Uncertainty-aware predictions of molecular X-ray absorption spectra using neural network ensembles

As machine learning (ML) methods continue to be applied to a broad scope of problems in the physical sciences, uncertainty quantification is becoming correspondingly more important for their robust application. Uncertainty aware machine learning methods have been used in select applications, but largely for scalar properties. In this work, we showcase an exemplary study in which neural network ensembles are used to predict the X-ray absorption spectra of small molecules, as well as their point-wise uncertainty, from local atomic environments. The performance of the resulting surrogate clearly demonstrates quantitative correlation between errors relative to ground truth and the predicted uncertainty estimates. Significantly, the model provides an upper bound on the expected error. Specifically, an important quality of this uncertainty-aware model is that it can indicate when the model is predicting on out-of-sample data. This allows for its integration with large scale sampling of structures together with active learning or other techniques for structure refinement. Additionally, our models can be generalized to larger molecules than those used for training, and also successfully track uncertainty due to random distortions in test molecules. While we demonstrate this workflow on a specific example, ensemble learning is completely general. We believe it could have significant impact on ML-enabled forward modeling of a broad array of molecular and materials properties.Comment: 24 pages, 16 figure

Higher Spins from Tensorial Charges and OSp(N|2n) Symmetry

It is shown that the quantization of a superparticle propagating in an N=1, D=4 superspace extended with tensorial coordinates results in an infinite tower of massless spin states satisfying the Vasiliev unfolded equations for free higher spin fields in flat and AdS_4 N=1 superspace. The tensorial extension of the AdS_4 superspace is proved to be a supergroup manifold OSp(1|4). The model is manifestly invariant under an OSp(N|8) (N=1,2) superconformal symmetry. As a byproduct, we find that the Cartan forms of arbitrary Sp(2n) and OSp(1|2n) groups are GL(2n) flat, i.e. they are equivalent to flat Cartan forms up to a GL(2n) rotation. This property is crucial for carrying out the quantization of the particle model on OSp(1|4) and getting the higher spin field dynamics in super AdS_4, which can be performed in a way analogous to the flat case.Comment: LaTeX, 21 page (JHEP style), misprints corrected, added comments on the relation of results of hep-th/0106149 with hep-th/9904109 and hep-th/9907113, references adde

A Critical Perspective on Moral Neuroscience

In this paper, we highlight several historical developments in the neuroscience of ethics as well as recent advances that forecast the experimental research to come. We argue, in particular, that our understanding of the moral brain will benefit from the further use of a formal, mathematical approach to the construction and testing of alternative theories, such as that found in the field of neuroeconomics. The use of economic modeling to understand the psychological processes underlying distributional preferences and charitable giving is reviewed to illustrate this potential. We also consider some obstacles to such an approach, notably the challenge of capturing substantive moral values within a mathematical model

Integrative Genome Comparison of Primary and Metastatic Melanomas

A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of effective therapeutics and prognostic diagnostics for melanoma patients. In this study, we conducted global genomic characterization of primary and metastatic melanomas to examine the genomic landscape associated with metastatic progression. In addition to uncovering three genomic subclasses of metastastic melanomas, we delineated 39 focal and recurrent regions of amplification and deletions, many of which encompassed resident genes that have not been implicated in cancer or metastasis. To identify progression-associated metastasis gene candidates, we applied a statistical approach, Integrative Genome Comparison (IGC), to define 32 genomic regions of interest that were significantly altered in metastatic relative to primary melanomas, encompassing 30 resident genes with statistically significant expression deregulation. Functional assays on a subset of these candidates, including MET, ASPM, AKAP9, IMP3, PRKCA, RPA3, and SCAP2, validated their pro-invasion activities in human melanoma cells. Validity of the IGC approach was further reinforced by tissue microarray analysis of Survivin showing significant increased protein expression in thick versus thin primary cutaneous melanomas, and a progression correlation with lymph node metastases. Together, these functional validation results and correlative analysis of human tissues support the thesis that integrated genomic and pathological analyses of staged melanomas provide a productive entry point for discovery of melanoma metastases genes

CNS Penetration of Intrathecal-Lumbar Idursulfase in the Monkey, Dog and Mouse: Implications for Neurological Outcomes of Lysosomal Storage Disorder

A major challenge for the treatment of many central nervous system (CNS) disorders is the lack of convenient and effective methods for delivering biological agents to the brain. Mucopolysaccharidosis II (Hunter syndrome) is a rare inherited lysosomal storage disorder resulting from a deficiency of iduronate-2-sulfatase (I2S). I2S is a large, highly glycosylated enzyme. Intravenous administration is not likely to be an effective therapy for disease-related neurological outcomes that require enzyme access to the brain cells, in particular neurons and oligodendrocytes. We demonstrate that intracerebroventricular and lumbar intrathecal administration of recombinant I2S in dogs and nonhuman primates resulted in widespread enzyme distribution in the brain parenchyma, including remarkable deposition in the lysosomes of both neurons and oligodendrocytes. Lumbar intrathecal administration also resulted in enzyme delivery to the spinal cord, whereas little enzyme was detected there after intraventricular administration. Mucopolysaccharidosis II model is available in mice. Lumbar administration of recombinant I2S to enzyme deficient animals reduced the storage of glycosaminoglycans in both superficial and deep brain tissues, with concurrent morphological improvements. The observed patterns of enzyme transport from cerebrospinal fluid to the CNS tissues and the resultant biological activity (a) warrant further investigation of intrathecal delivery of I2S via lumbar catheter as an experimental treatment for the neurological symptoms of Hunter syndrome and (b) may have broader implications for CNS treatment with biopharmaceuticals

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren’s syndrome

Sjögren’s syndrome is a common autoimmune disease (~0.7% of European Americans) typically presenting as keratoconjunctivitis sicca and xerostomia. In addition to strong association within the HLA region at 6p21 (Pmeta=7.65×10−114), we establish associations with IRF5-TNPO3 (Pmeta=2.73×10−19), STAT4 (Pmeta=6.80×10−15), IL12A (Pmeta =1.17×10−10), FAM167A-BLK (Pmeta=4.97×10−10), DDX6-CXCR5 (Pmeta=1.10×10−8), and TNIP1 (Pmeta=3.30×10−8). Suggestive associations with Pmeta<5×10−5 were observed with 29 regions including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2, and PHIP amongst others. These results highlight the importance of genes involved in both innate and adaptive immunity in Sjögren’s syndrome

Iron Oxide Superparamagnetic Nanocarriers Bearing Amphiphilic N-Heterocyclic Choline Analogues as Potential Antimicrobial Agents

Magnetic nanoparticles represent an advanced tool in biomedicine because they can be simultaneously functionalized and guided using a magnetic field. Iron oxide magnetic nanoparticles precoated with oleic acid and bearing novel antimicrobial N-heterocyclic choline analogues, namely O-, N- and O,N-bis-undecyl-substituted N-(2-hydroxyethyl)-1,2,3,4-tetrahydroisoquinolinium derivatives, have been obtained as potential biomedical agents for drug delivery and antimicrobial therapy. Structural and size determinations for the novel synthesized magnetic nanosystems were carried out based upon magnetogranulometry, dynamic light-scattering measurements and X-ray diffraction analysis. The most expected iron oxide core diameter was 6.2-10.5 nm. The magnetization analyses showed that the particles are superparamagnetic at room temperature. Aqueous magnetic fluids of the synthesized nanoparticles were examined in vitro concerning Gram-positive (Staphylococcus aureus MSCL 334, Bacillus cereus MSCL 330) and Gram-negative (Escherichia coli MSCL 332, Pseudomonas aeruginosa MSCL 331, Proteus mirabilis MSCL 590) bacterial strains and fungi (Candida albicans MSCL 378, Aspergillus niger MSCL 324). It was found that the samples have magnetic properties and possess antimicrobial activity. The minimum inhibitory concentration against S. aureus for the most active magnetic fluid was determined as 16 μg ml^-1

Serum Levels of Lipids, Calcium and Magnesium in Women with Hypothyroidism and Cardiovascular Diseases

Lipid abnormalities in hypothyroidism contribute to the disproportionate increase in cardiovascular risk. A possible relationship between serum level of magnesium (Mg) and calcium (Ca) and cardiovascular disease was recorded. In this work, the possible correlation between lipid profile components and serum cations Ca and Mg was investigated. Matched healthy women were evaluated in a cross-sectional study. All parameters were measured spectrophotometrically. The results showed a significant decrease (P < 0.05) in high-density lipoprotein-cholesterol (HDL-C), total and ionized Mg in hypothyroid patients in comparing with control group. There was a significant increase (P <0.05) in serum total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C) and (LDL-C)/(HDL-C) ratio in hypothyroid patients as compared with control group. However, no correlation was found between the cation levels and lipid profile of the studied groups. It can be concluded that patients with hypothyroidism exhibited elevated atherogenic parameters (TC and LDL-C) and high risk of cardiovascular diseases