Learning to rank from medical imaging data

Medical images can be used to predict a clinical score coding for the severity of a disease, a pain level or the complexity of a cognitive task. In all these cases, the predicted variable has a natural order. While a standard classifier discards this information, we would like to take it into account in order to improve prediction performance. A standard linear regression does model such information, however the linearity assumption is likely not be satisfied when predicting from pixel intensities in an image. In this paper we address these modeling challenges with a supervised learning procedure where the model aims to order or rank images. We use a linear model for its robustness in high dimension and its possible interpretation. We show on simulations and two fMRI datasets that this approach is able to predict the correct ordering on pairs of images, yielding higher prediction accuracy than standard regression and multiclass classification techniques

Risk and Ambiguity in Information Seeking:Eye Gaze Patterns Reveal Contextual Behavior in Dealing with Uncertainty

Information foraging connects optimal foraging theory in ecology with how humans search for information. The theory suggests that, following an information scent, the information seeker must optimize the tradeoff between exploration by repeated steps in the search space vs. exploitation, using the resources encountered. We conjecture that this tradeoff characterizes how a user deals with uncertainty and its two aspects, risk and ambiguity in economic theory. Risk is related to the perceived quality of the actually visited patch of information, and can be reduced by exploiting and understanding the patch to a better extent. Ambiguity, on the other hand, is the opportunity cost of having higher quality patches elsewhere in the search space. The aforementioned tradeoff depends on many attributes, including traits of the user: at the two extreme ends of the spectrum, analytic and wholistic searchers employ entirely different strategies. The former type focuses on exploitation first, interspersed with bouts of exploration, whereas the latter type prefers to explore the search space first and consume later. Based on an eye-tracking study of experts' interactions with novel search interfaces in the biomedical domain, we demonstrate that perceived risk shifts the balance between exploration and exploitation in either type of users, tilting it against vs. in favour of ambiguity minimization. Since the pattern of behaviour in information foraging is quintessentially sequential, risk and ambiguity minimization cannot happen simultaneously, leading to a fundamental limit on how good such a tradeoff can be. This in turn connects information seeking with the emergent field of quantum decision theory.Comment: 20 pages, 3 figure

Sterilization of lung matrices by supercritical carbon dioxide

Lung engineering is a potential alternative to transplantation for patients with end-stage pulmonary failure. Two challenges critical to the successful development of an engineered lung developed from a decellularized scaffold include (i) the suppression of resident infectious bioburden in the lung matrix, and (ii) the ability to sterilize decellularized tissues while preserving the essential biological and mechanical features intact. To date, the majority of lungs are sterilized using high concentrations of peracetic acid (PAA) resulting in extracellular matrix (ECM) depletion. These mechanically altered tissues have little to no storage potential. In this study, we report a sterilizing technique using supercritical carbon dioxide (ScCO(2)) that can achieve a sterility assurance level 10(−6) in decellularized lung matrix. The effects of ScCO(2) treatment on the histological, mechanical, and biochemical properties of the sterile decellularized lung were evaluated and compared with those of freshly decellularized lung matrix and with PAA-treated acellular lung. Exposure of the decellularized tissue to ScCO(2) did not significantly alter tissue architecture, ECM content or organization (glycosaminoglycans, elastin, collagen, and laminin), observations of cell engraftment, or mechanical integrity of the tissue. Furthermore, these attributes of lung matrix did not change after 6 months in sterile buffer following sterilization with ScCO(2), indicating that ScCO(2) produces a matrix that is stable during storage. The current study's results indicate that ScCO(2) can be used to sterilize acellular lung tissue while simultaneously preserving key biological components required for the function of the scaffold for regenerative medicine purposes

Inhibition of cPLA2 has neuroprotective effects on motoneuron and muscle atrophy following spinal cord injury

Surviving motoneurons undergo dendritic atrophy after spinal cord injury (SCI), suggesting an important therapeutic target for neuroprotective strategies to improve recovery of function after SCI. Our previous studies showed that phospholipase A2 (PLA2) may play an important role in the pathogenesis of SCI. In the present study, we investigated whether blocking cPLA2 pharmacologically with arachidonyl trifluoromethyl ketone (ATK) or genetically using cPLA2 knockout (KO) mice attenuates motoneuron atrophy following SCI. C57BL/6 mice received either sham or contusive SCI at the T10 level. At 30 min after SCI, mice were treated with ATK or vehicle. Four weeks later, motoneurons innervating the vastus lateralis muscle of the quadriceps were labeled with cholera toxin-conjugated horseradish peroxidase, and dendritic arbors were reconstructed in three dimensions. Soma volume, motoneuron number, lesion volume, and tissue sparing were also assessed, as were muscle weight, fiber cross-sectional area, and motor endplate size and density. ATK administration reduced percent lesion volume and increased percent volume of spared white matter compared to the vehicle-treated control animals. SCI with or without ATK treatment had no effect on the number or soma volume of quadriceps motoneurons. However, SCI resulted in a decrease in dendritic length of quadriceps motoneurons in untreated animals, and this decrease was completely prevented by treatment with ATK. Similarly, the vastus lateralis muscle weights of untreated SCI animals were smaller than those of sham-surgery controls, and these reductions were prevented by ATK treatment. No effects on fiber cross-sectional areas, motor endplate area or density were observed across treatment groups. Remarkably, genetically deleting cPLA2 in cPLA2 KO mice attenuated dendritic atrophy after SCI. These findings suggest that after SCI, cord tissue damage and regressive changes in motoneuron and muscle morphology can be reduced by inhibition of cPLA2, further supporting a role for cPLA2 as a neurotherapeutic target for SCI treatment

Finding predictive models for singlet fission by machine learning

Singlet fission (SF), the conversion of one singlet exciton into two triplet excitons, could significantly enhance solar cell efficiency. Molecular crystals that undergo SF are scarce. Computational exploration may accelerate the discovery of SF materials. However, many-body perturbation theory (MBPT) calculations of the excitonic properties of molecular crystals are impractical for large-scale materials screening. We use the sure-independence-screening-and-sparsifying-operator (SISSO) machine-learning algorithm to generate computationally efficient models that can predict the MBPT thermodynamic driving force for SF for a dataset of 101 polycyclic aromatic hydrocarbons (PAH101). SISSO generates models by iteratively combining physical primary features. The best models are selected by linear regression with cross-validation. The SISSO models successfully predict the SF driving force with errors below 0.2 eV. Based on the cost, accuracy, and classification performance of SISSO models, we propose a hierarchical materials screening workflow. Three potential SF candidates are found in the PAH101 set

The diet-derived short chain fatty acid propionate improves beta-cell function in humans and stimulates insulin secretion from human islets in vitro

Aims: Diet-derived short chain fatty acids (SCFAs) improve glucose homeostasis in vivo, but the role of individual SCFAs and their mechanisms of action have not been defined. This study evaluated the effects of increasing colonic delivery of the SCFA propionate on β-cell function in humans and the direct effects of propionate on isolated human islets in vitro. Materials and Methods: For 24 weeks human subjects ingested an inulin-propionate ester that delivers propionate to the colon. Acute insulin, GLP-1 and non-esterified fatty acid (NEFA) levels were quantified pre- and post-supplementation in response to a mixed meal test. Expression of the SCFA receptor FFAR2 in human islets was determined by western blotting and immunohistochemistry. Dynamic insulin secretion from perifused human islets was quantified by radioimmunoassay and islet apoptosis was determined by quantification of caspase 3/7 activities. Results: Colonic propionate delivery in vivo was associated with improved β-cell function with increased insulin secretion that was independent of changes in GLP-1 levels. Human islet β-cells expressed FFAR2 and propionate potentiated dynamic glucose-stimulated insulin secretion in vitro, an effect that was dependent on signalling via protein kinase C. Propionate also protected human islets from apoptosis induced by the NEFA sodium palmitate and inflammatory cytokines. Conclusions: Our results indicate that propionate has beneficial effects on β-cell function in vivo, and in vitro analyses demonstrated that it has direct effects to potentiate glucose-stimulated insulin release and maintain β-cell mass through inhibition of apoptosis. These observations support ingestion of propiogenic dietary fibres to maintain healthy glucose homeostasis

Vasoplegic Shock treated with Methylene Blue complicated by Severe Serotonin Syndrome.

Introduction: Management of severe vasoplegic shock in overdose can be very challenging. We describe a case of severe refractory vasodilatory shock in poisoning where methylene blue (MB) was used with success. Case Report. A 70kg 15-year-old male presented 1.5 hours post ingestion of a large polypharmacy overdose of quetiapine slow release 1.5g, quetiapine immediate release 12g, desvenlafaxine slow release 5.6g, venlafaxine 1050mg, amlodipine 290mg, ramipril 100mg, fluoxetine 560mg, promethazine 500mg and an unknown amount of lithium. He developed severe vasoplegic shock that was resistant to maximal doses of noradrenaline and vasopressin. MB was administered 6.5 hour post ingestion. Within 1 hour there was an improvement in his haemodynamic status and reduction of catecholamine requirements. Twelve hours post ingestion, he developed severe serotonin syndrome that lasted 5 days as a result of interaction between MB, a reversible monoamine oxidase inhibitor, and the antidepressants taken in overdose. MB had a calculated half-life of 38 hours. Conclusion MB is a useful second or third line strategy for severe drug induced vasodilatory shock, and may be potentially life-saving. Conversely, physicians should be aware that it can interact with other drugs and cause life-threatening serotonin syndrome. Lower doses or shorter durations may be wise in patients at risk of this interaction

Decoupling carrier concentration and electron-phonon coupling in oxide heterostructures observed with resonant inelastic x-ray scattering

We report the observation of multiple phonon satellite features in ultra thin superlattices of form $n$SrIrO$_3$/$m$SrTiO$_3$ using resonant inelastic x-ray scattering. As the values of $n$ and $m$ vary the energy loss spectra show a systematic evolution in the relative intensity of the phonon satellites. Using a closed-form solution for the cross section, we extract the variation in the electron-phonon coupling strength as a function of $n$ and $m$. Combined with the negligible carrier doping into the SrTiO$_3$ layers, these results indicate that tuning of the electron-phonon coupling can be effectively decoupled from doping. This work showcases both a feasible method to extract the electron-phonon coupling in superlattices and unveils a potential route for tuning this coupling which is often associated with superconductivity in SrTiO$_3$-based systems.Comment: 4 pages, 5 figure

Non-classical ProIL-1beta activation during mammary gland infection is pathogen-dependent but caspase-1 independent

Infection of the mammary gland with live bacteria elicits a pathogen-specific host inflammatory response. To study these host-pathogen interactions wild type mice, NF-kappaB reporter mice as well as caspase-1 and IL-1beta knockout mice were intramammarily challenged with Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). The murine mastitis model allowed to compare the kinetics of the induced cytokine protein profiles and their underlying pathways. In vivo and ex vivo imaging showed that E. coli rapidly induced NF-kappaB inflammatory signaling concomitant with high mammary levels of TNF-alpha, IL-1 alpha and MCP-1 as determined by multiplex analysis. In contrast, an equal number of S. aureus bacteria induced a low NF-kappaB activity concomitant with high mammary levels of the classical IL-1beta fragment. These quantitative and qualitative differences in local inflammatory mediators resulted in an earlier neutrophil influx and in a more extensive alveolar damage post-infection with E. coli compared to S. aureus. Western blot analysis revealed that the inactive proIL-1beta precursor was processed into pathogen-specific IL-1beta fragmentation patterns as confirmed with IL-1beta knockout animals. Additionally, caspase-1 knockout animals allowed to investigate whether IL-1beta maturation depended on the conventional inflammasome pathway. The lack of caspase-1 did not prevent extensive proIL-1beta fragmentation by either of S. aureus or E. coli. These non-classical IL-1beta patterns were likely caused by different proteases and suggest a sentinel function of IL-1beta during mammary gland infection. Thus, a key signaling nodule can be defined in the differential host innate immune defense upon E. coli versus S. aureus mammary gland infection, which is independent of caspase-1