Joint Embedding Predictive Architectures Focus on Slow Features

Many common methods for learning a world model for pixel-based environments use generative architectures trained with pixel-level reconstruction objectives. Recently proposed Joint Embedding Predictive Architectures (JEPA) offer a reconstruction-free alternative. In this work, we analyze performance of JEPA trained with VICReg and SimCLR objectives in the fully offline setting without access to rewards, and compare the results to the performance of the generative architecture. We test the methods in a simple environment with a moving dot with various background distractors, and probe learned representations for the dot's location. We find that JEPA methods perform on par or better than reconstruction when distractor noise changes every time step, but fail when the noise is fixed. Furthermore, we provide a theoretical explanation for the poor performance of JEPA-based methods with fixed noise, highlighting an important limitation.Comment: 4 pages (3 figures) short paper for SSL Theory and Practice workshop at NeurIPS 2022. Code is available at https://github.com/vladisai/JEPA_SSL_NeurIPS_202

Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs

Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 x R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization

Quantum dot loaded immunomicelles for tumor imaging

<p>Abstract</p> <p>Background</p> <p>Optical imaging is a promising method for the detection of tumors in animals, with speed and minimal invasiveness. We have previously developed a lipid coated quantum dot system that doubles the fluorescence of PEG-grafted quantum dots at half the dose. Here, we describe a tumor-targeted near infrared imaging agent composed of cancer-specific monoclonal anti-nucleosome antibody 2C5, coupled to quantum dot (QD)-containing polymeric micelles, prepared from a polyethylene glycol/phosphatidylethanolamine (PEG-PE) conjugate. Its production is simple and involves no special equipment. Its imaging potential is great since the fluorescence intensity in the tumor is twofold that of non-targeted QD-loaded PEG-PE micelles at one hour after injection.</p> <p>Methods</p> <p>Para-nitrophenol-containing (5%) PEG-PE quantum dot micelles were produced by the thin layer method. Following hydration, 2C5 antibody was attached to the PEG-PE micelles and the QD-micelles were purified using dialysis. 4T1 breast tumors were inoculated subcutaneously in the flank of the animals. A lung pseudometastatic B16F10 melanoma model was developed using tail vein injection. The contrast agents were injected via the tail vein and mice were depilated, anesthetized and imaged on a Kodak Image Station. Images were taken at one, two, and four hours and analyzed using a methodology that produces normalized signal-to-noise data. This allowed for the comparison between different subjects and time points. For the pseudometastatic model, lungs were removed and imaged <it>ex vivo </it>at one and twenty four hours.</p> <p>Results</p> <p>The contrast agent signal intensity at the tumor was double that of the passively targeted QD-micelles with equally fast and sharply contrasted images. With the side views of the animals only tumor is visible, while in the dorsal view internal organs including liver and kidney are visible. <it>Ex vivo </it>results demonstrated that the agent detects melanoma nodes in a lung pseudometastatic model after a 24 hours wash-out period, while at one hour, only a uniform signal is detected.</p> <p>Conclusions</p> <p>The targeted agent produces ultrabright tumor images and double the fluorescence intensity, as rapidly and at the same low dose as the passively targeted agents. It represents a development that may potentially serve to enhance early detection for metastases.</p

Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs

Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 x R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization

Istraživanje mehanizma toksičnosti anilina u eritrocitima

Strategies for the use of bio-indicators in the prediction of environmental damage should include mechanistic research. This study involves the relationship between the chemical structure and hemotoxic markers of aniline and its halogenated analogs. Aniline-induced methemoglobinemia, loss of circulating blood cells, blood stability, glutathione depletion and membrane cytoskeletal changes were assessed following exposure to phenylhydroxylamine (PHA), para-fluoro-, para-bromo-, and para-iodo in male Sprague-Dawley rats. Methemoglobin was determined spectrophotometrically at 635 nm. Erythrocyte depletion was investigated by loss of radioactivity in chromium-labeled red blood cells in vivo. Membrane proteins were analyzed by SDS-PAGE using red blood ghost cells treated with various aniline analogs. Results showed dose- and time-dependent changes in the induction of methemoglobin of up to 78 % with para-bromo PHA and 75 % with para-iodo PHA compared to 3 % to 5 % in control. Treated animals lost up to three times more blood from circulation compared to control within 14 days after treatment. Erythrocytes were more stable in buffer solution than in para-iodo-treated cells. Depletion of reduced glutathione in PHA and para-iodo-PHA treated red cells was also observed. Analysis of red cell skeletal membrane treated with para-iodo-PHA showed that protein band 2.1 became broader and band 2.2 diminished completely in some treatments. Dose- and time-dependent changes suggested the use of hemotoxic endpoints as potential biomarkers for assessing chemical and drug safetyStrategije primjene biopokazatelja za predviđanje štete u okolišu trebaju u obzir uzeti istraživanja mehanizama djelovanja. Ovo istraživanje propituje odnos između kemijske strukture i hemotoksičnih pokazatelja djelovanja anilina i njegovh halogeniranih analoga. Nakon izlaganja mužjaka štakora soja Sprague-Dawley para-fluoro-, para-bromo- i para-jodofenilhidroksilaminu, utvrđena je methemoglobinemija uzrokovana anilinom te pad broja krvnih stanica u krvotoku i stabilnosti krvi, gubitak glutationa i promjene na membrani stanice. Methemoglobin je određivan spektrofotometrijski na 635 nm. Pad broja eritrocita mjeren je in vivo s pomoću eritrocita obilježenih radioaktivnim kromom. Membranske su bjelančevine analizirane s pomoću SDS-PAGE, rabeći eritrocite bez hemoglobina (engl. ghost cells) kojima su dodani različiti analozi anilina. Nalazi upućuju na promjene indukcije methemoglobina ovisno o dozi i vremenu djelovanja do 78 % s para-bromo-fenilhidroksilaminom te do 75 % s para-jodofenilhidroksilaminom u usporedbi s 3 % do 5 % u kontrolnih uzoraka. U razdoblju od 14 dana nakon tretiranja izložene životinje izgubile su tri puta više krvi iz krvotoka od kontrolnih. Eritrociti su bili stabilniji u puferskoj otopini negoli u stanicama kojima je dodan para-jodofenilhidroksilamin. Zamijećen je i pad glutationa u eritrocitima kojima je dodan fenilhidroksilamin odnosno para-jodofenilhidroksilamin. Analizom membrane eritrocita kojima je dodan para-jodofenilhidroksilamin zamijećeno je da se u pojedinih obrada raširila proteinska vrpca 2.1, a potpuno smanjila proteinska vrpca 2.2. Zamijećene promjene uvjetovane dozom i vremenom upućuju na primjenu hemotoksičnih parametara kao mogućih biopokazatelja u procjeni sigurnosti lijeka odnosno kemikalije

The ring current model of the pentaprismane molecule

Three-dimensional models of the quantum-mechanical current density J(B), induced in the electron cloud of the C10H10 pentaprismane molecule by a magnetic field B applied along the C-5 (a C-2) symmetry axis, orthogonal to the pentagonal (a rectangular) face, and denoted by B-parallel to (B-perpendicular to), have been constructed. Predictions of near Hartree-Fock quality are reported for the diagonal components of magnetic tensors, magnetizability (xi), nuclear shielding of carbon (sigma(C)) and hydrogen (sigma(H)), and virtual shielding at the center of mass (sigma(CM)). The complicated spatial features of the induced electronic current-density field have been rationalized and compactly described via stagnation graphs that elucidate the details of its topological structure. A representation of JB is obtained by three-dimensional perspective plots and by planar maps visualizing phase portraits of electron flow in a series of molecular domains. Both streamline J(B)/|J(B)| and modulus |J(B)| are analyzed. These graphic tools illustrate the competition between diatropic and paratropic regimes which determine the magnitude of various components of magnetizability and magnetic shielding of hydrogen and carbon nuclei. Shielding density maps show that the differential Biot-Savart law explains magnetic shielding at hydrogen and carbon nuclei, and virtual shielding at ring and cage centers. Similarities and/or contrasting ring current effects on magnetotropicity are discussed by a comparison with triprismane C6H6 and cubane C8H8