Cancellation of lateral displacement noise of 3-port gratings for coupling light to cavities

Reflection gratings enable light coupling to optical cavities without transmission through substrates. Gratings that have three ports and are mounted in second-order Littrow configuration even allow the coupling to high-finesse cavities using low diffraction efficiencies. In contrast to conventional transmissive cavity couplers, however, the phase of the diffracted light depends on the lateral position of the grating, which introduces an additional noise coupling. Here we experimentally demonstrate that this kind of noise cancels out once both diffracted output ports of the grating are combined. We achieve the same signal-to-shot-noise ratio as for a conventional coupler. From this perspective, 3-port grating couplers in second-order Littrow configuration remain a valuable approach to reducing optical absorption of cavity coupler substrates in future gravitational wave detectors

A single-molecule method for measuring fluorophore labeling yields for the study of membrane protein oligomerization in membranes

Membrane proteins are often observed as higher-order oligomers, and in some cases in multiple stoichiometric forms, raising the question of whether dynamic oligomerization can be linked to modulation of function. To better understand this potential regulatory mechanism, there is an ongoing effort to quantify equilibrium reactions of membrane protein oligomerization directly in membranes. Single-molecule photobleaching analysis is particularly useful for this as it provides a binary readout of fluorophores attached to protein subunits at dilute conditions. However, any quantification of stoichiometry also critically requires knowing the probability that a subunit is fluorescently labeled. Since labeling uncertainty is often unavoidable, we developed an approach to estimate labeling yields using the photobleaching probability distribution of an intrinsic dimeric control. By iterative fitting of an experimental dimeric photobleaching probability distribution to an expected dimer model, we estimate the fluorophore labeling yields and find agreement with direct measurements of labeling of the purified protein by UV-VIS absorbance before reconstitution. Using this labeling prediction, similar estimation methods are applied to determine the dissociation constant of reactive CLC-ec1 dimerization constructs without prior knowledge of the fluorophore labeling yield. Finally, we estimate the operational range of subunit labeling yields that allows for discrimination of monomer and dimer populations across the reactive range of mole fraction densities. Thus, our study maps out a practical method for quantifying fluorophore labeling directly from single-molecule photobleaching data, improving the ability to quantify reactive membrane protein stoichiometry in membranes

DDR2 controls breast tumor stiffness and metastasis by regulating integrin mediated mechanotransduction in CAFs

Biomechanical changes in the tumor microenvironment influence tumor progression and metastases. Collagen content and fiber organization within the tumor stroma are major contributors to biomechanical changes (e., tumor stiffness) and correlated with tumor aggressiveness and outcome. What signals and in what cells control collagen organization within the tumors, and how, is not fully understood. We show in mouse breast tumors that the action of the collagen receptor DDR2 in CAFs controls tumor stiffness by reorganizing collagen fibers specifically at the tumor-stromal boundary. These changes were associated with lung metastases. The action of DDR2 in mouse and human CAFs, and tumors in vivo, was found to influence mechanotransduction by controlling full collagen-binding integrin activation via Rap1-mediated Talin1 and Kindlin2 recruitment. The action of DDR2 in tumor CAFs is thus critical for remodeling collagen fibers at the tumor-stromal boundary to generate a physically permissive tumor microenvironment for tumor cell invasion and metastases

Comparing estimates of child mortality reduction modelled in LiST with pregnancy history survey data for a community-based NGO project in Mozambique

<p>Abstract</p> <p>Background</p> <p>There is a growing body of evidence that integrated packages of community-based interventions, a form of programming often implemented by NGOs, can have substantial child mortality impact. More countries may be able to meet Millennium Development Goal (MDG) 4 targets by leveraging such programming. Analysis of the mortality effect of this type of programming is hampered by the cost and complexity of direct mortality measurement. The Lives Saved Tool (LiST) produces an estimate of mortality reduction by modelling the mortality effect of changes in population coverage of individual child health interventions. However, few studies to date have compared the LiST estimates of mortality reduction with those produced by direct measurement.</p> <p>Methods</p> <p>Using results of a recent review of evidence for community-based child health programming, a search was conducted for NGO child health projects implementing community-based interventions that had independently verified child mortality reduction estimates, as well as population coverage data for modelling in LiST. One child survival project fit inclusion criteria. Subsequent searches of the USAID Development Experience Clearinghouse and Child Survival Grants databases and interviews of staff from NGOs identified no additional projects. Eight coverage indicators, covering all the project’s technical interventions were modelled in LiST, along with indicator values for most other non-project interventions in LiST, mainly from DHS data from 1997 and 2003.</p> <p>Results</p> <p>The project studied was implemented by World Relief from 1999 to 2003 in Gaza Province, Mozambique. An independent evaluation collecting pregnancy history data estimated that under-five mortality declined 37% and infant mortality 48%. Using project-collected coverage data, LiST produced estimates of 39% and 34% decline, respectively.</p> <p>Conclusions</p> <p>LiST gives reasonably accurate estimates of infant and child mortality decline in an area where a package of community-based interventions was implemented. This and other validation exercises support use of LiST as an aid for program planning to tailor packages of community-based interventions to the epidemiological context and for project evaluation. Such targeted planning and assessments will be useful to accelerate progress in reaching MDG4 targets.</p

Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction

<p>Abstract</p> <p>Background</p> <p>The hepatocyte growth factor (HGF) stimulates mitogenesis, motogenesis, and morphogenesis in a wide range of tissues, including epithelial cells, on binding to the receptor tyrosine kinase c-Met. Abnormal c-Met signalling contributes to tumour genesis, in particular to the development of invasive and metastatic phenotypes. The human microbial pathogen <it>Helicobacter pylori </it>can induce chronic gastritis, peptic ulceration and more rarely, gastric adenocarcinoma. The <it>H. pylori </it>effector protein cytotoxin associated gene A (CagA), which is translocated via a type IV secretion system (T4SS) into epithelial cells, intracellularly modulates the c-Met receptor and promotes cellular processes leading to cell scattering, which could contribute to the invasiveness of tumour cells. Using a logical modelling framework, the presented work aims at analysing the c-Met signal transduction network and how it is interfered by <it>H. pylori </it>infection, which might be of importance for tumour development.</p> <p>Results</p> <p>A logical model of HGF and <it>H. pylori </it>induced c-Met signal transduction is presented in this work. The formalism of logical interaction hypergraphs (LIH) was used to construct the network model. The molecular interactions included in the model were all assembled manually based on a careful meta-analysis of published experimental results. Our model reveals the differences and commonalities of the response of the network upon HGF and <it>H. pylori </it>induced c-Met signalling. As another important result, using the formalism of minimal intervention sets, phospholipase Cγ1 (PLCγ1) was identified as knockout target for repressing the activation of the extracellular signal regulated kinase 1/2 (ERK1/2), a signalling molecule directly linked to cell scattering in <it>H. pylori </it>infected cells. The model predicted only an effect on ERK1/2 for the <it>H. pylori </it>stimulus, but not for HGF treatment. This result could be confirmed experimentally in MDCK cells using a specific pharmacological inhibitor against PLCγ1. The <it>in silico </it>predictions for the knockout of two other network components were also verified experimentally.</p> <p>Conclusion</p> <p>This work represents one of the first approaches in the direction of host-pathogen systems biology aiming at deciphering signalling changes brought about by pathogenic bacteria. The suitability of our network model is demonstrated by an <it>in silico </it>prediction of a relevant target against pathogen infection.</p

Diagnostic Performance of Ultrasonography-Based Risk Models in Differentiating Between Benign and Malignant Ovarian Tumors in a US Cohort

Importance: Ultrasonography-based risk models can help nonexpert clinicians evaluate adnexal lesions and reduce surgical interventions for benign tumors. Yet, these models have limited uptake in the US, and studies comparing their diagnostic accuracy are lacking. Objective: To evaluate, in a US cohort, the diagnostic performance of 3 ultrasonography-based risk models for differentiating between benign and malignant adnexal lesions: International Ovarian Tumor Analysis (IOTA) Simple Rules with inconclusive cases reclassified as malignant or reevaluated by an expert, IOTA Assessment of Different Neoplasias in the Adnexa (ADNEX), and Ovarian-Adnexal Reporting and Data System (O-RADS). Design, setting, and participants: This retrospective diagnostic study was conducted at a single US academic medical center and included consecutive patients aged 18 to 89 years with adnexal masses that were managed surgically or conservatively between January 2017 and October 2022. Exposure: Evaluation of adnexal lesions using the Simple Rules, ADNEX, and O-RADS. Main outcomes and measures: The main outcome was diagnostic performance, including area under the receiver operating characteristic (ROC) curve (AUC), sensitivity, specificity, positive and negative predictive values, and positive and negative likelihood ratios. Surgery or follow-up were reference standards. Secondary analyses evaluated the models' performances stratified by menopause status and race. Results: The cohort included 511 female patients with a 15.9% malignant tumor prevalence (81 patients). Mean (SD) ages of patients with benign and malignant adnexal lesions were 44.1 (14.4) and 52.5 (15.2) years, respectively, and 200 (39.1%) were postmenopausal. In the ROC analysis, the AUCs for discriminative performance of the ADNEX and O-RADS models were 0.96 (95% CI, 0.93-0.98) and 0.92 (95% CI, 0.90-0.95), respectively. After converting the ADNEX continuous individualized risk into the discrete ordinal categories of O-RADS, the ADNEX performance was reduced to an AUC of 0.93 (95% CI, 0.90-0.96), which was similar to that for O-RADS. The Simple Rules combined with expert reevaluation had 93.8% sensitivity (95% CI, 86.2%-98.0%) and 91.9% specificity (95% CI, 88.9%-94.3%), and the Simple Rules combined with malignant classification had 93.8% sensitivity (95% CI, 86.2%-98.0%) and 88.1% specificity (95% CI, 84.7%-91.0%). At a 10% risk threshold, ADNEX had 91.4% sensitivity (95% CI, 83.0%-96.5%) and 86.3% specificity (95% CI, 82.7%-89.4%) and O-RADS had 98.8% sensitivity (95% CI, 93.3%-100%) and 74.4% specificity (95% CI, 70.0%-78.5%). The specificities of all models were significantly lower in the postmenopausal group. Subgroup analysis revealed high performances independent of race. Conclusions and relevance: In this diagnostic study of a US cohort, the Simple Rules, ADNEX, and O-RADS models performed well in differentiating between benign and malignant adnexal lesions; this outcome has been previously reported primarily in European populations. Risk stratification models can lead to more accurate and consistent evaluations of adnexal masses, especially when used by nonexpert clinicians, and may reduce unnecessary surgeries.</p

Scaling up contrast-enhanced micro-CT imaging:Optimizing contrast and acquisition for large ex-vivo human samples

Microfocus Computed Tomography (Micro-CT) is a novel method for non-destructive 3D imaging of samples, reaching microscale resolutions. While initially prominent in material sciences for small samples, micro-CT now gains significance in biological and medical studies. Here we present our utilization of micro-CT for imaging large ex-vivo human samples for anatomical and forensic research in three recent experiments and discuss the fundamentals of micro-CT imaging. For pelvic anatomical research, whole human pelvises were imaged to explore nerve anatomy around the prostate using various concentrations of buffered lugol (B-lugol). Advanced acquisition protocols were essential due to X-ray attenuation properties of the sample, which required higher energy for sufficient photon transmission. For fetal research, B-lugol stained fetuses of 20–24 gestational weeks underwent full body imaging. However, this led to challenging acquisition parameters and images of insufficient quality. Subsequent destaining yielded less dense, yet contrast-maintaining samples allowing higher quality images. Refined acquisition protocols with reduced energy improved image quality. For forensic research, explanted hyoid-larynx complexes were imaged. Micro-CT imaging showed potential in visualizing micro-fractures. The addition of B-lugol allowed for excellent soft tissue contrast and promising possibilities for forensic evaluation. In conclusion, micro-CT imaging accommodates a diversity of large ex-vivo human samples for anatomical and forensic purposes, though challenges arise with optimal soft tissue staining and acquisition protocols. We describe partial destaining as a new possibility to alleviate scanning issues to improve scan quality and highlight topics for future research. Micro-CT imaging is a promising new avenue for medical research and forensic evaluation.</p