Seeing the advantage: Visually grounding word embeddings to better capture human semantic knowledge

Distributional semantic models capture word-level meaning that is useful in many natural language processing tasks and have even been shown to capture cognitive aspects of word meaning. The majority of these models are purely text based, even though the human sensory experience is much richer. In this paper we create visually grounded word embeddings by combining English text and images and compare them to popular text-based methods, to see if visual information allows our model to better capture cognitive aspects of word meaning. Our analysis shows that visually grounded embedding similarities are more predictive of the human reaction times in a large priming experiment than the purely text-based embeddings. The visually grounded embeddings also correlate well with human word similarity ratings.Importantly, in both experiments we show that he grounded embeddings account for a unique portion of explained variance, even when we include text-based embeddings trained on huge corpora. This shows that visual grounding allows our model to capture information that cannot be extracted using text as the only source of information

Language learning using speech to image retrieval

Humans learn language by interaction with their environment and listening to other humans. It should also be possible for computational models to learn language directly from speech but so far most approaches require text. We improve on existing neural network approaches to create visually grounded embeddings for spoken utterances. Using a combination of a multi-layer GRU, importance sampling, cyclic learning rates, ensembling and vectorial self-attention our results show a remarkable increase in image-caption retrieval performance over previous work. Furthermore, we investigate which layers in the model learn to recognise words in the input. We find that deeper network layers are better at encoding word presence, although the final layer has slightly lower performance. This shows that our visually grounded sentence encoder learns to recognise words from the input even though it is not explicitly trained for word recognition

His-tags as Zn(II) binding motifs in a protein-based fluorescent sensor

Fluorescent indicators that allow real-time imaging of Zn(II) in living cells are invaluable tools for understanding Zn(II) homeostasis. Genetically encoded sensors based on fluorescence resonance energy transfer between fluorescent protein domains have important advantages over synthetic probes. We discovered that hexahistidine tags have a strong tendency to dimerize upon binding of Zn(II) in solution and we used this principle to develop a new protein-based sensor for Zn(II). Enhanced cyan and yellow fluorescent proteins were connected by long flexible peptide linkers and His-tags were incorporated at both termini of this fusion protein. The resulting sensor CLY9-2His allows the ratiometric fluorescent detection of Zn(II) in the nanomolar range. In addition, CLY9-2His is selective over the physiologically relevant metal ions Fe(II), Mn(II), Ca(II) and Mg(II). Our approach demonstrates the potential of using small peptides as metal-binding ligands in chelating fluorescent protein chimeras

Relation between Reactive Surface Sites and Precursor Choice for Area-Selective Atomic Layer Deposition Using Small Molecule Inhibitors

Implementation of vapor/phase dosing of small molecule inhibitors (SMIs) in advanced atomic layer deposition (ALD) cycles is currently being considered for bottom-up fabrication by area-selective ALD. When SMIs are used, it can be challenging to completely block precursor adsorption due to the inhibitor size and the relatively short vapor/phase exposures. Two strategies for precursor blocking are explored: (i) physically covering precursor adsorption sites, i.e., steric shielding, and (ii) eliminating precursor adsorption sites from the surface, i.e., chemical passivation. In this work, it is determined whether steric shielding is enough for effective precursor blocking during area-selective ALD or whether chemical passivation is required as well. At the same time, we address why some ALD precursors are more difficult to block than others. To this end, the blocking of the Al precursor molecules trimethylaluminum (TMA), dimethylaluminum isopropoxide (DMAI), and tris(dimethylamino)aluminum (TDMAA) was studied by using acetylacetone (Hacac) as inhibitor. It was found that DMAI and TDMAA are more easily blocked than TMA because they adsorb on the same surface sites as Hacac, while TMA is also reactive with other surface sites. This work shows that chemical passivation plays a crucial role for precursor blocking in concert with steric shielding. Moreover, the reactivity of the precursor with the surface groups on the non-growth area dictates the effectiveness of blocking precursor adsorption

High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hypridization

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, and miscarriages. Automated detection of subtle deletions or duplications involving telomeres is essential for high-throughput diagnosis, but impossible when conventional cytogenetic methods are used. Array-based comparative genomic hybridization (CGH) allows high-resolution screening of copy number abnormalities by hybridizing differentially labeled test and reference genomes to arrays of robotically spotted clones. To assess the applicability of this technique in the diagnosis of (sub)telomeric imbalances, we here describe a blinded study, in which DNA from 20 patients with known cytogenetic abnormalities involving one or more telomeres was hybridized to an array containing a validated set of human-chromosome–specific (sub)telomere probes. Single-copy-number gains and losses were accurately detected on these arrays, and an excellent concordance between the original cytogenetic diagnosis and the array-based CGH diagnosis was obtained by use of a single hybridization. In addition to the previously identified cytogenetic changes, array-based CGH revealed additional telomere rearrangements in 3 of the 20 patients studied. The robustness and simplicity of this array-based telomere copy-number screening make it highly suited for introduction into the clinic as a rapid and sensitive automated diagnostic procedure

Macrocyclization of enzyme-based supramolecular polymers

AB type monomers for supramolecular polymers have been developed based on the strong and reversible noncovalent interaction between ribonuclease S-peptide (A) and S-protein (B), resulting in an active enzyme complex as the linking unit. Two AB-type protein constructs are synthesized differing in the length of the flexible oligo(ethylene glycol) spacer separating the two end groups. Using an experimental setup where size exclusion chromatography is directly coupled to Q-TOF mass spectrometry, we have analyzed the self-assembled architectures as a function of concentration. The theory of macrocyclization under thermodynamic control is used to quantitatively analyze the experimental data. Using this theory, we show that AB-type monomers linked by flexible linkers grow reversibly via ring-chain competition. Inherently the formation of linear polymeric assemblies is beyond the capability of these types of building blocks due to concentration limits of proteins. The results therefore contribute to the general understanding of supramolecular polymerization with biological building blocks and demonstrate design requirements for monomers if linear polymerization is desired

eZinCh-2: a versatile, genetically encoded FRET sensor for cytosolic and intraorganelle Zn2+ imaging

Zn2+ plays essential and diverse roles in numerous cellular processes. To get a better understanding of intracellular Zn2+ homeostasis and the putative signaling role of Zn2+, various fluorescent sensors have been developed that allow monitoring of Zn2+ concentrations in single living cells in real time. Thus far, two families of genetically encoded FRET-based Zn2+ sensors have been most widely applied, the eCALWY sensors developed by our group and the ZapCY sensors developed by Palmer and co-workers. Both have been successfully used to measure cytosolic free Zn2+, but distinctly different concentrations have been reported when using these sensors to measure Zn2+ concentrations in the ER and mitochondria. Here, we report the development of a versatile alternative FRET sensor containing a de novo Cys2His2 binding pocket that was created on the surface of the donor and acceptor fluorescent domains. This eZinCh-2 sensor binds Zn2+ with a high affinity that is similar to that of eCALWY-4 (Kd = 1 nM at pH 7.1), while displaying a substantially larger change in emission ratio. eZinCh-2 not only provides an attractive alternative for measuring Zn2+ in the cytosol but was also successfully used for measuring Zn2+ in the ER, mitochondria, and secretory vesicles. Moreover, organelle-targeted eZinCh-2 can also be used in combination with the previously reported redCALWY sensors to allow multicolor imaging of intracellular Zn2+ simultaneously in the cytosol and the ER or mitochondria

Integrated Bioluminescent Immunoassays for High-Throughput Sampling and Continuous Monitoring of Cytokines

Immunoassays show great potential for the detection of low levels of cytokines, due to their high sensitivity and excellent specificity. There is a particular demand for biosensors that enable both high-throughput screening and continuous monitoring of clinically relevant cytokines such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNFα). To this end, we here introduce a novel bioluminescent immunoassay based on the ratiometric plug-and-play immunodiagnostics (RAPPID) platform, with an improved intrinsic signal-to-background and an &gt;80-fold increase in the luminescent signal. The new dRAPPID assay, comprising a dimeric protein G adapter connected via a semiflexible linker, was applied to detect the secretion of IL-6 by breast carcinoma cells upon TNFα stimulation and the production of low concentrations of IL-6 (∼18 pM) in an endotoxin-stimulated human 3D muscle tissue model. Moreover, we integrated the dRAPPID assay in a newly developed microfluidic device for the simultaneous and continuous monitoring of changes in IL-6 and TNFα in the low-nanomolar range. The luminescence-based read-out and the homogeneous nature of the dRAPPID platform allowed for detection with a simple measurement setup, consisting of a digital camera and a light-sealed box. This permits the usage of the continuous dRAPPID monitoring chip at the point of need, without the requirement for complex or expensive detection techniques.</p