fault juxtaposing the permeable sandstone layers against low permeable clay-marl units is added to the base case model. The fault is located in distances varying from 4 to 118 m to the well to quantify the possible thermohydraulic response within the model. The variation in the distance between the fault and the well resulted in an insignificant change in the thermal recovery (∼ 1.5 %) but up to a ∼ 10.0 % pressure increase for the (shortest) distance of 4 m from the injection well. Modelling the pressure and temperature distribution in the 5° tilted reservoir, with a well placed in the centre of the model, reveals that heat tends to accumulate in the updip direction, while pressure increases in the downdip direction. [ABSTRACT FROM AUTHOR]

High-temperature aquifer thermal energy storage (HT-ATES) systems are designed for seasonal storage of large amounts of thermal energy to meet the demand of industrial processes or district heating systems at high temperatures (> 100 °C). The resulting high injection temperatures or pressures induce thermo- and poroelastic stress changes around the injection well. This study estimates the impact of stress changes in the reservoir on ground surface deformation and evaluates the corresponding risk. Using a simplified coupled thermo-hydraulic-mechanical (THM) model of the planned DeepStor demonstrator in the depleted Leopoldshafen oil field (Upper Rhine Graben, Germany), we show that reservoir heating is associated with stress changes of up to 6 MPa, which can cause vertical displacements at reservoir depth in the order of 10–3 m in the immediate vicinity of the hot injection well. Both the stress changes and the resulting displacements in the reservoir are dominated by thermoelasticity, which is responsible for up to 90% of the latter. Uplift at the surface, on the contrary, is primarily controlled by poroelasticity with by two orders of magnitude attenuated displacements of << 10–3 m. Our calculations further show that the reservoir depth, elastic modulus, and injection/production rates are the dominant controlling parameters for the uplift, showing variations of up to two order of magnitudes between shallower reservoirs with low elastic moduli and deeper and more competent reservoirs. In addition, our findings demonstrate that the cyclic operation of HT-ATES systems reduces the potential for uplift compared to the continuous injection and production of conventional geothermal doublets, hydrocarbon production, or CO2 storage. Consequently, at realistic production and injection rates and targeting reservoirs at depths of at least several hundred meters, the risk of ground surface movement associated with HT-ATES operations in depleted oil fields in, e.g., the Upper Rhine Graben is negligible. [ABSTRACT FROM AUTHOR]

Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml−1, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS. [ABSTRACT FROM AUTHOR]

Based on a newly developed geological 3D reservoir model for the demonstration site of the 'Freiburger Bucht' in the Upper Rhine Graben (SW Germany), geothermal development and realization concepts of an aquifer thermal energy storage (ATES) in the Buntsandstein aquifer were elaborated and energetically evaluated by numerical modeling. The thermal–hydraulic coupled modeling was performed with the FE-software OpenGeoSys and COMSOL. For this purpose, the geological model was converted into a numerical model and calibrated by local and regional, hydrogeological and geothermal measured values. A detailed study based on two-phase storage-heating cycles per year with constant injection temperature on the 'hot side' of the ATES, different volumetric flow rates, and temperature spreads was performed to quantify possible storage capacities, energies, and efficiencies. The calculated efficiency of the cyclic storage operation in this study, averaged over 10 storage heating cycles, are between 50 and 85%, depending on flow rate and temperature spread. The efficiency of the individual storage heating cycles increases from year to year in all scenarios considered, as the 'hot side' of the storage heats up in the long term. To increase ATES' efficiency, also horizontal wells were integrated into the numerical model and the results were compared with those of inclined wells. [ABSTRACT FROM AUTHOR]

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Background: The purpose of this report is to describe the seminal case of a near-term human fetus with a life-threatening left diaphragmatic hernia that underwent fetoscopic tracheal occlusion (FETO) combined with fetoscopic partial removal of herniated bowel from the fetal chest by fetoscopic laparoschisis (FETO-LAP). Case summary: A life-threatening left diaphragmatic hernia (liver-up; o/e LHR of ≤25%; MRI lung volume ≤ 20%) was observed in a human fetus at 34 weeks of gestation. After counselling the mother about the high risks of postnatal demise if left untreated, the expected limitations of fetoscopic tracheal occlusion (FETO), and the previously untested option of combining FETO with fetoscopic laparoschisis, i.e., partial removal of the herniated bowel from the fetal chest (FETO-LAP), she consented to the latter novel treatment approach. FETO-LAP was performed at 36 + 5 weeks of gestation under general maternofetal anesthesia. Mother and fetus tolerated the procedure well. The neonate was delivered and the balloon removed on placental support at 37 + 2 weeks of gestation. On ECMO, a rapid increase in tidal volume was seen over the next eight days. Unfortunately, after this period, blood clots obstructed the ECMO circuit and the neonate passed away. Discussion: This seminal case shows that in a fetus with severe left diaphragmatic hernia, partial removal of the herniated organs from the fetal chest is not only possible by minimally invasive fetoscopic techniques but also well tolerated. As the effect of FETO alone is limited in saving severely affected fetuses, combining FETO with fetoscopic laparoschisis (FETO-LAP) offers a new therapeutic route with multiple, potentially life-saving implications. [ABSTRACT FROM AUTHOR]

Background: Microbiome dysbiosis can have long-lasting effects on our health and induce the development of various diseases. Bronchopulmonary dysplasia (BPD) is a multifactorial disease with pre- and postnatal origins including intra-amniotic infection as main risk factor. Recently, postnatal pathologic lung microbiota colonization was associated with BPD. The objectives of this prospective observational cohort study were to describe differences in bacterial signatures in the amniotic fluid (AF) of intact pregnancies without clinical signs or risk of preterm delivery and AF samples obtained during preterm deliveries and their variations between different BPD disease severity stages. Methods: AF samples were collected under sterile conditions during fetal intervention from intact pregnancies (n = 17) or immediately before preterm delivery < 32 weeks (n = 126). Metabarcoding based approaches were used for the molecular assessment of bacterial 16S rRNA genes to describe bacterial community structure. Results: The absolute amount of 16S rRNA genes was significantly increased in AF of preterm deliveries and detailed profiling revealed a reduced alpha diversity and a significant change in beta diversity with a reduced relative abundance of 16S rRNA genes indicative for Lactobacillus and Acetobacter while Fusobacterium, Pseudomonas, Ureaplasma and Staphylococcus 16S rRNA gene prevailed. Although classification of BPD by disease severity revealed equivalent absolute 16S rRNA gene abundance and alpha and beta diversity in no, mild and moderate/severe BPD groups, for some 16S rRNA genes differences were observed in AF samples. Bacterial signatures of infants with moderate/severe BPD showed predominance of 16S rRNA genes belonging to the Escherichia-Shigella cluster while Ureaplasma and Enterococcus species were enriched in AF samples of infants with mild BPD. Conclusions: Our study identified distinct and diverse intrauterine 16S rRNA gene patterns in preterm infants immediately before birth, differing from the 16S rRNA gene signature of intact pregnancies. The distinct 16S rRNA gene signatures at birth derive from bacteria with varying pathogenicity to the immature lung and are suited to identify preterm infants at risk. Our results emphasize the prenatal impact to the origins of BPD. [ABSTRACT FROM AUTHOR]

Accurate quantification of spatially resolved fluid flow within fractures is crucial for successful reservoir development, such as Enhanced Geothermal Systems. This study presents an innovative workflow designed to model and characterize preferential flow paths (channels) within rough‐walled shear fractures. A set of 30 rough‐walled self‐affine fractures, all possessing identical roughness characteristics, is stochastically generated. By solving the nonlinear Navier‐Stokes equations in 420 individual realizations, the transition from linear to nonlinear flow regimes and the two extreme flow directions perpendicular and parallel to the shearing are numerically captured. A distinguishing feature of this approach is its comprehensive statistical analysis, which encompasses both the geometric and transport properties of flow paths in the non‐simplified three‐dimensional fractured void space under typical geothermal flow conditions. In a perpendicular orientation of flow and shearing, fluid flow exhibits pronounced localization, with more than one‐third of the volumetric flow concentrated within 15% of the fracture volume. In contrast, parallel to the shearing, a complex pattern of individual tortuous channels emerges, with flow occurring in 22% of the void space. Nonlinear effects primarily manifest outside these channels, suggesting that complex flow phenomena may dominate irregular fracture structures, such as contact zones or asperities. In the parallel case, increased flow rates lead to an amplification of channeling processes resulting in less affected volume and diminished tortuosity of the main flow path, while in perpendicular orientation nonlinear effects are only of minor importance. The small‐scale flow regime of both extreme cases tends to converge with increasing flow rates. Plain Language Summary: Understanding fluid flow in subsurface rock is important to successful geothermal operations. In Enhanced Geothermal Systems, the water flows in special paths within the rocks. These paths are like shortcuts that fluid takes because they're easier to move through. It is therefore important to quantify these emerging channels in terms of their geometric appearance as well as their transport properties. This study could show that the extent of channeling depends strongly on the flow direction along or perpendicular to the shearing. Tortuous and geometry‐dependent flow paths are formed parallel to the shearing, whereas perpendicular to the shearing, channels tend to be straight and highly localized. Furthermore, channeling depends on the volumetric flow in the fracture, as higher fluid flow and rising nonlinear effects favor increased channeling with less heat exchange area and less tortuous paths. Key Points: Sheared rough fractures exhibit preferential flow paths that localize a large part of the volume flow in small fracture void spaceThe 3D analysis shows that the geometric properties (height differences, tortuosity, and aperture) strongly affect the local flow regimeIncreasing flow rates cause an increase in channeling with a simultaneous decrease in flow path length [ABSTRACT FROM AUTHOR]

Lithium (Li) is considered a crucial element for energy transition due to its current irreplaceability in Li-ion batteries, particularly in electric vehicles. Market analysis indicates that Germany's future automotive sector and planned battery cell production will necessitate significant quantities of global lithium production. At the same time, only 1% of the world's Li production is currently sourced from Europe. Recently, geothermal brines in Germany have gained attention as a potential local raw material source. These brines exhibit elevated Li concentrations and substantial flow rates in geothermal plants, suggesting the possibility of viable local production. However, a comprehensive full-scale Li extraction process from geothermal brines is yet to be established, and uncertainties persist regarding its long-term behavior. To address this, a generic model based on the geothermal settings of the Upper Rhine Graben was developed, simulating a 30-year operational period for Li extraction. The simulation revealed a 40% depletion of lithium during the observation period, while heat production remained constant. Nonetheless, the model also demonstrated a mean Li production of 231 t per year (equivalent to 1230 t per year of lithium carbonate equivalent), which could significantly enhance the economic prospects of a geothermal power plant and, if applied to multiple plants, reduce Germany's dependence on global lithium imports. The primary factor influencing productivity is the achievable flow rate, as it directly impacts access to the raw material, hence, emphasizing the importance of detailed reservoir exploration and development in optimizing future lithium production from geothermal brines. [ABSTRACT FROM AUTHOR]

Background The recently published 2023 Duke-ISCVID Criteria for Infective Endocarditis for the first time consider mycobacteria (esp. Mycobacterium chimaera) as 'typical' microorganisms for prosthetic valve endocarditis (major criteria). This reflects the ongoing worldwide outbreak of M. chimaera prosthetic valve endocarditis. Case summary Our case series demonstrates a diagnostic pathway for mycobacterial endocarditis. Symptoms are unspecific, and standard microbiological testing does not result in identification of the causative agent (see Graphical Abstract); therefore patients require special microbiological and imaging diagnostics. One patient with early diagnosis and stringent antibiotic and surgical therapy survived. Two patients with disseminated infection at the time point of diagnosis had fatal outcomes. Discussion The diagnostic approach in our small retrospective case series is in line with the new modified Duke criteria and underlines the diagnostic gap in the previous definitions. Outcome of M. chimaera prosthetic valve endocarditis is related to timely diagnosis and anti-mycobacterial as well as surgical treatment. Non-tuberculous mycobacteria should be given more attention in future endocarditis guidelines. [ABSTRACT FROM AUTHOR]

The article focuses on the analysis of Mycobacterium tuberculosis whole-genome data to determine drug resistance profiles more quickly and reliably than traditional phenotypic resistance testing. It discusses the challenges of tuberculosis, especially the rise of drug-resistant cases, and emphasizes the importance of genomic sequencing for identifying and characterizing resistance mutations. The article also introduces the MTBseq software program for automated analysis.

Evaluating uncertainties of geological features on temperature and pressure changes in reservoir's fluids are crucial for a safe and sustainable operation of the High-Temperature Aquifer Thermal Energy Storage (HT-ATES). This study uses a new automated surface fitting function in Python API of GMSH (v. 4.11) to model the impact of arbitrary structural barriers and variations of roof and floor geometries on temperature and pressure in heat storage application. A workflow is developed in Python to implement an automated mesh generation routine for varying geological scenarios that cannot be predicted by surface-based exploration methods. This way, the geologic models and their underlying uncertainties are transferred into reservoir simulations. We applied our modelling approach on two case studies: 1) Greater Geneva Basin with the Upper Jurassic ("Malm") limestone reservoir of 100 m thickness and 2) the DeepStor project in the Upper Rhine Graben with an Oligocene sandstone reservoir of 10 m thickness. In the Greater Geneva Basin showcase, the upper and lower surfaces of the reservoir are shifted ± 8 and ± 10 m, respectively to perturb topology of the thick reservoir. Independence of the heat plume from reservoir's topology indicates the limited propagation of the induced thermal regime in thick reservoirs and redundancy of the advanced exploration campaigns like 3D seismic. In DeepStor, an arbitrary sub-seismic fault juxtaposing the permeable sandstone layers against low-permeable clay-marl units is introduced to the base case model. The arbitrary fault is located in distances varying 4 m to 118 m from the borehole and resulted in a ~10% difference in the pressure field of the cases. Modelling the pressure and temperature in the tilted reservoir reveals that heat tends to accumulate updip while pressure values are higher in the downdip side. [ABSTRACT FROM AUTHOR]

Motivated by the unknown reasons for a kilometre-scale high-temperature overprint of 270–300 ∘ C in a reservoir outcrop analogue (Piesberg quarry, northwestern Germany), numerical simulations are conducted to identify the transport mechanisms of the fault-related hydrothermal convection system. The system mainly consists of a main fault and a sandstone reservoir in which transfer faults are embedded. The results show that the buoyancy-driven convection in the main fault is the basic requirement for elevated temperatures in the reservoir. We studied the effects of permeability variations and lateral regional flow (LRF) mimicking the topographical conditions on the preferential fluid-flow pathways, dominant heat-transfer types, and mutual interactions among different convective and advective flow modes. The sensitivity analysis of permeability variations indicates that lateral convection in the sandstone and advection in the transfer faults can efficiently transport fluid and heat, thus causing elevated temperatures (≥269 ∘ C) in the reservoir at a depth of 4.4 km compared to purely conduction-dominated heat transfer (≤250 ∘ C). Higher-level lateral regional flow interacts with convection and advection and changes the dominant heat transfer from conduction to advection in the transfer faults for the low permeability cases of sandstone and main fault. Simulations with anisotropic permeabilities detailed the dependence of the onset of convection and advection in the reservoir on the spatial permeability distribution. The depth-dependent permeabilities of the main fault reduce the amount of energy transferred by buoyancy-driven convection. The increased heat and fluid flows resulting from the anisotropic main fault permeability provide the most realistic explanation for the thermal anomalies in the reservoir. Our numerical models can facilitate exploration and exploitation workflows to develop positive thermal anomaly zones as geothermal reservoirs. These preliminary results will stimulate further petroleum and geothermal studies of fully coupled thermo–hydro–mechanical–chemical processes in faulted tight sandstones. [ABSTRACT FROM AUTHOR]

Silica nanoparticles have become an important tool in material sciences, nanomedicine, biotechnology, and pharmaceutics, with recent suggested applications also in environmental sciences. In life and environmental sciences, the application field is usually aqueous media; however, the crucial issue of silica nanoparticle dissolution behavior and rate in the target medium is often neglected, overlooked, or taken for granted. Silica nanoparticles are not stable in aqueous solutions until equilibrium silica concentrations are reached. While for life science applications, the degradability of silica nanoparticles is prerequisite for biocompatibility, this characteristic impedes the successful application of silica nanoparticles as environmental tracer, where long-term stability is needed. In this study, the impact of external (temperature, pH values, salinity, availability of silica) and internal (degree of condensation, size, porosity) parameters on the stability of ~ 45-nm-sized silica nanoparticles is characterized. Results show that external factors such as elevated temperature and alkaline pH-values accelerate the dissolution, acidic pH, high salinities, and high initial silica concentrations exhibit a contrary effect. Consequently, in applications, where external parameters cannot be controlled (e.g., in vivo, subsurface reservoirs), dissolution control and stability improvement of silica nanoparticles can be achieved by various means, such as adding a protective layer or by condensation of the silanol bonds through calcination. [ABSTRACT FROM AUTHOR]

Fetal surgery has become a lifesaving reality for hundreds of fetuses each year. The development of a formidable spectrum of safe and effective minimally invasive techniques for fetal interventions since the early 1990s until today has led to an increasing acceptance of novel procedures by both patients and health care providers. From his vast personal experience of more than 20 years as one of the pioneers at the forefront of clinical minimally invasive fetal surgery, the author describes and comments on old and new minimally invasive approaches, highlighting their lifesaving or quality-of-life-improving potential. He provides easy-to-use practical information on how to perform partial amniotic carbon dioxide insufflation (PACI), how to assess lung function in fetuses with pulmonary hypoplasia, how to deal with giant CPAMS, how to insert shunts into fetuses with LUTO and hydrothorax when conventional devices are not available, and how to resuscitate a fetus during fetal cardiac intervention. Furthermore, the author proposes a curriculum for future fetal surgeons, solicits for the centralization of patients, for adequate maternal counseling, for adequate pain management and adequate hygienic conditions during interventions, and last but not least for starting the process of academic recognition of the matured field as an independent specialty. These steps will allow more affected expectant women and their unborn children to gain access to modern minimally invasive fetal surgery and therapy. The opportunity to treat more patients at dedicated centers will also result in more opportunities for the research of rare diseases and conditions, promising even better pre- and postnatal care in the future. [ABSTRACT FROM AUTHOR]

Motivated by the unknown reasons for a kilometer-scale high-temperature overprint of 270 ~ 300 °C in a reservoir outcrop analog (Piesberg Quarry, northwest Germany), numerical simulations are conducted to identify the transport mechanisms of the fault-related hydrothermal convection system. The system mainly consists of a main fault and a sandstone reservoir in which transfer faults are embedded. The results show that the buoyancy-driven convection in the main fault is the basic requirement for elevated temperatures in the reservoir. We studied the effects of permeability variations and lateral regional flow on the preferential fluid flow pathways, dominant heat transfer types, and mutual interactions among different convective and advective flow modes. The sensitivity analysis of permeability variations indicates that lateral convection in the sandstone and advection in the transfer faults can efficiently transport fluid and heat, thus causing elevated temperatures (= 269 °C) in the reservoir compared to purely conduction-dominated heat transfer (= 250 °C). Higher-level lateral regional flow interacts with convection and advection and changes the dominant heat transfer from conduction to advection in the transfer faults for the low permeability cases of sandstone and main fault. Simulations with anisotropic permeabilities detailed the dependence of the onset of convection and advection in the reservoir on the directional permeability distribution. The depth-dependent permeabilities of the main fault reduce the amount of energy transferred by buoyancy-driven convection. The increased heat and fluid flows resulting from the anisotropic main fault permeability provide the most realistic explanation for the thermal anomalies in the reservoir. Our numerical models can facilitate exploration and exploitation workflows to develop positive thermal anomalies zones as geothermal reservoirs. These preliminary results will stimulate further petroleum and geothermal studies of fully coupled thermo-hydro-mechanical-chemical processes in faulted tight sandstones. [ABSTRACT FROM AUTHOR]

Motivated by the unknown reasons for a kilometer-scale high-temperature overprint of 270 ~ 300 °C in a reservoir outcrop analog (Piesberg Quarry, northwest Germany), numerical simulations are conducted to identify the transport mechanisms of the fault-related hydrothermal convection system. The system mainly consists of a main fault and a sandstone reservoir in which transfer faults are embedded. The results show that the buoyancy-driven convection in the main fault is the basic requirement for elevated temperatures in the reservoir. We studied the effects of permeability variations and lateral regional flow on the preferential fluid flow pathways, dominant heat transfer types, and mutual interactions among different convective and advective flow modes. The sensitivity analysis of permeability variations indicates that lateral convection in the sandstone and advection in the transfer faults can efficiently transport fluid and heat, thus causing elevated temperatures (≥ 269 °C) in the reservoir compared to purely conduction-dominated heat transfer (≤ 250 °C). Higher-level lateral regional flow interacts with convection and advection and changes the dominant heat transfer from conduction to advection in the transfer faults for the low permeability cases of sandstone and main fault. Simulations with anisotropic permeabilities detailed the dependence of the onset of convection and advection in the reservoir on the directional permeability distribution. The depth-dependent permeabilities of the main fault reduce the amount of energy transferred by buoyancy-driven convection. The increased heat and fluid flows resulting from the anisotropic main fault permeability provide the most realistic explanation for the thermal anomalies in the reservoir. Our numerical models can facilitate exploration and exploitation workflows to develop positive thermal anomalies zones as geothermal reservoirs. These preliminary results will stimulate further petroleum and geothermal studies of fully coupled thermo-hydro-mechanical-chemical processes in faulted tight sandstones. [ABSTRACT FROM AUTHOR]

Transmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a "perfect storm" that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens. An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations. [ABSTRACT FROM AUTHOR]

Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes. Mycobacterium abscessus is an emerging infection of increasing public health concern due to outbreaks and intrinsic multidrug-resistance. Here, the authors develop and evaluate a core-genome multilocus sequence typing scheme for this pathogen to facilitate standardised molecular surveillance. [ABSTRACT FROM AUTHOR]

Simple Summary: Tuberculosis still causes 1.5 million deaths annually and is mainly caused by Mycobacterium tuberculosis complex strains belonging to three evolutionary modern lineages (Lineages 2–4). While Lineage 2 and Lineage 4 virtually conquered the world, Lineage 3 is particularly successful in Northern and Eastern Africa, as well as in Southern Asia, the suspected evolutionary origin of these strains. Here, we sought to understand how Lineage 3 strains came to the African continent. To this end, we performed routine genotyping to characterize over 2500 clinical isolates from 38 countries. We then selected a representative collection of 373 isolates for a whole-genome analysis and a modeling approach to infer the geographic origin of different sublineages. In fact, the origin of Lineage 3 could be located in India, and we found evidence for independent introductions of four distinct sublineages into North/East Africa, in line with known ancient exchanges and migrations between both world regions. Our study illustrates that the evolutionary history of humans and their pathogens are closely connected and further provides a systematic understanding of the genomic diversity of Lineage 3, which could be important for the development of new tuberculosis vaccines or new therapeutics. Mycobacterium tuberculosis complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates. [ABSTRACT FROM AUTHOR]

Objectives: To develop a robust phenotypic antimicrobial susceptibility testing (AST) method with a correctly set breakpoint for pretomanid (Pa), the most recently approved anti-tuberculosis drug.Methods: The Becton Dickinson Mycobacterial Growth Indicator Tube™ (MGIT) system was used at six laboratories to determine the MICs of a phylogenetically diverse collection of 356 Mycobacterium tuberculosis complex (MTBC) strains to establish the epidemiological cut-off value for pretomanid. MICs were correlated with WGS data to study the genetic basis of differences in the susceptibility to pretomanid.Results: We observed ancient differences in the susceptibility to pretomanid among various members of MTBC. Most notably, lineage 1 of M. tuberculosis, which is estimated to account for 28% of tuberculosis cases globally, was less susceptible than lineages 2, 3, 4 and 7 of M. tuberculosis, resulting in a 99th percentile of 2 mg/L for lineage 1 compared with 0.5 mg/L for the remaining M. tuberculosis lineages. Moreover, we observed that higher MICs (≥8 mg/L), which probably confer resistance, had recently evolved independently in six different M. tuberculosis strains. Unlike the aforementioned ancient differences in susceptibility, these recent differences were likely caused by mutations in the known pretomanid resistance genes.Conclusions: In light of these findings, the provisional critical concentration of 1 mg/L for MGIT set by EMA must be re-evaluated. More broadly, these findings underline the importance of considering the global diversity of MTBC during clinical development of drugs and when defining breakpoints for AST. [ABSTRACT FROM AUTHOR]

Background: Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods: A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results: The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions: Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. [ABSTRACT FROM AUTHOR]

Carcassonne G 6, preserving a judicial oath from 833, is an exceptional source for the history of the Spanish March and more generally the workings of power in the Carolingian world. The oath, concerning at first glance a very local dispute, links a body of royal charters with the precepts for the hispani issued by Charlemagne, Louis the Pious and Charles the Bald. This link reveals the close entanglement of localities and centre that structured the better part of western Europe into a political entity. A critical edition, which was not available for this text before, is provided as an appendix. [ABSTRACT FROM AUTHOR]

"Ancestral" Mycobacterium tuberculosis complex (MTBC) strains of Lineage 1 (L1, East African Indian) are a prominent tuberculosis (TB) cause in countries around the Indian Ocean. However, the pathobiology of L1 strains is insufficiently characterized. Here, we used whole genome sequencing (WGS) of 312 L1 strains from 43 countries to perform a characterization of the global L1 population structure and correlate this to the analysis of the synthesis of phenolic glycolipids (PGL) – known MTBC polyketide-derived virulence factors. Our results reveal the presence of eight major L1 sub-lineages, whose members have specific mutation signatures in PGL biosynthesis genes, e.g., pks15/1 or glycosyltransferases Rv2962c and/or Rv2958c. Sub-lineage specific PGL production was studied by NMR-based lipid profiling and strains with a completely abolished phenolphthiocerol dimycoserosate biosynthesis showed in average a more prominent growth in human macrophages. In conclusion, our results show a diverse population structure of L1 strains that is associated with the presence of specific PGL types. This includes the occurrence of mycoside B in one sub-lineage, representing the first description of a PGL in an M. tuberculosis lineage other than L2. Such differences may be important for the evolution of L1 strains, e.g., allowing adaption to different human populations. [ABSTRACT FROM AUTHOR]

2 Decision algorithm to classify human-related strains of Haemophilus spp. based on whole genome sequencing data. Reference 1 Diricks M. Whole genome sequencing-based classifcation of human-related Haemophilus species and detection of antimicrobial resistance genes. [Extracted from the article]

Background: Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods: A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results: The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions: Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. [ABSTRACT FROM AUTHOR]

Background: Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods: A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results: The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions: Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. [ABSTRACT FROM AUTHOR]

Conventional methods to estimate the static formation temperature (SFT) require borehole temperature data measured during thermal recovery periods. This can be both economically and technically prohibitive under real operational conditions, especially for high-temperature boreholes. This study investigates the use of temperature logs obtained under injection conditions to determine SFT through inverse modelling. An adaptive sampling approach based on machine-learning techniques is applied to explore the model space efficiently by iteratively proposing samples based on the results of previous runs. Synthetic case studies are conducted with rigorous evaluation of factors affecting the quality of SFT estimates for deep hot wells. The results show that using temperature data measured at higher flow rates or after longer injection times could lead to less-reliable results. Furthermore, the estimation error exhibits an almost linear dependency on the standard error of the measured borehole temperatures. In addition, potential flow loss zones in the borehole would lead to increased uncertainties in the SFT estimates. Consequently, any prior knowledge about the amount of flow loss could improve the estimation accuracy considerably. For formations with thermal gradients varying with depth, prior information on the depth of the gradient change is necessary to avoid spurious results. The inversion scheme presented is demonstrated as an efficient tool for quantifying uncertainty in the interpretation of borehole data. Although only temperature data are considered in this work, other types of data such as flow and transport measurements can also be included in this method for geophysical and rock physics studies. [ABSTRACT FROM AUTHOR]

Background Comprehensive and reliable drug susceptibility testing (DST) is urgently needed to provide adequate treatment regimens for patients with multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB). We determined whether next-generation sequencing (NGS) analysis of Mycobacterium tuberculosis complex isolates and genes implicated in drug resistance can guide the design of effective MDR/RR-TB treatment regimens. Methods NGS-based genomic DST predictions of M. tuberculosis complex isolates from MDR/RR-TB patients admitted to a TB reference center in Germany between 1 January 2015 and 30 April 2019 were compared with phenotypic DST results of mycobacteria growth indicator tubes (MGIT). Standardized treatment algorithms were applied to design individualized therapies based on either genomic or phenotypic DST results, and discrepancies were further evaluated by determination of minimal inhibitory drug concentrations (MICs) using Sensititre MYCOTBI and UKMYC microtiter plates. Results In 70 patients with MDR/RR-TB, agreement among 1048 pairwise comparisons of genomic and phenotypic DST was 86.3%; 76 (7.2%) results were discordant, and 68 (6.5%) could not be evaluated due to the presence of polymorphisms with yet unknown implications for drug resistance. Importantly, 549 of 561 (97.9%) predictions of drug susceptibility were phenotypically confirmed in MGIT, and 27 of 64 (42.2%) false-positive results were linked to previously described mutations mediating a low or moderate MIC increase. Virtually all drugs (99.0%) used in combination therapies that were inferred from genomic DST were confirmed to be susceptible by phenotypic DST. Conclusions NGS-based genomic DST can reliably guide the design of effective MDR/RR-TB treatment regimens. [ABSTRACT FROM AUTHOR]

Background: Determining factors affecting the transmission of rifampicin (RR) and multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains under standardized tuberculosis (TB) treatment is key to control TB and prevent the evolution of drug resistance.Methods: We combined bacterial whole genome sequencing (WGS) and epidemiological investigations for 37% (n = 195) of all RR/MDR-TB patients in Cameroon (2012-2015) to identify factors associated with recent transmission.Results: Patients infected with a strain resistant to high-dose isoniazid, and ethambutol had 7.4 (95% CI 2.6-21.4), and 2.4 (95% CI 1.2-4.8) times increased odds of being in a WGS-cluster, a surrogate for recent transmission. Furthermore, age between 30 and 50 was positively correlated with recent transmission (adjusted OR 3.8, 95% CI 1.3-11.4). We found high drug-resistance proportions against three drugs used in the short standardized MDR-TB regimen in Cameroon, i.e. high-dose isoniazid (77.4%), ethambutol (56.9%), and pyrazinamide (43.1%). Virtually all strains were susceptible to fluoroquinolones, kanamycin, and clofazimine, and treatment outcomes were mostly favourable (87.5%).Conclusion: Pre-existing resistance to high-dose isoniazid, and ethambutol is associated with recent transmission of RR/MDR strains in our study. A possible contributing factor for this observation is the absence of universal drug susceptibility testing in Cameroon, likely resulting in prolonged exposure of new RR/MDR-TB patients to sub-optimal or failing first-line drug regimens. [ABSTRACT FROM AUTHOR]

Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project's timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results. [ABSTRACT FROM AUTHOR]

Background: Mycobacterium abscessus (MAB) is a widely disseminated pathogenic non-tuberculous mycobacterium (NTM). Like with the M. tuberculosis complex (MTBC), excreted / secreted (ES) proteins play an essential role for its virulence and survival inside the host. Here, we used a robust bioinformatics pipeline to predict the secretome of the M. abscessus ATCC 19977 reference strain and 15 clinical isolates belonging to all three MAB subspecies, M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. Results: We found that ~ 18% of the proteins encoded in the MAB genomes were predicted as secreted and that the three MAB subspecies shared > 85% of the predicted secretomes. MAB isolates with a rough (R) colony morphotype showed larger predicted secretomes than isolates with a smooth (S) morphotype. Additionally, proteins exclusive to the secretomes of MAB R variants had higher antigenic densities than those exclusive to S variants, independent of the subspecies. For all investigated isolates, ES proteins had a significantly higher antigenic density than non-ES proteins. We identified 337 MAB ES proteins with homologues in previously investigated M. tuberculosis secretomes. Among these, 222 have previous experimental support of secretion, and some proteins showed homology with protein drug targets reported in the DrugBank database. The predicted MAB secretomes showed a higher abundance of proteins related to quorum-sensing and Mce domains as compared to MTBC indicating the importance of these pathways for MAB pathogenicity and virulence. Comparison of the predicted secretome of M. abscessus ATCC 19977 with the list of essential genes revealed that 99 secreted proteins corresponded to essential proteins required for in vitro growth. Conclusions: This study represents the first systematic prediction and in silico characterization of the MAB secretome. Our study demonstrates that bioinformatics strategies can help to broadly explore mycobacterial secretomes including those of clinical isolates and to tailor subsequent, complex and time-consuming experimental approaches accordingly. This approach can support systematic investigation exploring candidate proteins for new vaccines and diagnostic markers to distinguish between colonization and infection. All predicted secretomes were deposited in the Secret-AAR web-server (http://microbiomics.ibt.unam.mx/tools/aar/index.php). [ABSTRACT FROM AUTHOR]

This study presents a probabilistic analysis of 3D Navier‐Stokes (NS) fluid flow through 30 randomly generated sheared fractures with equal roughness properties (Hurst exponent = 0.8). The results of numerous 3D NS realizations are compared with the highly simplified local cubic law (LCL) solutions regarding flow orientations and regimes. The transition between linear and nonlinear flow conditions cannot be described with a generally valid critical Reynolds number (Recrit), but rather depends on the individual fracture's void geometry. Over 10% reduction in flow is observed for increased global Re (>100) due to the increasing impact of nonlinear conditions. Furthermore, the fracture geometry promotes flow anisotropy and the formation of channels. Flow perpendicular to the shearing leads to increased channeling and fluid flow (∼40% higher) compared to flow parallel to the shearing. In the latter case, dispersed flow and irregular flow paths cause a reduction of LCL validity. Plain Language Summary: The movement of fluid and heat through fractured rocks is massively affected by the void space of the contributing fractures and the velocity of the fluid. The opposing offset of the two fracture surfaces creates complex and variable void geometries. A calculation of the expected flow rates is very difficult. In most studies, simplifications are adopted neglecting these complex features by using a plane surface and assuming that the flow is taking place smoothly. We therefore simulate the real flow using the three‐dimensional fracture void space and compare the results with simpler two‐dimensional models. It can be demonstrated that the difference between the two types of simulations depends not only on the local simplification but also on the flow direction within the fractures and that the difference increases with higher flow velocities. If the fractures are not considered as a whole continuum but on the local scale, preferential fluid pathways or channels are formed in which most of the flow takes place. Depending on the flow direction, channels are more or less pronounced. We can show that in well‐developed channels the differences between the calculation methods are much smaller than in the other parts of the domain. Key Points: Shearing of fractures generates a directional flow anisotropy, with an increased flow rate perpendicular to the shearingPreferential channels are formed which localize the largest part of the volumetric flow in small parts of the entire fracture domainSpatial differences between the complex Navier‐Stokes equations and the local cubic law can be explained by channeling processes [ABSTRACT FROM AUTHOR]