Saccadic latency in amblyopia.

We measured saccadic latencies in a large sample (total n = 459) of individuals with amblyopia or risk factors for amblyopia, e.g., strabismus or anisometropia, and normal control subjects. We presented an easily visible target randomly to the left or right, 3.5° from fixation. The interocular difference in saccadic latency is highly correlated with the interocular difference in LogMAR (Snellen) acuity-as the acuity difference increases, so does the latency difference. Strabismic and strabismic-anisometropic amblyopes have, on average, a larger difference between their eyes in LogMAR acuity than anisometropic amblyopes and thus their interocular latency difference is, on average, significantly larger than anisometropic amblyopes. Despite its relation to LogMAR acuity, the longer latency in strabismic amblyopes cannot be attributed either to poor resolution or to reduced contrast sensitivity, because their interocular differences in grating acuity and in contrast sensitivity are roughly the same as for anisometropic amblyopes. The correlation between LogMAR acuity and saccadic latency arises because of the confluence of two separable effects in the strabismic amblyopic eye-poor letter recognition impairs LogMAR acuity while an intrinsic sluggishness delays reaction time. We speculate that the frequent microsaccades and the accompanying attentional shifts, made while strabismic amblyopes struggle to maintain fixation with their amblyopic eyes, result in all types of reactions being irreducibly delayed

Stimulation by a low-molecular-weight angiogenic factor of capillary endothelial cells in culture.

A low-mol.-wt compound isolated from rat Walker 256 carcinoma and found to induce neovascularization in vivo was tested on cultures of cow brain-derived endothelial cells (CBEC) growing on plastic and collagen substrates. This factor had a mitogenic effect on CBEC cultured on native collagen gels and for this reason has been called "endothelial-cell-stimulating angiogenesis factor" (ESAF). CBEC growing on plastic culture dishes or denatured collagen films were not stimulated by ESAF. The mitogenic effect of ESAF was equally apparent when added to cells already attached to the native collagen substrate or when the collagen substrate was pre-incubated with ESAF before plating the cells. A floating collagen gel pre-incubated with ESAF in cultures of CBEC growing on plastic dishes did not stimulate cell growth. Our data indicate that the substrate influences cell behaviour and that CBEC only respond to ESAF when growing on a native collagen substrate

AI for predicting chemical-effect associations at the chemical universe level – deepFPlearn

Many chemicals are out there in our environment, and all living species are exposed. However, numerous chemicals pose risks, such as developing severe diseases, if they occur at the wrong time in the wrong place. For the majority of the chemicals, these risks are not known. Chemical risk assessment and subsequent regulation of use require efficient and systematic strategies. Lab-based methods – even if high throughput – are too slow to keep up with the pace of chemical innovation. Existing computational approaches are designed for specific chemical classes or sub-problems but not usable on a large scale. Further, the application range of these approaches is limited by the low amount of available labeled training data.We present the ready-to-use and stand-alone program deepFPlearn that predicts the association between chemical structures and effects on the gene/pathway level using a combined deep learning approach. deepFPlearn uses a deep autoencoder for feature reduction before training a deep feedforward neural network to predict the target association. We received good prediction qualities and showed that our feature compression preserves relevant chemical structural information. Using a vast chemical inventory (unlabeled data) as input for the autoencoder did not reduce our prediction quality but allowed capturing a much more comprehensive range of chemical structures. We predict meaningful - experimentally verified-associations of chemicals and effects on unseen data. deepFPlearn classifies hundreds of thousands of chemicals in seconds.We provide deepFPlearn as an open-source and flexible tool that can be easily retrained and customized to different application settings at https://github.com/yigbt/deepFPlearn.Supplementary information Supplementary data are available at bioRxiv online.Contact jana.schor{at}ufz.deCompeting Interest StatementThe authors have declared no competing interest

AI for predicting chemical-effect associations at the chemical universe level: DeepFPlearn

Many chemicals are present in our environment, and all living species are exposed to them. However, numerous chemicals pose risks, such as developing severe diseases, if they occur at the wrong time in the wrong place. For the majority of the chemicals, these risks are not known. Chemical risk assessment and subsequent regulation of use require efficient and systematic strategies. Lab-based methods-even if high throughput-are too slow to keep up with the pace of chemical innovation. Existing computational approaches are designed for specific chemical classes or sub-problems but not usable on a large scale. Further, the application range of these approaches is limited by the low amount of available labeled training data. We present the ready-to-use and stand-alone program deepFPlearn that predicts the association between chemical structures and effects on the gene/pathway level using a combined deep learning approach. deepFPlearn uses a deep autoencoder for feature reduction before training a deep feed-forward neural network to predict the target association. We received good prediction qualities and showed that our feature compression preserves relevant chemical structural information. Using a vast chemical inventory (unlabeled data) as input for the autoencoder did not reduce our prediction quality but allowed capturing a much more comprehensive range of chemical structures. We predict meaningful-experimentally verified-associations of chemicals and effects on unseen data. deepFPlearn classifies hundreds of thousands of chemicals in seconds. We provide deepFPlearn as an open-source and flexible tool that can be easily retrained and customized to different application settings at https://github.com/yigbt/deepFPlearn

Chromatin and alternative splicing

Alternative splicing affects more than 90% of human genes. Coupling between transcription and splicing has become crucial in the complex network underlying alternative splicing regulation. Because chromatin is the real template for nuclear transcription, changes in its structure, but also in the "reading" and "writing" of the histone code, could modulate splicing choices. Here, we discuss the evidence supporting these ideas, from the first proposal of chromatin affecting alternative splicing, performed 20 years ago, to the latest findings including genome-wide evidence that nucleosomes are preferentially positioned in exons. We focus on two recent reports from our laboratories that add new evidence to this field. The first report shows that a physiological stimulus such as neuron depolarization promotes intragenic histone acetylation (H3K9ac) and chromatin relaxation, causing the skipping of exon 18 of the neural cell adhesion molecule gene. In the second report, we show how specific histone modifications can be created at targeted gene regions as a way to affect alternative splicing: Using small interfering RNAs (siRNAs), we increased the levels of H3K9me2 and H3K27me3 in the proximity of alternative exon 33 of the human fibronectin gene, favoring its inclusion into mature messenger RNA (mRNA) through a mechanism that recalls RNAmediated transcriptional gene silencing. © 2010 Cold Spring Harbor Laboratory Press.Fil:Alló, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Schor, I.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Muñoz, M.J. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:De La Mata, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.Fil:Kornblihtt, A.R. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Smoke gets in your eyes:what is sociological about cigarettes?

Contemporary public health approaches increasingly draw attention to the unequal social distribution of cigarette smoking. In contrast, critical accounts emphasize the importance of smokers’ situated agency, the relevance of embodiment and how public health measures against smoking potentially play upon and exacerbate social divisions and inequality. Nevertheless, if the social context of cigarettes is worthy of such attention, and sociology lays a distinct claim to understanding the social, we need to articulate a distinct, positive and systematic claim for smoking as an object of sociological enquiry. This article attempts to address this by situating smoking across three main dimensions of sociological thinking: history and social change; individual agency and experience; and social structures and power. It locates the emergence and development of cigarettes in everyday life within the project of modernity of the nineteenth and twentieth centuries. It goes on to assess the habituated, temporal and experiential aspects of individual smoking practices in everyday lifeworlds. Finally, it argues that smoking, while distributed in important ways by social class, also works relationally to render and inscribe it

Superconducting crossed correlations in ferromagnets: implications for thermodynamics and quantum transport

It is demonstrated that non local Cooper pairs can propagate in ferromagnetic electrodes having an opposite spin orientation. In the presence of such crossed correlations, the superconducting gap is found to depend explicitly on the relative orientation of the ferromagnetic electrodes. Non local Cooper pairs can in principle be probed with dc-transport. With two ferromagnetic electrodes, we propose a ``quantum switch'' that can be used to detect correlated pairs of electrons. With three or more ferromagnetic electrodes, the Cooper pair-like state is a linear superposition of Cooper pairs which could be detected in dc-transport. The effect also induces an enhancement of the ferromagnetic proximity effect on the basis of crossed superconducting correlations propagating along domain walls.Comment: 4 pages, RevTe

Accommodation and vergence response gains to different near cues characterize specific esotropias

Aim. To describe preliminary findings of how the profile of the use of blur, disparity and proximal cues varies between non-strabismic groups and those with different types of esotropia. Design. Case control study Methodology. A remote haploscopic photorefractor measured simultaneous convergence and accommodation to a range of targets containing all combinations of binocular disparity, blur and proximal (looming) cues. 13 constant esotropes, 16 fully accommodative esotropes, and 8 convergence excess esotropes were compared with age and refractive error matched controls, and 27 young adult emmetropic controls. All wore full refractive correction if not emmetropic. Response AC/A and CA/C ratios were also assessed. Results. Cue use differed between the groups. Even esotropes with constant suppression and no binocular vision (BV) responded to disparity in cues. The constant esotropes with weak BV showed trends for more stable responses and better vergence and accommodation than those without any BV. The accommodative esotropes made less use of disparity cues to drive accommodation (p=0.04) and more use of blur to drive vergence (p=0.008) than controls. All esotropic groups failed to show the strong bias for better responses to disparity cues found in the controls, with convergence excess esotropes favoring blur cues. AC/A and CA/C ratios existed in an inverse relationship in the different groups. Accommodative lag of >1.0D at 33cm was common (46%) in the pooled esotropia groups compared with 11% in typical children (p=0.05). Conclusion. Esotropic children use near cues differently from matched non-esotropic children in ways characteristic to their deviations. Relatively higher weighting for blur cues was found in accommodative esotropia compared to matched controls

Biological activity differences between TGF-β1 and TGF-β3 correlate with differences in the rigidity and arrangement of their component monomers

[Image: see text] TGF-β1, -β2, and -β3 are small, secreted signaling proteins. They share 71–80% sequence identity and signal through the same receptors, yet the isoform-specific null mice have distinctive phenotypes and are inviable. The replacement of the coding sequence of TGF-β1 with TGF-β3 and TGF-β3 with TGF-β1 led to only partial rescue of the mutant phenotypes, suggesting that intrinsic differences between them contribute to the requirement of each in vivo. Here, we investigated whether the previously reported differences in the flexibility of the interfacial helix and arrangement of monomers was responsible for the differences in activity by generating two chimeric proteins in which residues 54–75 in the homodimer interface were swapped. Structural analysis of these using NMR and functional analysis using a dermal fibroblast migration assay showed that swapping the interfacial region swapped both the conformational preferences and activity. Conformational and activity differences were also observed between TGF-β3 and a variant with four helix-stabilizing residues from TGF-β1, suggesting that the observed changes were due to increased helical stability and the altered conformation, as proposed. Surface plasmon resonance analysis showed that TGF-β1, TGF-β3, and variants bound the type II signaling receptor, TβRII, nearly identically, but had small differences in the dissociation rate constant for recruitment of the type I signaling receptor, TβRI. However, the latter did not correlate with conformational preference or activity. Hence, the difference in activity arises from differences in their conformations, not their manner of receptor binding, suggesting that a matrix protein that differentially binds them might determine their distinct activities

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Long non-coding RNAs (lncRNAs) can often function in the regulation of gene expression during development; however, their generality as essential regulators in developmental processes and organismal phenotypes remains unclear. Here, we performed a tailored investigation of lncRNA expression and function during Drosophila embryogenesis, interrogating multiple stages, tissue specificity, nuclear localization, and genetic backgrounds. Our results almost double the number of annotated lncRNAs expressed at these embryonic stages. lncRNA levels are generally positively correlated with those of their neighboring genes, with little evidence of transcriptional interference. Using fluorescent in situ hybridization, we report the spatiotemporal expression of 15 new lncRNAs, revealing very dynamic tissue-specific patterns. Despite this, deletion of selected lncRNA genes had no obvious developmental defects or effects on viability under standard and stressed conditions. However, two lncRNA deletions resulted in modest expression changes of a small number of genes, suggesting that they fine-tune expression of non-essential genes. Several lncRNAs have strain-specific expression, indicating that they are not fixed within the population. This intra-species variation across genetic backgrounds may thereby be a useful tool to distinguish rapidly evolving lncRNAs with as yet non-essential roles.Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. European Molecular Biology Laboratory; AlemaniaFil: Bussotti, Giovanni. European Bioinformatics Institute; Reino UnidoFil: Maleš, Matilda. European Molecular Biology Laboratory; AlemaniaFil: Forneris, Mattia. European Molecular Biology Laboratory; AlemaniaFil: Viales, Rebecca R.. European Molecular Biology Laboratory; AlemaniaFil: Enright, Anton J.. European Bioinformatics Institute; Reino UnidoFil: Furlong, Eileen E. M.. European Molecular Biology Laboratory; Alemani