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In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22–1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms. [ABSTRACT FROM AUTHOR]

The digitization of medicine will play an increasingly significant role in future years. In particular, telemedicine, Virtual Reality (VR) and innovative Artificial Intelligence (AI) systems offer tremendous potential in imaging diagnostics and are expected to shape ultrasound diagnostics and teaching significantly. However, it is crucial to consider the advantages and disadvantages of employing these new technologies and how best to teach and manage their use. This paper provides an overview of telemedicine, VR and AI in student ultrasound education, presenting current perspectives and controversies. [ABSTRACT FROM AUTHOR]

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics. [ABSTRACT FROM AUTHOR]

Background: Laparoscopic cholecystectomy is a very frequent surgical procedure. However, in an ageing society, less surgical staff will need to perform surgery on patients. Collaborative surgical robots (cobots) could address surgical staff shortages and workload. To achieve context-awareness for surgeon-robot collaboration, the intraoperative action workflow recognition is a key challenge. Methods: A surgical process model was developed for intraoperative surgical activities including actor, instrument, action and target in laparoscopic cholecystectomy (excluding camera guidance). These activities, as well as instrument presence and surgical phases were annotated in videos of laparoscopic cholecystectomy performed on human patients (n = 10) and on explanted porcine livers (n = 10). The machine learning algorithm Distilled-Swin was trained on our own annotated dataset and the CholecT45 dataset. The validation of the model was conducted using a fivefold cross-validation approach. Results: In total, 22,351 activities were annotated with a cumulative duration of 24.9 h of video segments. The machine learning algorithm trained and validated on our own dataset scored a mean average precision (mAP) of 25.7% and a top K = 5 accuracy of 85.3%. With training and validation on our dataset and CholecT45, the algorithm scored a mAP of 37.9%. Conclusions: An activity model was developed and applied for the fine-granular annotation of laparoscopic cholecystectomies in two surgical settings. A machine recognition algorithm trained on our own annotated dataset and CholecT45 achieved a higher performance than training only on CholecT45 and can recognize frequently occurring activities well, but not infrequent activities. The analysis of an annotated dataset allowed for the quantification of the potential of collaborative surgical robots to address the workload of surgical staff. If collaborative surgical robots could grasp and hold tissue, up to 83.5% of the assistant's tissue interacting tasks (i.e. excluding camera guidance) could be performed by robots. [ABSTRACT FROM AUTHOR]

The H1 Collaboration reports the first measurement of the 1-jettiness event shape observable τ 1 b in neutral-current deep-inelastic electron-proton scattering (DIS). The observable τ 1 b is equivalent to a thrust observable defined in the Breit frame. The data sample was collected at the HERA ep collider in the years 2003–2007 with center-of-mass energy of s = 319 GeV , corresponding to an integrated luminosity of 351.1 pb - 1 . Triple differential cross sections are provided as a function of τ 1 b , event virtuality Q 2 , and inelasticity y, in the kinematic region Q 2 > 150 GeV 2 . Single differential cross sections are provided as a function of τ 1 b in a limited kinematic range. Double differential cross sections are measured, in contrast, integrated over τ 1 b and represent the inclusive neutral-current DIS cross section measured as a function of Q 2 and y. The data are compared to a variety of predictions and include long-standing and more recent Monte Carlo event generators, predictions in fixed-order perturbative QCD where calculations up to O (α s 3) are available for τ 1 b or inclusive DIS, and resummed predictions at next-to-leading logarithmic accuracy matched to fixed order predictions at O (α s 2) . These comparisons reveal sensitivity of the 1-jettiness observable to QCD parton shower and resummation effects, as well as the modeling of hadronization and fragmentation. Within their range of validity, the fixed-order predictions provide a good description of the data. Monte Carlo event generators are predictive over the full measured range and hence their underlying models and parameters can be constrained by comparing to the presented data. [ABSTRACT FROM AUTHOR]

The Breit frame provides a natural frame to analyze lepton–proton scattering events. In this reference frame, the parton model hard interactions between a quark and an exchanged boson defines the coordinate system such that the struck quark is back-scattered along the virtual photon momentum direction. In Quantum Chromodynamics (QCD), higher order perturbative or non-perturbative effects can change this picture drastically. As Bjorken-x decreases below one half, a rather peculiar event signature is predicted with increasing probability, where no radiation is present in one of the two Breit-frame hemispheres and all emissions are to be found in the other hemisphere. At higher orders in α s or in the presence of soft QCD effects, predictions of the rate of these events are far from trivial, and that motivates measurements with real data. We report on the first observation of the empty current hemisphere events in electron–proton collisions at the HERA collider using data recorded with the H1 detector at a center-of-mass energy of 319 GeV. The fraction of inclusive neutral-current DIS events with an empty hemisphere is found to be 0.0112 ± 3.9 % stat ± 4.5 % syst ± 1.6 % mod in the selected kinematic region of 150 < Q 2 < 1500 GeV 2 and inelasticity 0.14 < y < 0.7 . The data sample corresponds to an integrated luminosity of 351.1 pb - 1 , sufficient to enable differential cross section measurements of these events. The results show an enhanced discriminating power at lower Bjorken-x among different Monte Carlo event generator predictions. [ABSTRACT FROM AUTHOR]

The H1 Collaboration at HERA reports the first measurement of groomed event shape observables in deep inelastic electron-proton scattering (DIS) at s = 319 GeV, using data recorded between the years 2003 and 2007 with an integrated luminosity of 351 pb - 1 . Event shapes provide incisive probes of perturbative and non-perturbative QCD. Grooming techniques have been used for jet measurements in hadronic collisions; this paper presents the first application of grooming to DIS data. The analysis is carried out in the Breit frame, utilizing the novel Centauro jet clustering algorithm that is designed for DIS event topologies. Events are required to have squared momentum-transfer Q 2 > 150 GeV 2 and inelasticity 0.2 < y < 0.7 . We report measurements of the production cross section of groomed event 1-jettiness and groomed invariant mass for several choices of grooming parameter. Monte Carlo model calculations and analytic calculations based on Soft Collinear Effective Theory are compared to the measurements. [ABSTRACT FROM AUTHOR]

Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types of T4P, namely the archaellum, the UV-inducible pilus system (Ups) and the archaeal adhesive pilus (Aap). Whereas the archaellum functions primarily in swimming motility, and the Ups in UV-induced cell aggregation and DNA-exchange, the Aap plays an important role in adhesion and twitching motility. Here, we present a cryoEM structure of the Aap of the archaeal model organism Sulfolobus acidocaldarius. We identify the component subunit as AapB and find that while its structure follows the canonical T4P blueprint, it adopts three distinct conformations within the pilus. The tri-conformer Aap structure that we describe challenges our current understanding of pilus structure and sheds new light on the principles of twitching motility. The cells of many archaeal species display surface appendages that closely resemble bacterial Type IV pili (T4P). Here, Gaines et al. present a cryoEM structure of the archaeal adhesive pilus from Sulfolobus acidocaldarius, showing that the structure of the component subunit follows the canonical T4P blueprint but adopts three distinct conformations within the pilus. [ABSTRACT FROM AUTHOR]

The Indo-Gangetic Plains represents one of South Asia’s most productive agricultural regions, yet it is highly vulnerable to climate change and requires the widespread adoption of Climate-Smart Agriculture. Although farmers understand the benefits of such technologies, financial constraints often undermine adoption. Using a case study from Haryana, we assess the opportunities and challenges aligned with the different pathways available for farmers to adopt and finance two capital-intensive technologies: laser land levelers and happy seeders. Our analysis uses unique data from Karnal, where stakeholders have partnered in Climate-Smart-Villages, and combines a household survey from 120 farmers, interviews, and focus group discussions with banks and cooperatives. Our results indicate adoption rates of 77% for laser land levelers and 52% for happy seeders, with only 7% and 21% of farmers owning the technologies, respectively. Hiring is highly preferred over purchase, mainly due to the flourishing of Custom-Hiring Centers, which are vital in driving large-scale implementation. We find that farmers prefer funding from family, savings, and moneylenders (indirect pathways) rather than from commercial banks (direct pathways) to get immediate access to credit and avoid bureaucratic procedures. Our study offers broader insights into the state of agricultural finance in India and adaptation to climate change and reveals that institutional innovations can enhance the financing of CSA technologies for smallholder farmers. Our findings have important implications for decision-makers seeking to streamline credit access for CSA machinery rental. Future research should focus on the efficacy of different finance channels and their causal impact on pathways for technology adoption. [ABSTRACT FROM AUTHOR]

We would like to provide an updated comprehensive perspective and identify the components linked to chronic spontaneous urticaria (CSU) without specific triggers in autoimmune atrophic gastritis (AAG). AAG is an organ-specific autoimmune disease that affects the corpus-fundus gastric mucosa. Although we lack a unified explanation of the underlying pathways, when considering all paediatric patients reported in the literature, alterations result in gastric neuroendocrine enterochromaffin-like (ECL) cell proliferation and paracrine release of histamine. Several mechanisms have been proposed for the pathogenesis of CSU, with much evidence pointing towards AAG and ECL cell responses, which may be implicated as potential factors contributing to CSU. The excessive production/release of histamine into the bloodstream could cause or trigger exacerbations of CSU in AAG, independent of Helicobacter pylori; thus, the release of histamine from ECL cells may be the primary modulator. Conclusion: Considering the understanding of these interactions, recognising the respective roles of AAG in the pathogenesis of CSU may strongly impact the diagnostic workup and management of unexplained/refractory CSU and may inform future research and interventions in the paediatric population. What is Known: • Autoimmune atrophic gastritis is a chronic immune-mediated inflammatory disease characterised by the destruction of the oxyntic mucosa in the gastric body and fundus, mucosal atrophy, and metaplastic changes. • Autoimmune atrophic gastritis in paediatric patients is important because of the poor outcome and risk of malignancy and possibly underestimated entities primarily reported in single-case reports. What is New: • Upper gastrointestinal inflammatory disorders, independent of H. pylori, have been implicated as potential inducing factors in the development of chronic spontaneous urticaria. • If a paediatric patient presents with symptoms such as anaemia, reduced vitamin B12 levels, recurrent urticaria with no other detectable aetiology, positive anti-parietal cell antibodies, and elevated gastrin levels, autoimmune atrophic gastritis should be considered a possible cause of chronic urticaria. [ABSTRACT FROM AUTHOR]

In this work, we explore the nonlinear dynamics for capturing energy from a device, which is considered support with cantilever beam ferromagnetic containing piezoceramic patches connected to an electrical circuit that collects energy for capture. The free end of the ferromagnetic cantilever beam is under the effect of two magnetic poles, and we consider an asymmetric potential for the magnetic poles. However, the influence of asymmetry in bi-stable energy collectors can change the potential well and adjust the distribution of its potential energy. Charging in the potential well also modifies the unstable equilibrium positions thus altering the dynamic characteristics of the device and thus benefiting the use of energy under various excitation conditions. Furthermore, asymmetric potentials combine with the movement of human lower limbs for applications in energy harvesting devices in such displacement. As numerical results, we explored the nonlinear dynamics and established the sets of parameters for the convergence of the trajectories and the regions of maximum average output power. [ABSTRACT FROM AUTHOR]

ADP-ribosylation factor 1 (Arf1) interacts with multiple cellular partners and membranes to regulate intracellular traffic, organelle structure and actin dynamics. Defining the dynamic conformational landscape of Arf1 in its active form, when bound to the membrane, is of high functional relevance and key to understanding how Arf1 can alter diverse cellular processes. Through concerted application of nuclear magnetic resonance (NMR), neutron reflectometry (NR) and molecular dynamics (MD) simulations, we show that, while Arf1 is anchored to the membrane through its N-terminal myristoylated amphipathic helix, the G domain explores a large conformational space, existing in a dynamic equilibrium between membrane-associated and membrane-distal conformations. These configurational dynamics expose different interfaces for interaction with effectors. Interaction with the Pleckstrin homology domain of ASAP1, an Arf-GTPase activating protein (ArfGAP), restricts motions of the G domain to lock it in what seems to be a conformation exposing functionally relevant regions. An integrated approach combing solution and solid-state NMR, molecular dynamics simulations and neutron reflectometry is applied to characterize dynamic membrane bound forms of ADP-ribosylation factor 1 (Arf1). [ABSTRACT FROM AUTHOR]

Background: With Surgomics, we aim for personalized prediction of the patient's surgical outcome using machine-learning (ML) on multimodal intraoperative data to extract surgomic features as surgical process characteristics. As high-quality annotations by medical experts are crucial, but still a bottleneck, we prospectively investigate active learning (AL) to reduce annotation effort and present automatic recognition of surgomic features. Methods: To establish a process for development of surgomic features, ten video-based features related to bleeding, as highly relevant intraoperative complication, were chosen. They comprise the amount of blood and smoke in the surgical field, six instruments, and two anatomic structures. Annotation of selected frames from robot-assisted minimally invasive esophagectomies was performed by at least three independent medical experts. To test whether AL reduces annotation effort, we performed a prospective annotation study comparing AL with equidistant sampling (EQS) for frame selection. Multiple Bayesian ResNet18 architectures were trained on a multicentric dataset, consisting of 22 videos from two centers. Results: In total, 14,004 frames were tag annotated. A mean F1-score of 0.75 ± 0.16 was achieved for all features. The highest F1-score was achieved for the instruments (mean 0.80 ± 0.17). This result is also reflected in the inter-rater-agreement (1-rater-kappa > 0.82). Compared to EQS, AL showed better recognition results for the instruments with a significant difference in the McNemar test comparing correctness of predictions. Moreover, in contrast to EQS, AL selected more frames of the four less common instruments (1512 vs. 607 frames) and achieved higher F1-scores for common instruments while requiring less training frames. Conclusion: We presented ten surgomic features relevant for bleeding events in esophageal surgery automatically extracted from surgical video using ML. AL showed the potential to reduce annotation effort while keeping ML performance high for selected features. The source code and the trained models are published open source. [ABSTRACT FROM AUTHOR]

We present a novel Active Magnetic Shield (AMS), designed and implemented for the n2EDM experiment at the Paul Scherrer Institute. The experiment will perform a high-sensitivity search for the electric dipole moment of the neutron. Magnetic-field stability and control is of key importance for n2EDM. A large, cubic, 5 m side length, magnetically shielded room (MSR) provides a passive, quasi-static shielding-factor of about 10 5 for its inner sensitive volume. The AMS consists of a system of eight complex, feedback-controlled compensation coils constructed on an irregular grid spanned on a volume of less than 1000 m 3 around the MSR. The AMS is designed to provide a stable and uniform magnetic-field environment around the MSR, while being reasonably compact. The system can compensate static and variable magnetic fields up to ± 50 μ T (homogeneous components) and ± 5 μ T/m (first-order gradients), suppressing them to a few μ T in the sub-Hertz frequency range. The presented design concept and implementation of the AMS fulfills the requirements of the n2EDM experiment and can be useful for other applications, where magnetically silent environments are important and spatial constraints inhibit simpler geometrical solutions. [ABSTRACT FROM AUTHOR]

Goals constitute an important construct in developmental psychology. They represent a central way in which individuals shape their development. Here, we present two studies on age-related differences in one important goal dimension, goal focus, that is, the relative salience of the means and ends of goal pursuit. Extant studies on age-related differences in adults suggest a shift from focusing on the ends to focusing on the means across adulthood. The current studies aimed to expand this research to encompass the entire lifespan including childhood. The first cross-sectional study included participants spanning from early childhood into old age (N = 312, age range: 3–83 years) and used a multimethodological approach comprising eye tracking, behavioral, and verbal measures of goal focus. The second study investigated the verbal measures of the first study in more detail in an adult sample (N = 1550, age range: 17–88 years). Overall, the results do not show a clear pattern, making them difficult to interpret. There was little convergence of the measures, pointing to the difficulties in assessing a construct such as goal focus across a large range of age groups differing in social-cognitive and verbal skills. [ABSTRACT FROM AUTHOR]

Upper tract urothelial carcinoma (UTUC) is the third most common malignancy associated with Lynch syndrome (LS). The current European urology guidelines recommend screening for LS in patients with UTUC up to the age of 60 years. In this study, we examined a cohort of patients with UTUC for potential association with LS in order to establish the sensitivity of current guidelines in detecting LS. A total of 180 patients with confirmed diagnosis of UTUC were enrolled in the study during a 12-year period (2010–2022). Loss of DNA-mismatch repair proteins (MMRp) expression was identified in 15/180 patients (8.3%). Germline analysis was eventually performed in 8 patients confirming LS in 5 patients (2.8%), including 4 germline mutations in MSH6 and 1 germline mutation in MSH2. LS-related UTUC included 3 females and 2 males, with a mean age of 66.2 years (median 71 years, range 46–75 years). Four of five LS patients (all with MSH6 mutation) were older than 65 years (mean age 71.3, median 72 years). Our findings indicate that LS-associated UTUCs can occur in patients with LS older than 60 years. In contrast to previous studies which used mainly highly pre-selected populations with already diagnosed LS, the most frequent mutation in our cohort involved MSH6 gene. All MSH6 mutation carriers were > 65 years, and UTUC was the first LS manifestation in 2/4 patients. Using current screening guidelines, a significant proportion of patients with LS-associated UTUC may be missed. We suggest universal immunohistochemical MMRp screening for all UTUCs, regardless of age and clinical history. [ABSTRACT FROM AUTHOR]

Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts. Probing the evolution of bacterial endosymbionts in Mucoromycota - Mollicutes-related endobacteria (MRE) - reveals that the genera Linnemannia and Benniella acquired MRE after host divergence from a common ancestor. [ABSTRACT FROM AUTHOR]

The ultracold neutron (UCN) source at the Paul Scherrer Institute (PSI) provides high intensities of storable neutrons for fundamental physics experiments. The neutron velocity spectrum parallel to the beamline axis was determined by time-of-flight spectroscopy using a neutron chopper. In particular, the temporal evolution of the spectrum during neutron production and UCN storage in the source storage volume was investigated and compared to Monte Carlo simulation results. A softening of the measured spectrum from a mean velocity of 7.7(1)–5.1(1) m s - 1 occurred within the first 30 s after the proton beam pulse had impinged on the spallation target. A spectral hardening was observed over longer time scales of one measurement day, consistent with the effect of surface degradation of the solid deuterium moderator. [ABSTRACT FROM AUTHOR]

Purpose: Hematotoxicity is a common side-effect of cytotoxic gastrointestinal (GI) cancer therapies. An unsolved problem is to predict the individual risk therefore to decide on treatment adaptions. We applied an established biomathematical prediction model and primarily evaluated its predictive value in patients undergoing chemotherapy for GI cancers in curative intent. Methods: In a prospective, observational multicenter study on patients with gastro-esophageal or pancreatic cancer (n = 28) receiving myelosuppressive adjuvant or neoadjuvant chemotherapy (FLO(T) or FOLFIRINOX), individual model parameters were learned based on patients' observed laboratory values during the first chemotherapy cycle and further external data resources. Grades of hematotoxicity of subsequent cycles were predicted by model simulation and compared with observed data. Results: The most common high-grade hematological toxicity was neutropenia [19/28 patients (68%)]. For the FLO(T) regimen, individual grades of thrombocytopenia and leukopenia could be well predicted for cycles 2–4, as well as grades of neutropenia for cycle 2. Prediction accuracy for neutropenia in the third and fourth cycle differed by one toxicity grade on average. For the FOLFIRINOX-regimen, thrombocytopenia predictions showed a maximum deviation of one toxicity grade up to the end of therapy (8 cycles). Deviations of predictions were less than one degree on average up to cycle 4 for neutropenia, and up to cycle 6 for leukopenia. Conclusion: The biomathematical model showed excellent short-term and decent long-term prediction performance for all relevant hematological side effects associated with FLO(T)/FOLFIRINOX. Clinical utility of this precision-medicine approach needs to be further investigated in a larger cohort. [ABSTRACT FROM AUTHOR]

Background: Laparoscopic videos are increasingly being used for surgical artificial intelligence (AI) and big data analysis. The purpose of this study was to ensure data privacy in video recordings of laparoscopic surgery by censoring extraabdominal parts. An inside-outside-discrimination algorithm (IODA) was developed to ensure privacy protection while maximizing the remaining video data. Methods: IODAs neural network architecture was based on a pretrained AlexNet augmented with a long-short-term-memory. The data set for algorithm training and testing contained a total of 100 laparoscopic surgery videos of 23 different operations with a total video length of 207 h (124 min ± 100 min per video) resulting in 18,507,217 frames (185,965 ± 149,718 frames per video). Each video frame was tagged either as abdominal cavity, trocar, operation site, outside for cleaning, or translucent trocar. For algorithm testing, a stratified fivefold cross-validation was used. Results: The distribution of annotated classes were abdominal cavity 81.39%, trocar 1.39%, outside operation site 16.07%, outside for cleaning 1.08%, and translucent trocar 0.07%. Algorithm training on binary or all five classes showed similar excellent results for classifying outside frames with a mean F1-score of 0.96 ± 0.01 and 0.97 ± 0.01, sensitivity of 0.97 ± 0.02 and 0.0.97 ± 0.01, and a false positive rate of 0.99 ± 0.01 and 0.99 ± 0.01, respectively. Conclusion: IODA is able to discriminate between inside and outside with a high certainty. In particular, only a few outside frames are misclassified as inside and therefore at risk for privacy breach. The anonymized videos can be used for multi-centric development of surgical AI, quality management or educational purposes. In contrast to expensive commercial solutions, IODA is made open source and can be improved by the scientific community. [ABSTRACT FROM AUTHOR]

We present a case of mild radiation recall dermatitis triggered by cisplatin chemotherapy given simultaneously to re-irradiation. The dermatitis area correlated to skin exposure of the previous radiation therapy, characterizing the reaction clearly as a recall. Cisplatin has not yet been recognized as a potential trigger for recall reactions. Although it was part of several reported multidrug trigger combinations, all review works referred to cisplatin as not suspicious, suggesting the combination partner as the effector. We performed a focused systematic literature review aiming to re-evaluate the real role of cisplatin as a (co-)triggering factor. In total, 30 reported cases were found, 90% triggered by multidrug combinations. The latter tended to cause more severe symptoms. Besides findings supporting the 20 Gy-threshold theory, no correlation between radiation dose and severity or prevalence was found. Recognition of cisplatin as a trigger of the recall phenomenon and its supportive management may prevent unnecessary cessation of systemic chemotherapy. Systematic reporting of recall events as a secondary endpoint of prospective clinical trials applying radiation therapy could support understanding the recall phenomenon. [ABSTRACT FROM AUTHOR]

Background: Detection of circulating tumour DNA (ctDNA) in biological fluids is a minimally invasive alternative to tissue biopsy for therapy monitoring. Cytokines are released in the tumour microenvironment to influence inflammation and tumorigenic mechanisms. Here, we investigated the potential biomarker utility of circulating cytokines vis-à-vis ctDNA in ALK-rearranged+ lung adenocarcinoma (ALK + NSCLC) and explored the optimal combination of molecular parameters that could indicate disease progression. Methods: Longitudinal serum samples (n = 296) were collected from ALK + NSCLC patients (n = 38) under tyrosine kinase inhibitor (TKI) therapy and assayed to quantify eight cytokines: IFN-γ, IL-1β, IL-6, IL-8, IL-10, IL-12p70, MCP1 and TNF-α. Generalised linear mixed-effect modelling was performed to test the performance of different combinations of cytokines and previously determined ctDNA parameters in identifying progressive disease. Results: Serum IL-6, IL-8 and IL-10 were elevated at progressive disease, with IL-8 having the most significant impact as a biomarker. Integrating changes in IL-8 with ctDNA parameters maximised the performance of the classifiers in identifying disease progression, but this did not significantly outperform the model based on ctDNA alone. Conclusions: Serum cytokine levels are potential disease progression markers in ALK + NSCLC. Further validation in a larger and prospective cohort is necessary to determine whether the addition of cytokine evaluation could improve current tumour monitoring modalities in the clinical setting. [ABSTRACT FROM AUTHOR]

Background: Hyperglycaemia is common in critically ill patients, but blood glucose and insulin management may differ widely among intensive care units (ICUs). We aimed to describe insulin use practices and the resulting glycaemic control in French ICUs. We conducted a multicentre 1-day observational study on November 23, 2021, in 69 French ICUs. Adult patients hospitalized for an acute organ failure, severe infection or post-operative care were included. Data were recorded from midnight to 11:59 p.m. the day of the study by 4-h periods. Results: Two ICUs declared to have no insulin protocol. There was a wide disparity in blood glucose targets between ICUs with 35 different target ranges recorded. In 893 included patients we collected 4823 blood glucose values whose distribution varied significantly across ICUs (P < 0.0001). We observed 1135 hyperglycaemias (> 1.8 g/L) in 402 (45.0%) patients, 35 hypoglycaemias (≤ 0.7 g/L) in 26 (2.9%) patients, and one instance of severe hypoglycaemia (≤ 0.4 g/L). Four hundred eight (45.7%) patients received either IV insulin (255 [62.5%]), subcutaneous (SC) insulin (126 [30.9%]), or both (27 [6.6%]). Among patients under protocolized intravenous (IV) insulin, 767/1681 (45.6%) of glycaemias were above the target range. Among patients receiving insulin, short- and long-acting SC insulin use were associated with higher counts of hyperglycaemias as assessed by multivariable negative binomial regression adjusted for the propensity to receive SC insulin: incidence rate ratio of 3.45 (95% confidence interval [CI] 2.97–4.00) (P < 0.0001) and 3.58 (95% CI 2.84–4.52) (P < 0.0001), respectively. Conclusions: Practices regarding blood glucose management varied widely among French ICUs. Administration of short or long-acting SC insulin was not unusual and associated with more frequent hyperglycaemia. The protocolized insulin algorithms used failed to prevent hyperglycaemic events. [ABSTRACT FROM AUTHOR]

Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle. In this work, the authors report a system for production of short versions of a filamentous phage enables the structure to be determined by cryo-electron microscopy. Structure combined with mutagenesis allows the identification of phage domains that are important in bacterial attack and for release of new viral progeny. [ABSTRACT FROM AUTHOR]

Normothermic machine perfusion (NMP) has emerged as an innovative organ preservation technique. Developing an understanding for the donor organ immune cell composition and its dynamic changes during NMP is essential. We aimed for a comprehensive characterization of immune cell (sub)populations, cell trafficking and cytokine release during liver NMP. Single-cell transcriptome profiling of human donor livers prior to, during NMP and after transplantation shows an abundance of CXC chemokine receptor 1+/2+ (CXCR1+/CXCR2+) neutrophils, which significantly decreased during NMP. This is paralleled by a large efflux of passenger leukocytes with neutrophil predominance in the perfusate. During NMP, neutrophils shift from a pro-inflammatory state towards an aged/chronically activated/exhausted phenotype, while anti-inflammatory/tolerogenic monocytes/macrophages are increased. We herein describe the dynamics of the immune cell repertoire, phenotypic immune cell shifts and a dominance of neutrophils during liver NMP, which potentially contribute to the inflammatory response. Our findings may serve as resource to initiate future immune-interventional studies. Normothermic machine perfusion (NMP) is a method of keeping transplant organs maintained closer to physiological conditions. Here the authors analyse the immune cell dynamics during NMP in human donor livers using scRNA sequencing as a way of assessing the effects of NMP upon the immune status of the organ. [ABSTRACT FROM AUTHOR]

Objectives: Perioperative chemo-(radio-) therapy is the accepted standard in European patients with locally advanced adenocarcinoma of the esophagogastric junction or stomach (AEG/AS). However, 30–85% of patients do not respond to this treatment. The aim of our study was the identification of predictive biomarkers in pre-therapeutic endoscopic tumor biopsies from patients with histopathologic response (Becker-1) versus non-response (Becker-2/3) to preoperative chemotherapy. Methods: Formalin-fixed paraffin-embedded biopsies from 36 Caucasian patients (Becker-1 n = 11, Becker-2 n = 7, Becker-3 n = 18) with AEG/AS, taken prior to neoadjuvant chemotherapy were selected. For RNA expression analysis, we employed the NanoString nCounter System. To identify genomic alterations like single nucleotide variants (SNV), copy number variation (CNV) and fusion events, we used Illumina TST170 gene panel. For HER2 and FGFR2 protein expression, immunostaining was performed. Furthermore, we analyzed the microsatellite instability (MSI) and Epstein–Barr virus (EBV) infection status by EBER in situ hybridization. Results: Heat map and principal component analyses showed no clustering by means of gene expression according to regression grade. Concerning two recently proposed predictive markers, our data showed equal distribution for MSI (Becker-1: 2; Becker-2: 1; Becker-3: 3; out of 29 tested) and EBV infection was rare (1/32). We could not reveal discriminating target genes concerning SNV, but found a higher mutational burden in non-responders versus responders and fusion (in 6/14) and CNV events (in 5/14) exclusively in Becker-3. Conclusions: Although we could not identify discriminating target genes, our data suggest that molecular alterations are in general more prevalent in patients with AEG/AS belonging to the non-responding Becker group 3. [ABSTRACT FROM AUTHOR]

Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen. Zymoseptoria tritici is an important fungal pathogen of wheat which has spread globally. Here, the authors perform genomic analyses on a collection of ~1100 Z. tritici samples from 42 countries to describe its global spread and elucidate mechanisms of adaptation to different environmental conditions. [ABSTRACT FROM AUTHOR]

There is an urgent need for agri-food system transformation to achieve global sustainability goals. Innovations can play a key role in this transformation but often come with both sustainability synergies and trade-offs. One such innovation is agricultural mechanization, which is spreading rapidly in parts of the Global South and is high on the policy agenda in others. The rapid spread of mechanization is fundamentally changing the character of agri-food systems in the Global South, with both positive and negative effects. However, while some of these effects have been well explored, no study so far has systematically reviewed the sustainability synergies and trade-offs associated with mechanization, undermining necessary accompanying research and policy efforts. This review provides an overview of the progress toward mechanization across the Global South, identifies drivers and barriers, assesses sustainability synergies and trade-offs, and discusses options to maximize sustainability outcomes. The review is the first to holistically assess the potentials and risks of agricultural mechanization for the sustainable transformation of agri-food systems in the Global South, taking into account all pillars of sustainability. The review suggests that agricultural mechanization is needed to make agri-food systems more sustainable concerning various economic and social aspects, such as labor productivity, poverty reduction, food security, and health and well-being. However, there are also sustainability risks concerning environmental aspects such as biodiversity loss and land degradation, and economic and social concerns related to lacking inclusiveness and growing inequalities, among others. A wide range of technological and institutional solutions is identified to harness the potential of agricultural mechanization for sustainable agri-food system transformation, while at the same time minimizing the risks. However, more efforts are needed to implement such solutions at scale and ensure that mechanization contributes to agri-food systems that respect all pillars of sustainability. [ABSTRACT FROM AUTHOR]

A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation. Paspalum vaginatum is a stress tolerant wild relative of maize and sorghum. Here, the authors assemble its genome at pseudomolecule level and reveal the role of trehalose mediated autophagy in increasing maize biomass productivity under nutrient-deficit conditions. [ABSTRACT FROM AUTHOR]

Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament's flexibility. The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins. [ABSTRACT FROM AUTHOR]

Background: Personalized medicine requires the integration and analysis of vast amounts of patient data to realize individualized care. With Surgomics, we aim to facilitate personalized therapy recommendations in surgery by integration of intraoperative surgical data and their analysis with machine learning methods to leverage the potential of this data in analogy to Radiomics and Genomics. Methods: We defined Surgomics as the entirety of surgomic features that are process characteristics of a surgical procedure automatically derived from multimodal intraoperative data to quantify processes in the operating room. In a multidisciplinary team we discussed potential data sources like endoscopic videos, vital sign monitoring, medical devices and instruments and respective surgomic features. Subsequently, an online questionnaire was sent to experts from surgery and (computer) science at multiple centers for rating the features' clinical relevance and technical feasibility. Results: In total, 52 surgomic features were identified and assigned to eight feature categories. Based on the expert survey (n = 66 participants) the feature category with the highest clinical relevance as rated by surgeons was "surgical skill and quality of performance" for morbidity and mortality (9.0 ± 1.3 on a numerical rating scale from 1 to 10) as well as for long-term (oncological) outcome (8.2 ± 1.8). The feature category with the highest feasibility to be automatically extracted as rated by (computer) scientists was "Instrument" (8.5 ± 1.7). Among the surgomic features ranked as most relevant in their respective category were "intraoperative adverse events", "action performed with instruments", "vital sign monitoring", and "difficulty of surgery". Conclusion: Surgomics is a promising concept for the analysis of intraoperative data. Surgomics may be used together with preoperative features from clinical data and Radiomics to predict postoperative morbidity, mortality and long-term outcome, as well as to provide tailored feedback for surgeons. [ABSTRACT FROM AUTHOR]

Today, a vast number of tools exist to measure development in early childhood in a variety of domains such as cognition, language, or motor, cognition. These tools vary in different aspects. Either children are examined by a trained experimenter, or caregivers fill out questionnaires. The tools are applied in the controlled setting of a laboratory or in the children's natural environment. While these tools provide a detailed picture of the current state of children's development, they are at the same time subject to several constraints. Furthermore, the measurement of an individual child's change of different skills over time requires not only one measurement but high-density longitudinal assessments. These assessments are time-consuming, and the breadth of developmental domains assessed remains limited. In this paper, we present a novel tool to assess the development of skills in different domains, a smartphone-based developmental diary app (the kleineWeltentdecker App, henceforth referred to as the APP (The German expression "kleine Weltentdecker" can be translated as "young world explorers".)). By using the APP, caregivers can track changes in their children's skills during development. Here, we report the construction and validation of the questionnaires embedded in the APP as well as the technical details. Empirical validations with children of different age groups confirmed the robustness of the different measures implemented in the APP. In addition, we report preliminary findings, for example, on children's communicative development by using existing APP data. This substantiates the validity of the assessment. With the APP, we put a portable tool for the longitudinal documentation of individual children's development in every caregiver's pocket, worldwide. [ABSTRACT FROM AUTHOR]

Schizotypy constitutes a susceptibility to beneficial and deleterious schizotypal traits, ranging from coping mechanisms to schizotypal personality disorder on a psychosis continuum. Growing evidence indicates a relationship between childhood adversity and trauma and schizotypy. However, the exact influence of childhood adversity and trauma on schizotypy and its relation to sex is not sufficiently understood. Therefore, we investigated sex-adjusted connections between childhood adversity and trauma subdomains (emotional/physical/sexual abuse, emotional/physical neglect) and positive (magical ideation, perceptual aberration) as well as negative schizotypy (physical/social anhedonia). In total, 240 outpatients of the Early Detection and Intervention Centre of the University Hospital Cologne were assessed with the Trauma and Distress Scale for childhood adversity and trauma and the Wisconsin Schizotypy Scales for schizotypy. Path analyses were performed to investigate sex-adjusted correlations. The well-fitting path model of the total sample linked emotional abuse to magical ideation (p = 0.03; SE = 0.20) and emotional neglect to social anhedonia (p = 0.01; SE = 0.26). In females, physical abuse predicted magical ideation (p = 0.01; SE = 0.33), while emotional neglect forecasted physical anhedonia (p = 0.03; SE = 0.34) and social anhedonia (p = 0.03; SE = 0.32). In males, sexual abuse predicted perceptive aberration (p = 0.04; SE = 0.19) and emotional abuse forecasted magical ideation (p = 0.03; SE = 0.27). Overall, the significance of sex-specific interrelations between trauma and schizotypy were highlighted. Magical ideation and perceptive aberration occurred prominently in the absence of negative and disorganized schizotypy, thus positive schizotypy could be discussed as a beneficial expression of coping with emotional, physical and sexual abuse. Furthermore, emotional neglect should be addressed particularly to prevent deleterious negative schizotypy in females. Trial registration number (20-1243), date of registration (May 19th 2020), retrospectively registered. [ABSTRACT FROM AUTHOR]

Efficient neutron transport is a key ingredient to the performance of ultracold neutron (UCN) sources, important to meeting the challenges placed by high precision fundamental physics experiments. At the Paul Scherrer Institute's UCN source we have been continuously improving our understanding of the UCN source parameters by performing a series of studies to characterize neutron production and moderation, and UCN production, extraction, and transport efficiency to the beamport. The present study on the absolute UCN transport efficiency completes our previous publications. We report on complementary measurements, namely one on the height-dependent UCN density and a second on the transmission of a calibrated quantity of UCN over a ∼ 16 m long UCN guide section connecting one beamport via the source storage vessel to another beamport. These allow us quantifying and optimizing the performance of the guide system based on extensive Monte Carlo simulations. [ABSTRACT FROM AUTHOR]

In this paper, an electronic circuit based on Macek equations was developed in which the phenomenon of hyperchaos was observed. Synchronization of signals was applied using the technique optimal linear feedback control (OLFC) and embedded in digital signal processor (DSP), with the circuit with hyperchaotic behavior as a master system and a periodic slave system embedded in the DSP along with the applied control technique. Within the context presented, it was possible to carry out the synchronization in phase between the systems, i.e., taking the system with periodic behavior to hyperchaos. [ABSTRACT FROM AUTHOR]

The reported incidence of incisional hernia following repair of abdominal aortic aneurysm (AAA) via midline laparotomy is up to 69%. This prospective, multicenter, double-blind, randomised controlled trial was conducted at eleven hospitals in Germany. Patients aged 18 years or older undergoing elective AAA-repair via midline incision were randomly assigned using a computer-generated randomisation sequence to one of three groups for fascial closure: with long-term absorbable suture (MonoPlus®, group I), long-term absorbable suture and onlay mesh reinforcement (group II) or extra long-term absorbable suture (MonoMax®, group III). The primary endpoint was the incidence of incisional hernia within 24 months of follow-up, analysed by intention to treat. Physicians conducting the postoperative visits and the patients were blinded. Between February 2011 and July 2013, 104 patients (69.8 ± 7.7 years) were randomised, 99 of them received a study intervention. The rate of incisional hernia within 24 months was not significantly reduced with onlay mesh augmentation compared to primary suture (p = 0.290). Furthermore, the rate of incisional hernia did not differ significantly between fascial closure with slow and extra long-term absorbable suture (p = 0.111). Serious adverse events related to study intervention occurred in five patients (5.1%) from treatment groups II and III. Wound healing disorders were more frequently seen after onlay mesh implantation on the day of discharge (p = 0.010) and three (p = 0.009) and six (p = 0.023) months postoperatively. The existing evidence on prophylactic mesh augmentation in patients undergoing AAA-repair via midline laparotomy probably needs critical review. As the implementation of new RCTs is considered difficult due to the increasing number of endovascular AAA treated, registry studies could help to collect and evaluate data in cases of open AAA-repair. Comparisons between prophylactic mesh implantation and the small bite technique are also required. Trial registration: ClinicalTrials.gov Identifier: NCT01353443. Funding Sources: Aesculap AG, Tuttlingen, Germany. [ABSTRACT FROM AUTHOR]

Fanconi anemia (FA) is a multisystem disease, characterized by the triad of physical abnormalities, bone marrow failure, and increased risk for malignancy. In the past few years, data has accumulated regarding fertility issues in FA patients, mostly due to gonadal dysfunction, which is prevalent in FA patients reaching puberty. It seems that attenuated FA phenotype lacking the classical manifestations often is presented with POI or azoospermia. Searching the literature, we summarized data regarding FA patients presenting as suffering from sub/infertility due to gonadal dysfunction, with or without other FA symptoms. We present a summary of the patients having biallelic pathogenic variants in FA genes FANCA, FANCM, BRCA2, and XRCC2 that presented with gonadal dysfunction with or without other phenotypic features of FA. Some were in mosaic, while some are considered hypomorphic, enabling residual protein function. There are also a few descriptions of POI associated with monoallelic pathogenic variants in FANCA, BRCA2, and FANCL. We conclude that the diagnosis of FA in gonadal dysfunction patients is of utmost importance due to its actionability. Follow-up strategies in FA patients are designed to discover early stages of leukemias and solid tumors and thus save lives. The feasibility of next-generation sequencing (NGS) can now ease this diagnostic procedure. An open question is the justification of performing NGS for all isolated azoospermia/POI patients. [ABSTRACT FROM AUTHOR]

Background: A recently developed haemostatic peptide gel for endoscopic application has been introduced to improve the management of gastrointestinal bleeding. The aim of this pilot study was to evaluate the feasibility, safety, efficacy and indication profiles of PuraStat in a clinical setting. Methods: In this prospective observational multicentre pilot study, patients with acute non-variceal gastrointestinal bleeding (upper and lower) were included. Primary and secondary application of PuraStat was evaluated. Haemoglobin, prothrombin time, platelets and transfusion behaviour were documented before and after haemostasis. The efficacy of PuraStat was assessed during the procedure, at 3 days and 1 week after application. Results: 111 patients with acute gastrointestinal bleeding were recruited into the study. 70 percent (78/111) of the patients had upper gastrointestinal bleeding and 30% (33/111) had lower gastrointestinal bleeding. After primary application of PuraStat, initial haemostatic success was achieved in 94% of patients (74/79, 95% CI 88–99%), and in 75% of the patients when used as a secondary haemostatic product, following failure of established techniques (24/32, 95% CI 59–91%). The therapeutic success rates (absence of rebleeding) after 3 and 7 days were 91% and 87% after primary use, and 87% and 81% in all study patients. Overall rebleeding rate at 30 day follow-up was 16% (18/111). In the 5 patients who finally required surgery (4.5%), PuraStat allowed temporary haemostasis and stabilisation. Conclusions: PuraStat expanded the therapeutic toolbox available for an effective treatment of gastrointestinal bleeding sources. It could be safely applied and administered without complications as a primary or secondary therapy. PuraStat may additionally serve as a bridge to surgery in order to achieve temporary haemostasis in case of refractory severe bleeding, possibly playing a role in preventing immediate emergency surgery. [ABSTRACT FROM AUTHOR]

In the quest to reduce global under- and malnutrition, which are particularly high among smallholder farmers, agriculture-nutrition linkages are receiving increasing attention. Researchers have analyzed the link between the quantity and diversity of food that farmers produce and nutritional outcomes but paid limited attention to a third agriculture-nutrition link: the link between how food is produced and nutritional outcomes. This neglect persists despite the majority of smallholder farmers relying on hand tools for farming, which implies heavy physical work and, thus, high energy requirements. To address this research gap, this study compares the energy requirements of farm households in rural Zambia that are characterized by three different levels of mechanization: hand tools, animal drought power, and tractors. 1638 days of detailed time-use and nutrition data were collected from 186 male and female adults and boys and girls during different seasons (land preparation, weeding, and harvesting/processing) using an innovative picture-based smartphone app called "Timetracker". This data served to calculate different proxies for physical activity and energy requirements using "Ainsworth's Compendium of Physical Activities". The results suggest that detailed time-use data offers great potentials to study physical activity and energy requirements. The findings show strong linkages between farm technologies, physical activity levels, and energy requirements, suggesting that this agriculture-nutrition link deserves more scientific and political attention to reduce under- and malnutrition among smallholder farmers. [ABSTRACT FROM AUTHOR]

Purpose: Studying the legume nodule microbiome is important for understanding the development and nutrition of the plants inhabited by the various microbes within and upon them. We analyzed the microbiomes of these underground organs from both an important crop plant (Medicago sativa) and a related legume (M. polymorpha) using metagenomic and culture-based techniques to identify the main cultivatable contributors to plant growth enhancement. Methods: Using high-throughput sequencing, culturing, and in planta techniques, we identified and analyzed a broad population of the bacterial taxa within Medicago nodules and the surrounding soil. Results: Fifty-one distinct bacterial strains were isolated and characterized from nodules of both Medicago species and their growth-promoting activities were studied. Sequencing of 16S rRNA gene amplicons showed that in addition to Ensifer, the dominant genus, a large number of Gram-positive bacteria belonging to the Firmicutes and Actinobacteria were also present. After performing ecological and plant growth-promoting trait analyses, selecting the most promising strains, and then performing in planta assays, we found that strains of Bacillus and Micromonospora among others could play important roles in supporting the growth, health, and productivity of the host plant. Conclusion: To our knowledge, the comparison of the biodiversity of the microbiota of undomesticated vs. cultivated Medicago roots and nodules is novel and shows the range of potential Plant Growth-Promoting Bacteria that could be used for plants of agricultural interest. These and other nodule-isolated microbes could also serve as inoculants with rhizobia with the goal of replacing synthetic fertilizers and pesticides for sustainable agriculture. [ABSTRACT FROM AUTHOR]

High-density lipoprotein (HDL), best known for cholesterol transport, also has anti-inflammatory effects. Previous studies suggest involvement of myeloperoxidase (MPO) in modification of HDL. HDL bound Sphingosine-1-phosphate (S1P) has been implied to be an essential protein regarding beneficial HDL effects. In this study, we analyzed anti-inflammatory HDL properties in patients with atrial fibrillation (AF), a disease involving atrial inflammation, compared to non-AF controls and whether anti-inflammatory properties improve upon catheter ablation. Additionally, association with serum concentrations of MPO and S1P were assessed. We isolated HDL from 25 AF patients, 13 non-AF individuals and 14 AF patients at follow-up (FU) after catheter ablation. S1P was measured in a cohort of 141 AF and 21 FU patients. Following preincubation with HDL from either group, bovine aortic endothelial cells were stimulated using tumor necrosis factor α and expression of pro-inflammatory genes intercellular adhesion molecule 1 (ICAM1), vascular cell adhesion molecule 1 (VCAM1), E-selectin (SELE) and P-selectin (SELP) was assessed using qPCR. Concentrations of circulating protein of these genes as well as MPO and S1P were measured in serum samples. Compared to non-AF individuals HDL from AF patients suppressed gene expression of the pro-inflammatory adhesion molecules ICAM1, VCAM1, SELE and SELP 27%, 18%, 21% and 57% less, respectively (p < 0.05 for all except SELE p = 0.06). In FU patients, the anti-inflammatory HDL activity was improved (suppression of ICAM1 + 22%, VCAM1 + 10%, SELE + 38% and SELP + 75%, p < 0.05 for all except VCAM1 p = 0.08). AF patients using angiotensin converting enzyme inhibitors or angiotensin receptor blockers had better anti-inflammatory HDL properties than non-users (gene expression suppression at least 28% more, p < 0.05 for all except ICAM1 p = 0.051). Circulating protein concentrations were not correlated with in vitro gene-expression, but circulating P-selectin was generally elevated in AF and FU patients compared to non-AF patients. MPO plasma concentration was positively associated with gene-expression of ICAM1, VCAM1 and SELP (r2 > 0.4, p < 0.05). Serum concentrations of S1P were increased in FU patients {1.201 µM [1.077–1.543]} compared to AF patients {0.953 µM [0.807–1.135], p < 0.01} but not correlated with ICAM1, VCAM1 and SELP gene expression. We conclude that the anti-inflammatory activity of HDL is impaired in AF patients, which might promote AF progression and AF-associated complications. [ABSTRACT FROM AUTHOR]

In this paper, the dynamical behavior of a four-dimensional magnetohydrodynamic model, consisting of a generalized Lorenz model, is investigated. A nonlinear dynamical analysis is performed using Lyapunov exponents and bifurcation diagrams, focusing on the chaotic and hyperchaotic behaviors associated with the bifurcation parameter k 1 that couples the equations of fluid displacement to the induced magnetic field. The State-dependent Riccati Equation (SDRE) and the Optimal Linear Feedback Control (OLFC) techniques are considered to design the state feedback control system that stabilizes the system to a previously defined orbit. The performance of the control systems are compared showing that the OLFC presents better results. [ABSTRACT FROM AUTHOR]

Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts. Marc Van Goethem et al. combine short- and long-read sequencing from biocrust samples to report nearly 3,000 biosynthetic gene clusters (BGCs) encoding microbial secondary metabolites. Their results demonstrate the advantage of integrated metatranscriptomic and long-read metagenomic sequencing in analyzing BGCs and provides insight into the role of secondary metabolites in maintaining phylogenetic niches in biocrusts. [ABSTRACT FROM AUTHOR]

The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins. New virions of Ff bacteriophages are extruded from the host cell via the channel built from phage protein pIV, homologous to bacterial secretins. Here, the authors report the structure of this channel from the f1 filamentous bacteriophage and propose its use as an adjuvant to increase the uptake and efficacy of antibiotics. [ABSTRACT FROM AUTHOR]

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change. Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients. [ABSTRACT FROM AUTHOR]

Carcinoma showing thymus-like elements (CASTLE) is an extremely rare malignant tumor of the thyroid gland and soft tissues of the neck with favorable prognosis. Histological features of the CASTLE are similar to thymic carcinoma, and it is assumed that it arises from the ectopic thymic tissue or the remnants of branchial pouches. The optimal treatment strategy is still uncertain because of the rarity of the tumor. The mainstay of treatment is surgery. The role of other modalities is unclear. We present a case report of a patient with locally advanced CASTLE of the thyroid gland who was not suitable for surgery and underwent radical radiotherapy with subsequent achievement of complete remission. We also present a literature review. [ABSTRACT FROM AUTHOR]