Miracle-dz/UniFAR-FTUs huggingface dataset:
A Super-Condenser for Labelfree Nanoscopy

Labelfree nanoscopy encompasses optical imaging with resolution in the 100 nm range using visible wavelengths. Here, we present a labelfree nanoscopy method that combines Fourier ptychography with waveguide microscopy to realize a 'super-condenser' featuring maximally inclined coherent darkfield illumination with artificially stretched wave vectors due to large refractive indices of the employed Si$_3$N$_4$ waveguide material. We produce the required coherent plane wave illumination for Fourier ptychography over imaging areas 400 $\mathrm{\mu}$m$^2$ in size via adiabatically tapered single-mode waveguides and tackle the overlap constraints of the Fourier ptychography phase retrieval algorithm two-fold: firstly, the directionality of the illumination wave vector is changed sequentially via a multiplexed input structure of the waveguide chip layout and secondly, the wave vector modulus is shortend via step-wise increases of the illumination light wavelength over the visible spectrum. We validate the method via in silico and in vitro experiments and provide details on the underlying image formation theory as well as the reconstruction algorithm.
Mixed-mode Bytecode Execution

Modern high-performance virtual machines use dynamic compilation. There is a tension between compilation speed and code quality. We argue that a highly-optimizing compiler is best deployed with both a fast, less-optimizing compiler and an interpreter. We present measurements showing that such a system can achieve the same peak performance as a system with just the optimizing compiler, and startup costs similar to a system with just the interpreter and fast compiler.
A case–control study of risk factors for sporadic campylobacter infections in Denmark

A case control study comprising 282 cases and 319 matched controls was conducted in Denmark during 1996–7. Two estimates of the odds ratio (OR) were determined for each risk factor with and without ‘protective factors’ fitted into the final model. Consumption of undercooked poultry (OR 4·5; 8·2), consumption of red meat at a barbecue (OR 2·3; 4·1), consumption of grapes (OR 1·6; 2·8) and drinking unpasteurized milk (OR 2·3; 11·8) were identified as risk factors in both models. Frequent consumption of pork chops (OR 4·4) and daily contact with domestic animals and pets were identified as risk factors in one of the two models only. Finally, foreign travel was found to be a significant risk factor (OR 2·5). Seasonal and regional interaction was observed for several risk factors and the time elapsed from interviewing of cases to interviewing of controls seemed to influence the effect of certain seasonal dependent risk factors.
Tackling the wicked problem of health networks: the design of an evaluation framework

Networks are everywhere. Health systems and public health settings are experimenting with multifarious forms. Governments and providers are heavily investing in networks with an expectation that they will facilitate the delivery of better services and improve health outcomes. Yet, we lack a suitable conceptual framework to evaluate the effectiveness and sustainability of clinical and health networks. This paper aims to present such a framework to assist with rigorous research and policy analysis. The framework was designed as part of a project to evaluate the effectiveness and sustainability of health networks. We drew on systematic reviews of the literature on networks and communities of practice in health care, and on theoretical and evidence-based studies of the evaluation of health and non-health networks. Using brainstorming and mind-mapping techniques in expert advisory group sessions, we assessed existing network evaluation frameworks and considered their application to extant health networks. Feedback from stakeholders in network studies that we conducted was incorporated. The framework encompasses network goals, characteristics and relationships at member, network and community levels, and then looks at network outcomes, taking into account intervening variables. Finally, the short-term, medium-term and long-term effectiveness of the network needs to be assessed. The framework provides an overarching contribution to network evaluation. It is sufficiently comprehensive to account for many theoretical and evidence-based contributions to the literature on how networks operate and is sufficiently flexible to assess different kinds of health networks across their life-cycle at community, network and member levels. We outline the merits and limitations of the framework and discuss how it might be further tested.
Fabrication, optimization, and in vitro evaluation of docetaxel-loaded nanostructured lipid carriers for improved anticancer activity

Abstract Lung cancer is the leading cause of cancer-related deaths in both men and women worldwide. It is the leading cancer killer in both men and women in every Ethnic Group. A major problem associated with chemotherapies against their lung cancer is the lack of selective toxicity, which results in a narrow therapeutic index thereby compromising clinical prognosis. To circumvent these challenges, the present investigation sought to develop a docetaxel-loaded nanostructured lipid carrier system (DTX-NLCS) for the treatment of lung cancer. A 3-factor/3-level Box-Behnken Design was applied to systematically optimize the DTX-NLCS parameters. The amount of drug, emulsifier concentration, and homogenization speed was selected as independent variables, while the particle size and % entrapment efficiency (%EE) were selected as dependent variables. The optimized batch parameters were 29.81 mg drug, 19.97% w/w emulsifier, and 13 200 (rpm) speed of homogenization with a mean particle size of 154.1 ± 3.13 nm and a mean %EE of 86.12 ± 3.48%. The in vitro lipolysis experiments revealed that the optimized DTX-NLCs were stabilized by 10% w/w PEG 4000 mono-stearate and exhibited an anti-lipolytic effect. Furthermore, the in vitro gastrointestinal stability studies (at pH-1.2, pH-4.5, pH-6.8, and pH-7.4) revealed that the optimized developed system could withstand various GI tract media. The in vitro dissolution studies depicted a pH-independent controlled-release consistent with the Weibull model. In vitro cytotoxicity studies using NCI-H460 cell lines further revealed that there was a reduction in IC50 values in the DTX-NLCS treated cells as compared to those treated with the pure drug, indicating an improved efficiency for the developed system. Graphical Abstract
A Rank Revealing Factorization Using Arbitrary Norms

The classic rank-revealing QR factorization factorizes a matrix $A$ as $AP=QR$ where $P$ permutes the columns of $A$, $Q$ is an orthogonal matrix, and $R$ is upper triangular with non-increasing diagonal entries. This is called rank-revealing because careful choice of $P$ allows the user to truncate the factorization for a low-rank approximation of $A$ with an error term computed in the $l^2$ norm. In this paper I generalize the QR factorization to use any arbitrary norm and prove analogous properties for $Q$ and $R$ in this setting. I then show an application of this algorithm to compute low-rank approximations to $A$ with error term in the $l^1$ norm instead of the $l^2$ norm. I provide Python code for the $l^1$ case as demonstration of the idea.
Idiopathic Pelvic Girdle Pain as it Relates to the Sacroiliac Joint Hip Radiograph Findings in Patients Aged 40 Years and Under with Posterior Pelvic Pain

Background: Several sacroiliac joint (SIJ) provocative tests used to assess posterior pelvic pain involve moving and stressing the hip. It is unknown if there is a subgroup of patients with posterior pelvic pain who have underlying hip deformity that could potentially influence performance and interpretation of these tests. Objective: To describe the prevalence of radiographic hip deformity and hip osteoarthritis in a group of adults 40 years old and under who met the clinical diagnostic criteria for treatment of posterior pelvic pain with an image guided intra-articular SIJ injection. Design: Retrospective cohort study. Setting: Tertiary university orthopedic department Patients (or Participants):One hundred and forty-eight patients were evaluated (83% (123/148) female;mean age 31.3 6.2 years). All had completed a trial of comprehensive noninvasive treatment for posterior pelvic pain and had a minimum of three positive SIJ provocative tests on physical examination. Methods: Retrospective review identified patients undergoing SIJ injection for pain recommended and performed by seven physiatrists between 2011 and 2017. Hip radiographs were read by a physician with expertise in hip measurements with previously demonstrated excellent intrarater reliability. Main Outcome Measurements: Percentage of patients with hip deformity findings. Results: No patients meeting the inclusion criteria had significant radiographic hip osteoarthritis (Tonnis ≥2 indicating moderate or greater radiographic hip osteoarthritis) and 4/148 (3%) were found to have mild radiographic hip osteoarthritis. Prearthritic hip disorders were identified in 123 (83%, 95% CI: 76, 89%) patients. For those patients with prearthritic hip disorders, measurements consistent with femoroacetabular impingement (FAI) were seen in 61 (41%) patients, acetabular dysplasia in 49 (33%) patients, and acetabular retroversion in 85 (57%) patients. Acetabular retroversion was identified in 43% (crossover sign) and 39% (prominent ischial spine) of patients. Conclusions: Approximately 57% of adult patients under the age of 40 years with the clinical symptom complex of SIJ pain were found to have radiographic acetabular retroversion. This is a higher percentage than the 5%-15% found in asymptomatic people in the current literature. Further study is needed to assess links between hip structure, hip motion, and links to pelvic pain including peri and intra-articular SIJ pain. Level of Evidence: III
On the geometry of stability regions of Smith predictors subject to delay uncertainty

In this paper, we present a geometric method for describing the effects of the ‘delay-induced uncertainty’ on the stability of a standard Smith predictor control scheme. The method consists of deriving the ‘stability crossing curves’ in the parameter space defined by the ‘nominal delay’ and ‘delay uncertainty’, respectively. More precisely, we start by computing the ‘crossing set’, which consists of all frequencies corresponding to all points on the stability crossing curve, and next we give their ‘complete classification’, including also the explicit characterization of the ‘directions’ in which the zeros cross the imaginary axis. This approach complements existing algebraic stability tests, and it allows some new insights in the stability analysis of such control schemes. Several illustrative examples are also included.
Wrinkles, Folds, Creases, Buckles: Small-Scale Surface Deformations as Periodic Functions on 3D Meshes

We propose a method for adding small-scale details to surfaces of 3D geometries in the context of interactive deformation computation of elastic objects. This is relevant in real-time applications, for instance, in surgical simulation or interactive animation. The key idea is the procedural generation of surface details via a weighted sum of periodic functions, applied as an on-surface displacement field. We first calculate local deformation strains of a low-resolution 3D input mesh, which are then employed to estimate amplitudes, orientations, and positions of high-resolution details. The shapes and spatial frequencies of the periodic details are obtained from mechanical parameters, assuming the physical model of a film-substrate aggregate. Finally, our approach creates the highly-detailed output mesh fully on the GPU. The performance is independent of the spatial frequency of the inserted details as well as, within certain limits, of the resolution of the output mesh. We can reproduce numerous commonly observed, characteristic surface deformation patterns, such as wrinkles or buckles, allowing for the representation of a wide variety of simulated materials and interaction processes. We highlight the performance of our method with several examples.
“Glyco‐peakfinder” – de novo composition analysis of glycoconjugates

Mass spectrometric techniques are the key technology for rapid and reliable glycan analysis. However, the lack of robust, dependable, and freely available software for the (semi‐) automatic annotation of mass spectra is still a severe bottleneck that hampers their rapid interpretation. In this article the “Glyco‐Peakfinder” web‐service is described allowing de novo determination of glycan compositions from their mass signals. Starting from a basic set of mandatory masses of glycan components, the calculation can be performed without any knowledge concerning the biological background of the sample or the fragmentation technique used. “Glyco‐Peakfinder” assigns all types of fragment ions including monosaccharide cross‐ring cleavage products and multiply charged ions. It provides full user control to handle modified glycans (persubstituted molecules, reducing‐end modifications, glycoconjugates) and ion types. The formula applied to calculate the fragment masses and an outline of the implemented algorithm are discussed. A systematic evaluation of the dependence of all factors influencing the computation time revealed strikingly different impact of the individual calculation steps. To provide access to known carbohydrate structures a “composition search” in the open access database GLYCOSCIENCES.de can be performed. The service is available at the URL: www.eurocarbdb. org/applications/ms‐tools.
jViz.RNA 4.0—Visualizing pseudoknots and RNA editing employing compressed tree graphs

Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs. However, the new RNA representation and visualization method required a sophisticated mechanism of pseudoknot visualization. In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model. We then compare our approach with other RNA visualization software, and demonstrate jViz.RNA 4.0’s benefits compared to other software. Additionally, we introduce interactive editing functionality into jViz.RNA and demonstrate its benefits in exploring and building RNA structures. The results presented highlight the new high degree of utility jViz.RNA 4.0 now offers. Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined. Care was taken to limit overlap between structural elements, particularly in the case of pseudoknots to ensure an intuitive and informative layout of the final RNA structure. Availability: The software is freely available at: https://jviz.cs. sfu.ca/.
Comparison of severity of asthma hospitalization between African American and Hispanic children in the Bronx

Abstract Objective: There are racial and ethnic disparities in childhood asthma burden and outcomes. Although there have been comparisons between whites and minorities, there are few between minority groups. This study aimed to compare characteristics of asthma hospitalizations in African American and Hispanic children. Methods: A retrospective chart review was conducted to compare asthma characteristics between African American and Hispanic children aged 2–18 years hospitalized at an urban, tertiary care hospital for an acute asthma exacerbation. Length of stay (LOS), need for intensive care unit (ICU), and need for additional medications or respiratory support were compared between the groups. Results: Of the 925 children that met the inclusion criteria, 64% were Hispanic and 36% were African American. The groups were similar in age, gender, insurance status, and weight classification. African American children were more likely to have severe persistent asthma (12% vs. 7%, p = .02). They were also more likely to require magnesium sulfate (45% vs. 32%, p < .001) and admission to the ICU from the emergency department (ED) (14% vs. 8%, p = .01), which were independent of asthma severity. There was no significant difference in LOS or other characteristics of hospitalization. Conclusions: African American children hospitalized for asthma have more severe exacerbations compared to Hispanic children, which is independent of their asthma severity. However, this was not associated with longer LOS, which may indicate greater responsiveness to inpatient asthma management. Further investigation is needed to understand the mechanisms underlying asthma and exacerbation severity among minority groups.
Limiting Neuronal Nogo Receptor 1 Signaling during Experimental Autoimmune Encephalomyelitis Preserves Axonal Transport and Abrogates Inflammatory Demyelination

We previously identified that ngr1 allele deletion limits the severity of experimental autoimmune encephalomyelitis (EAE) by preserving axonal integrity. However, whether this favorable outcome observed in EAE is a consequence of an abrogated neuronal-specific pathophysiological mechanism, is yet to be defined. Here we show that, Cre-loxP-mediated neuron-specific deletion of ngr1 preserved axonal integrity, whereas its re-expression in ngr1−/− female mice potentiated EAE-axonopathy. As a corollary, myelin integrity was preserved under Cre deletion in ngr1flx/flx, retinal ganglion cell axons whereas, significant demyelination occurred in the ngr1−/− optic nerves following the re-introduction of NgR1. Moreover, Cre-loxP-mediated axon-specific deletion of ngr1 in ngr1flx/flx mice also demonstrated efficient anterograde transport of fluorescently-labeled ChTxβ in the optic nerves of EAE-induced mice. However, the anterograde transport of ChTxβ displayed accumulation in optic nerve degenerative axons of EAE-induced ngr1−/− mice, when NgR1 was reintroduced but was shown to be transported efficiently in the contralateral non- recombinant adeno-associated virus serotype 2-transduced optic nerves of these mutant mice. We further identified that the interaction between the axonal motor protein, Kinesin-1 and collapsin response mediator protein 2 (CRMP2) was unchanged upon Cre deletion of ngr1. Whereas, this Kinesin-1/CRMP2 association was reduced when NgR1 was re-expressed in the ngr1−/− optic nerves. Our data suggest that NgR1 governs axonal degeneration in the context of inflammatory-mediated demyelination through the phosphorylation of CRMP2 by stalling axonal vesicular transport. Moreover, axon-specific deletion of ngr1 preserves axonal transport mechanisms, blunting the induction of inflammatory demyelination and limiting the severity of EAE. SIGNIFICANCE STATEMENT Multiple sclerosis (MS) is commonly induced by aberrant immune-mediated destruction of the protective sheath of nerve fibers (known as myelin). However, it has been shown that MS lesions do not only consist of this disease pattern, exhibiting heterogeneity with continual destruction of axons. Here we investigate how neuronal NgR1 can drive inflammatory-mediated axonal degeneration and demyelination within the optic nerve by analyzing its downstream signaling events that govern axonal vesicular transport. We identify that abrogating the NgR1/pCRMP2 signaling cascade can maintain Kinesin-1-dependent anterograde axonal transport to limit inflammatory-mediated axonopathy and demyelination. The ability to differentiate between primary and secondary mechanisms of axonal degeneration may uncover therapeutic strategies to limit axonal damage and progressive MS.
Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed.
Preoperative Plasma Endoglin Levels Predict Biochemical Progression After Radical Prostatectomy

Purpose: Endoglin (CD105) is a transmembrane glycoprotein expressed by human vascular endothelial cells thought to play a pivotal role in endothelial cell proliferation. The aim of this study was to evaluate the association of preoperative plasma endoglin levels with established clinical and pathologic features of prostate cancer and disease progression after radical prostatectomy. Experimental Design: Preoperative plasma endoglin levels were measured in 425 patients who underwent radical prostatectomy for clinically localized prostate cancer using a commercially available ELISA assay. Multivariate logistic regression was used to test the association of plasma endoglin levels with biochemical progression after radical prostatectomy. Results: Median follow-up for patients alive at the time of analysis was 36.8 months (interquartile range, 44.1). Of 425 patients, 77 patients (18.1%) experienced biochemical progression after radical prostatectomy. Preoperative plasma endoglin levels were significantly elevated in patients with higher preoperative total serum prostate-specific antigen (P < 0.001) and adverse pathologic features. Preoperative plasma endoglin was an independent predictor of biochemical progression after surgery after adjusting for the effects of standard preoperative and postoperative features (P < 0.001 and P = 0.026, respectively). Conclusions: Preoperative plasma endoglin levels are associated with established features of advanced prostate cancer. More importantly, higher preoperative plasma endoglin levels are independent predictors of an increased risk of biochemical progression in patients treated with radical prostatectomy and bilateral pelvic lymphadenectomy.