Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic emphysema detection using weakly labeled HRCT lung images

Purpose A method for automatically quantifying emphysema regions using High-Resolution Computed Tomography (HRCT) scans of patients with chronic obstructive pulmonary disease (COPD) that does not require manually annotated scans for training is presented. Methods HRCT scans of controls and of COPD patients with diverse disease severity are acquired at two different centers. Textural features from co-occurrence matrices and Gaussian filter banks are used to characterize the lung parenchyma in the scans. Two robust versions of multiple instance learning (MIL) classifiers that can handle weakly labeled data, miSVM and MILES, are investigated. Weak labels give information relative to the emphysema without indicating the location of the lesions. The classifiers are trained with the weak labels extracted from the forced expiratory volume in one minute (FEV1) and diffusing capacity of the lungs for carbon monoxide (DLCO). At test time, the classifiers output a patient label indicating overall COPD diagnosis and local labels indicating the presence of emphysema. The classifier performance is compared with manual annotations made by two radiologists, a classical density based method, and pulmonary function tests (PFTs). Results The miSVM classifier performed better than MILES on both patient and emphysema classification. The classifier has a stronger correlation with PFT than the density based method, the percentage of emphysema in the intersection of annotations from both radiologists, and the percentage of emphysema annotated by one of the radiologists. The correlation between the classifier and the PFT is only outperformed by the second radiologist. Conclusions The presented method uses MIL classifiers to automatically identify emphysema regions in HRCT scans. Furthermore, this approach has been demonstrated to correlate better with DLCO than a classical density based method or a radiologist, which is known to be affected in emphysema. Therefore, it is relevant to facilitate assessment of emphysema and to reduce inter-observer variability.
The Lantibiotic NAI-107 Efficiently Rescues Drosophila melanogaster from Infection with Methicillin-Resistant Staphylococcus aureus USA300

ABSTRACT We used the fruit fly Drosophila melanogaster as a cost-effective in vivo model to evaluate the efficacy of novel antibacterial peptides and peptoids for treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections. A panel of peptides with known antibacterial activity in vitro and/or in vivo was tested in Drosophila. Although most peptides and peptoids that were effective in vitro failed to rescue lethal effects of S. aureus infections in vivo, we found that two lantibiotics, nisin and NAI-107, rescued adult flies from fatal infections. Furthermore, NAI-107 rescued mortality of infection with the MRSA strain USA300 with an efficacy equivalent to that of vancomycin, a widely applied antibiotic for the treatment of serious MRSA infections. These results establish Drosophila as a useful model for in vivo drug evaluation of antibacterial peptides.
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. With the help of sliders, SlideBase enables users to define custom expression thresholds for individual cell types/tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS. Database URL: http://slidebase.binf. ku.dk
The TacTip Family: Soft Optical Tactile Sensors with 3D-Printed Biomimetic Morphologies

Abstract Tactile sensing is an essential component in human–robot interaction and object manipulation. Soft sensors allow for safe interaction and improved gripping performance. Here we present the TacTip family of sensors: a range of soft optical tactile sensors with various morphologies fabricated through dual-material 3D printing. All of these sensors are inspired by the same biomimetic design principle: transducing deformation of the sensing surface via movement of pins analogous to the function of intermediate ridges within the human fingertip. The performance of the TacTip, TacTip-GR2, TacTip-M2, and TacCylinder sensors is here evaluated and shown to attain submillimeter accuracy on a rolling cylinder task, representing greater than 10-fold super-resolved acuity. A version of the TacTip sensor has also been open-sourced, enabling other laboratories to adopt it as a platform for tactile sensing and manipulation research. These sensors are suitable for real-world applications in tactile perception, exploration, and manipulation, and will enable further research and innovation in the field of soft tactile sensing.
Let’s Not Waste Time: Using Temporal Information in Clustered Activity Estimation with Spatial Adjacency Restrictions (CAESAR) for Parcellating FMRI Data

We have proposed a Bayesian approach for functional parcellation of whole-brain FMRI measurements which we call Clustered Activity Estimation with Spatial Adjacency Restrictions (CAESAR). We use distance-dependent Chinese restaurant processes (dd-CRPs) to define a flexible prior which partitions the voxel measurements into clusters whose number and shapes are unknown a priori. With dd-CRPs we can conveniently implement spatial constraints to ensure that our parcellations remain spatially contiguous and thereby physiologically meaningful. In the present work, we extend CAESAR by using Gaussian process (GP) priors to model the temporally smooth haemodynamic signals that give rise to the measured FMRI data. A challenge for GP inference in our setting is the cubic scaling with respect to the number of time points, which can become computationally prohibitive with FMRI measurements, potentially consisting of long time series. As a solution we describe an efficient implementation that is practically as fast as the corresponding time-independent non-GP model with typically-sized FMRI data sets. We also employ a population Monte-Carlo algorithm that can significantly speed up convergence compared to traditional single-chain methods. First we illustrate the benefits of CAESAR and the GP priors with simulated experiments. Next, we demonstrate our approach by parcellating resting state FMRI data measured from twenty participants as taken from the Human Connectome Project data repository. Results show that CAESAR affords highly robust and scalable whole-brain clustering of FMRI timecourses.
Recombinant erythropoietin acutely decreases renal perfusion and decouples the renin‐angiotensin‐aldosterone system

The effect of recombinant erythropoietin (rhEPO) on renal and systemic hemodynamics was evaluated in a randomized double‐blinded, cross‐over study. Sixteen healthy subjects were tested with placebo, or low‐dose rhEPO for 2 weeks, or high‐dose rhEPO for 3 days. Subjects refrained from excessive salt intake, according to instructions from a dietitian. Renal clearance studies were done for measurements of renal plasma flow, glomerular filtration rate (GFR) and the segmentel tubular handling of sodium and water (lithium clearance). rhEPO increased arterial blood pressure, total peripheral resistance, and renal vascular resistance, and decreased renal plasma flow in the high‐dose rhEPO intervention and tended to decrease GFR. In spite of the decrease in renal perfusion, rhEPO tended to decrease reabsorption of sodium and water in the proximal tubule and induced a prompt decrease in circulating levels of renin and aldosterone, independent of changes in red blood cell mass, blood volumes, and blood pressure. We also found changes in biomarkers showing evidence that rhEPO induced a prothrombotic state. Our results suggest that rhEPO causes a direct downregulation in proximal tubular reabsorption that seems to decouple the activity of the renin‐angiotensin‐aldosterone system from changes in renal hemodynamics. This may serve as a negative feed‐back mechanism on endogenous synthesis of EPO when circulating levels of EPO are high. These results demonstrates for the first time in humans a direct effect of rhEPO on renal hemodynamics and a decoupling of the renin‐angiotensin‐aldosterone system.
Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies

Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.
Thermodynamics and Kinetics of Guest-Induced Switching between “Basket Handle” Porphyrin Isomers

The synthesis and switching properties of two “basket handle” porphyrin isomers is described. The cis-oriented meso-phenyl groups of these porphyrins are linked at their ortho-positons via benzocrown-ether-based spacers, which as a result of slow atropisomerization are located either on the same side of the porphyrin plane (cis), or on opposite sides (trans). In solution, the cis-linked isomer slowly isomerizes in the direction of the thermodynamically more stable trans-isomer. In the presence of viologen (N,N'-dialkyl-4,4'-bipyridinium) derivatives, which have different affinities for the two isomers, the isomerization equilibrium could be significantly influenced. In addition, the presence of these guests was found to enhance the rate of the switching process, which was suggested to be caused by favorable interactions between the positively charged guest and the crown ethers of the receptor, stabilizing the transition state energies of the isomerization reaction between the two isomers.
Evaluation of nurses’ changing perceptions when trained to implement a self-management programme for dual sensory impaired older adults in long-term care: a qualitative study

Objectives To gain insights into the process of nurses’ changing perceptions when trained to implement a self-management programme for dual sensory impaired older adults in long-term care, and into the factors that contributed to these changes in their perceptions. Design Qualitative study alongside a cluster randomised controlled trial. Setting 17 long-term care homes spread across the Netherlands. Participants 34 licensed practical nurses supporting 54 dual sensory impaired older adults. Intervention A 5-month training programme designed to enable nurses to support the self-management of dual sensory impaired older adults in long-term care. Primary outcomes Nurses’ perceptions on relevance and feasibility of the self-management programme collected from nurses’ semistructured coaching diaries over the 5-month training and intervention period, as well as from trainers’ reports. Results Nurses’ initial negative perceptions on relevance and feasibility of the intervention changed to positive as nurses better understood the concept of autonomy. Through interactions with older adults and by self-evaluations of the effect of their behaviour, nurses discovered that their usual care conflicted with client autonomy. From that moment, nurses felt encouraged to adapt their behaviour to the older adults’ autonomy needs. However, nurses’ initial unfamiliarity with conversation techniques required a longer exploration period than planned. Once client autonomy was understood, nurses recommended expanding the intervention as a generic approach to all their clients, whether dual sensory impaired or not. Conclusions Longitudinal data collection enabled exploration of nurses’ changes in perceptions when moving towards self-management support. The training programme stimulated nurses to go beyond ‘protocol thinking’, discovering client autonomy and exploring the need for their own behavioural adaptations. Educational programmes for practical nurses should offer more longitudinal coaching of autonomy supportive conversational skills. Intervention programming should acknowledge that change is a process rather than an event, and should include self-evaluations of professional behaviours over a period of time. Trial registration number NCT01217502, Post-results.
A multi-chamber microfluidic intestinal barrier model using Caco-2 cells for drug transport studies

This paper presents the design and fabrication of a multi-layer and multi-chamber microchip system using thiol-ene ‘click chemistry’ aimed for drug transport studies across tissue barrier models. The fabrication process enables rapid prototyping of multi-layer microfluidic chips using different thiol-ene polymer mixtures, where porous Teflon membranes for cell monolayer growth were incorporated by masked sandwiching thiol-ene-based fluid layers. Electrodes for trans-epithelial electrical resistance (TEER) measurements were incorporated using low-melting soldering wires in combination with platinum wires, enabling parallel real-time monitoring of barrier integrity for the eight chambers. Additionally, the translucent porous Teflon membrane enabled optical monitoring of cell monolayers. The device was developed and tested with the Caco-2 intestinal model, and compared to the conventional Transwell system. Cell monolayer differentiation was assessed via in situ immunocytochemistry of tight junction and mucus proteins, P-glycoprotein 1 (P-gp) mediated efflux of Rhodamine 123, and brush border aminopeptidase activity. Monolayer tightness and relevance for drug delivery research was evaluated through permeability studies of mannitol, dextran and insulin, alone or in combination with the absorption enhancer tetradecylmaltoside (TDM). The thiol-ene-based microchip material and electrodes were highly compatible with cell growth. In fact, Caco-2 cells cultured in the device displayed differentiation, mucus production, directional transport and aminopeptidase activity within 9–10 days of cell culture, indicating robust barrier formation at a faster rate than in conventional Transwell models. The cell monolayer displayed high TEER and tightness towards hydrophilic compounds, whereas co-administration of an absorption enhancer elicited TEER-decrease and increased permeability similar to the Transwell cultures. The presented cell barrier microdevice constitutes a relevant tissue barrier model, enabling transport studies of drugs and chemicals under real-time optical and functional monitoring in eight parallel chambers, thereby increasing the throughput compared to previously reported microdevices.
Novel role for endogenous mitochondrial formylated peptide-driven formyl peptide receptor 1 signalling in acute respiratory distress syndrome

Background Acute respiratory distress syndrome (ARDS) is an often fatal neutrophil-dominant lung disease. Although influenced by multiple proinflammatory mediators, identification of suitable therapeutic candidates remains elusive. We aimed to delineate the presence of mitochondrial formylated peptides in ARDS and characterise the functional importance of formyl peptide receptor 1 (FPR1) signalling in sterile lung inflammation. Methods Mitochondrial formylated peptides were identified in bronchoalveolar lavage fluid (BALF) and serum of patients with ARDS by liquid chromatography–tandem mass spectrometry. In vitro, human neutrophils were stimulated with mitochondrial formylated peptides and their effects assessed by flow cytometry and chemotaxis assay. Mouse lung injury was induced by mitochondrial formylated peptides or hydrochloric acid. Bone marrow chimeras determined the contribution of myeloid and parenchymal FPR1 to sterile lung inflammation. Results Mitochondrial formylated peptides were elevated in BALF and serum from patients with ARDS. These peptides drove neutrophil activation and chemotaxis through FPR1-dependent mechanisms in vitro and in vivo. In mouse lung injury, inflammation was attenuated in Fpr1−/− mice, effects recapitulated by a pharmacological FPR1 antagonist even when administered after the onset of injury. FPR1 expression was present in alveolar epithelium and chimeric mice demonstrated that both myeloid and parenchymal FPR1 contributed to lung inflammation. Conclusions We provide the first definitive evidence of mitochondrial formylated peptides in human disease and demonstrate them to be elevated in ARDS and important in a mouse model of lung injury. This work reveals mitochondrial formylated peptide FPR1 signalling as a key driver of sterile acute lung injury and a potential therapeutic target in ARDS.
Conveying facial expressions to blind and visually impaired persons through a wearable vibrotactile device

In face-to-face social interactions, blind and visually impaired persons (VIPs) lack access to nonverbal cues like facial expressions, body posture, and gestures, which may lead to impaired interpersonal communication. In this study, a wearable sensory substitution device (SSD) consisting of a head mounted camera and a haptic belt was evaluated to determine whether vibrotactile cues around the waist could be used to convey facial expressions to users and whether such a device is desired by VIPs for use in daily living situations. Ten VIPs (mean age: 38.8, SD: 14.4) and 10 sighted persons (SPs) (mean age: 44.5, SD: 19.6) participated in the study, in which validated sets of pictures, silent videos, and videos with audio of facial expressions were presented to the participant. A control measurement was first performed to determine how accurately participants could identify facial expressions while relying on their functional senses. After a short training, participants were asked to determine facial expressions while wearing the emotion feedback system. VIPs using the device showed significant improvements in their ability to determine which facial expressions were shown. A significant increase in accuracy of 44.4% was found across all types of stimuli when comparing the scores of the control (mean±SEM: 35.0±2.5%) and supported (mean±SEM: 79.4±2.1%) phases. The greatest improvements achieved with the support of the SSD were found for silent stimuli (68.3% for pictures and 50.8% for silent videos). SPs also showed consistent, though not statistically significant, improvements while supported. Overall, our study shows that vibrotactile cues are well suited to convey facial expressions to VIPs in real-time. Participants became skilled with the device after a short training session. Further testing and development of the SSD is required to improve its accuracy and aesthetics for potential daily use.
Polymorphisms in the GNAS Gene as Predictors of Ventricular Tachyarrhythmias and Sudden Cardiac Death: Results From the DISCOVERY Trial and Oregon Sudden Unexpected Death Study

Background Population‐based studies suggest that genetic factors contribute to sudden cardiac death (SCD). Methods and Results In the first part of the present study (Diagnostic Data Influence on Disease Management and Relation of Genetic Polymorphisms to Ventricular Tachy‐arrhythmia in ICD Patients [DISCOVERY] trial) Cox regression was done to determine if 7 single‐nucleotide polymorphisms (SNPs) in 3 genes coding G‐protein subunits (GNB3, GNAQ, GNAS) were associated with ventricular tachyarrhythmia (VT) in 1145 patients receiving an implantable cardioverter‐defibrillator (ICD). In the second part of the study, SNPs significantly associated with VT were further investigated in 1335 subjects from the Oregon SUDS, a community‐based study analyzing causes of SCD. In the DISCOVERY trial, genotypes of 2 SNPs in the GNAS gene were nominally significant in the prospective screening and significantly associated with VT when viewed as recessive traits in post hoc analyses (TT vs CC/CT in c.393C>T: HR 1.42 [CI 1.11‐1.80], P=0.005; TT vs CC/CT in c.2273C>T: HR 1.57 [CI 1.18‐2.09], P=0.002). TT genotype in either SNP was associated with a HR of 1.58 (CI 1.26‐1.99) (P=0.0001). In the Oregon SUDS cohort significant evidence for association with SCD was observed for GNAS c.393C>T under the additive (P=0.039, OR=1.21 [CI 1.05‐1.45]) and recessive (P=0.01, OR=1.52 [CI 1.10‐2.13]) genetic models. Conclusions GNAS harbors 2 SNPs that were associated with an increased risk for VT in ICD patients, of which 1 was successfully replicated in a community‐based population of SCD cases. To the best of our knowledge, this is the first example of a gene variant identified by ICD VT monitoring as a surrogate parameter for SCD and also confirmed in the general population. Clinical Trial Registration URL: http://www.clinicaltrials. gov. Unique identifier: NCT00478933.