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A research artifact associated with the paper "SecBench.js: An Executable Security Benchmark Suite for Server-Side JavaScript" (ICSE 2023).

Neocortical projection neurons are generated by neural progenitor cells (NPCs) within the ventricular and subventricular zone. While early NPCs can give rise to both deep and upper layer neurons, late progenitors are restricted to upper layer neurogenesis. The molecular mechanisms controlling the differentiation potential of early versus late NPCs are unknown. Here, we report a novel function for TrkC-T1, the non-catalytic isoform of the neurotrophin receptor TrkC, that is distinct from TrkC-TK+, the full-length isoform. We provide direct evidence that TrkC-T1 regulates the switch in NPC fate from deep to upper layer neuron production. Elevated levels of TrkC-T1 in early NPCs promote the generation of deep layer neurons. Conversely, downregulation of TrkC-T1 in these cells promotes upper layer neuron fate. Furthermore, we show that TrkC-T1 exerts this control by interaction with the signaling adaptor protein ShcA. TrkC-T1 prevents the phosphorylation of Shc and the downstream activation of the MAP kinase (Erk1/2) pathway. In vivo manipulation of the activity of ShcA or Erk1/2, directly affects cortical neuron cell fate. We thus show that the generation of upper layer neurons by late progenitors is dependent on the downregulation of TrkC-T1 in late progenitor cells and the resulting activation of the ShcA/Erk1/2 pathway.

SummaryPrairie voles are among a small group of mammals that display long-term social attachment between mating partners. Many pharmacological studies show that signaling via the oxytocin receptor (OxtR) is critical for the display of social monogamy in these animals. We used CRISPR-mutagenesis to independently generate three different OxtR null mutant prairie vole lines. OxtR mutants displayed social attachment such that males and females showed a behavioral preference for their mating partners over a stranger of the opposite sex when assayed using different paradigms. Mothers lacking OxtR delivered viable pups, and parents displayed care of their young and raised them to the weanling stage. Together, our studies unexpectedly reveal that OxtR-mediated signaling is genetically dispensable for social attachment, parturition, and parental behavior.

Deep learning models trained on audio-visual data have been successfully used to achieve state-of-the-art performance for emotion recognition. In particular, models trained with multitask learning have shown additional performance improvements. However, such multitask models entangle information between the tasks, encoding the mutual dependencies present in label distributions in the real world data used for training. This work explores the disentanglement of multimodal signal representations for the primary task of emotion recognition and a secondary person identification task. In particular, we developed a multitask framework to extract low-dimensional embeddings that aim to capture emotion specific information, while containing minimal information related to person identity. We evaluate three different techniques for disentanglement and report results of up to 13% disentanglement while maintaining emotion recognition performance., Accepted for ICASSP 2021, 5 pages

General embeddings like word2vec, GloVe and ELMo have shown a lot of success in natural language tasks. The embeddings are typically extracted from models that are built on general tasks such as skip-gram models and natural language generation. In this paper, we extend the work from natural language understanding to multi-modal architectures that use audio, visual and textual information for machine learning tasks. The embeddings in our network are extracted using the encoder of a transformer model trained using multi-task training. We use person identification and automatic speech recognition as the tasks in our embedding generation framework. We tune and evaluate the embeddings on the downstream task of emotion recognition and demonstrate that on the CMU-MOSEI dataset, the embeddings can be used to improve over previous state of the art results., To appear in Interspeech,2020

Emotion recognition is a challenging task due to limited availability of in-the-wild labeled datasets. Self-supervised learning has shown improvements on tasks with limited labeled datasets in domains like speech and natural language. Models such as BERT learn to incorporate context in word embeddings, which translates to improved performance in downstream tasks like question answering. In this work, we extend self-supervised training to multi-modal applications. We learn multi-modal representations using a transformer trained on the masked language modeling task with audio, visual and text features. This model is fine-tuned on the downstream task of emotion recognition. Our results on the CMU-MOSEI dataset show that this pre-training technique can improve the emotion recognition performance by up to 3% compared to the baseline., Comment: To appear in SLT2020

Neuropsychiatric developmental disorders, such as autism spectrum disorders (ASDs) and schizophrenia, are typically characterized by alterations in social behavior and have been linked to aberrant dendritic spine and synapse development. Here we show, using genetically engineered mice, that the Cdc42 GTPase-activating multiadaptor protein, NOMA-GAP, regulates autism-like social behavior in the mouse, as well as dendritic spine and synapse development. Surprisingly, we were unable to restore spine morphology or autism-associated social behavior in NOMA-GAP-deficient animals by Cre-mediated deletion of Cdc42 alone. Spine morphology can be restored in vivo by re-expression of wild-type NOMA-GAP or a mutant of NOMA-GAP that lacks the RhoGAP domain, suggesting that other signaling functions are involved. Indeed, we show that NOMA-GAP directly interacts with several MAGUK (membrane-associated guanylate kinase) proteins, and that this modulates NOMA-GAP activity toward Cdc42. Moreover, we demonstrate that NOMA-GAP is a major regulator of PSD-95 in the neocortex. Loss of NOMA-GAP leads to strong upregulation of serine 295 phosphorylation of PSD-95 and moreover to its subcellular mislocalization. This is associated with marked loss of surface α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor and defective synaptic transmission, thereby providing a molecular basis for autism-like social behavior in the absence of NOMA-GAP.

miR-128, a brain-enriched microRNA, has been implicated in the control of neurogenesis and synaptogenesis but its potential roles in intervening processes have not been addressed. We show that post-transcriptional mechanisms restrict miR-128 accumulation to post-mitotic neurons during mouse corticogenesis and in adult stem cell niches. Whereas premature miR-128 expression in progenitors for upper layer neurons leads to impaired neuronal migration and inappropriate branching, sponge-mediated inhibition results in overmigration. Within the upper layers, premature miR-128 expression reduces the complexity of dendritic arborization, associated with altered electrophysiological properties. We show that Phf6, a gene mutated in the cognitive disorder Börjeson-Forssman-Lehmann syndrome, is an important regulatory target for miR-128. Restoring PHF6 expression counteracts the deleterious effect of miR-128 on neuronal migration, outgrowth and intrinsic physiological properties. Our results place miR-128 upstream of PHF6 in a pathway vital for cortical lamination as well as for the development of neuronal morphology and intrinsic excitability. DOI: http://dx.doi.org/10.7554/eLife.04263.001, eLife digest The unique capabilities of the mammalian brain depend on the patterns formed by spatial arrangements and connections between millions (sometimes billions) of electrically active cells called neurons, and on the connections between these neurons. During the development of the cortex, the largest part of the brain, neurons are born in stem cell areas that lie deep inside the brain, and these newly made neurons then migrate outwards to their final positions close to the surface of the adult brain. Franzoni et al. have examined how two molecules, a small RNA called miR-128 and a protein called PHF6, control when and how neurons migrate through the cortex and then grow to form connections with other neurons as they mature. Mutations that disrupt PHF6 can cause intellectual disabilities, and one possible reason for this is that PHF6 is needed to ensure that the neurons migrate to the correction location. Franzoni et al. now show that miR-128 can reduce the production of PHF6 and is therefore responsible for controlling when and where PHF6 is active. Studying miR-128 in detail, they show that although an inactive precursor form of miR-128 is present in stem cells and migrating neurons, the active form of miR-128 is only found in neurons that have already reached their final position in the cortex. Franzoni et al. used genetic methods to override the switch that controls when miR-128 becomes active. When the amount of miR-128 was artificially reduced, the neurons migrated too far. Artificially increasing the amount of miR-128 had the opposite effect: both the movement of the neurons and, later, their growth were defective. PHF6 was the key to these effects: if PHF6 levels were kept close to normal, miR-128 could no longer interfere with the movement and growth of the neurons. Further work will be required to better understand how miR-128 is turned off and on, and how PHF6 acts to control neuronal movement and growth. DOI: http://dx.doi.org/10.7554/eLife.04263.002

The pyramidal neurons of the mammalian neocortex form two major types of long-range connections—corticocortical and cortico-subcortical. The transcription factors Satb2 and Ctip2 are critical regulators of neuronal cell fate that control interhemispheric versus corticofugal connections respectively. Here, we investigate the axon guidance molecules downstream of Satb2 and Ctip2 that establish these connections. We show that the expression of two Netrin1 receptors- DCC and Unc5C is under direct negative regulation by Satb2 and Ctip2, respectively. Further, we show that the Netrin1–Unc5C/DCC interaction is involved in controlling the interhemispherical projection in a subset of early born, deep layer callosal neurons., The neocortex is responsible for higher level cognitive functions and long-range neural connections are critical for mediating these functions. Here, Srivatsa et al. show that axon guidance molecules downstream of transcription factors Stab2 and Ctip2 play a role in the establishment of cortical connections during mouse brain development.

Neocortical neurons have highly branched dendritic trees that are essential for their function. Indeed, defects in dendritic arborization are associated with human neurodevelopmental disorders. The molecular mechanisms regulating dendritic arbor complexity, however, are still poorly understood. Here, we uncover the molecular basis for the regulation of dendritic branching during cortical development. We show that during development, dendritic branching requires post-mitotic suppression of the RhoGTPase Cdc42. By generating genetically modified mice, we demonstrate that this is catalyzed in vivo by the novel Cdc42-GAP NOMA-GAP. Loss of NOMA-GAP leads to decreased neocortical volume, associated specifically with profound oversimplification of cortical dendritic arborization and hyperactivation of Cdc42. Remarkably, dendritic complexity and cortical thickness can be partially restored by genetic reduction of post-mitotic Cdc42 levels. Furthermore, we identify the actin regulator cofilin as a key regulator of dendritic complexity in vivo. Cofilin activation during late cortical development depends on NOMA-GAP expression and subsequent inhibition of Cdc42. Strikingly, in utero expression of active cofilin is sufficient to restore postnatal dendritic complexity in NOMA-GAP-deficient animals. Our findings define a novel cell-intrinsic mechanism to regulate dendritic branching and thus neuronal complexity in the cerebral cortex.

First insights into the molecular programs orchestrating the progression from neural stem cells to cortical projection neurons are emerging. Loss of the transcriptional regulator Ski has been linked to the human 1p36 deletion syndrome, which includes central nervous system defects. Here, we report critical roles for Ski in the maintenance of the neural stem cell pool and the specification of callosal neurons. Ski -deficient callosal neurons lose their identity and ectopically express the transcription factor Ctip2. The misspecified callosal neurons largely fail to form the corpus callosum and instead redirect their axons toward subcortical targets. We identify the chromatin-remodeling factor Satb2 as a partner of Ski, and show that both proteins are required for transcriptional repression of Ctip2 in callosal neurons. We propose a model in which Satb2 recruits Ski to the Ctip2 locus, and Ski attracts histone deacetylases, thereby enabling the formation of a functional nucleosome remodeling and deacetylase repressor complex. Our findings establish a central role for Ski–Satb2 interactions in regulating transcriptional mechanisms of callosal neuron specification.

The rostral migratory stream (RMS) is composed of neuroblasts migrating from the striatal SVZ to the olfactory bulb through a meshwork of GFAP- expressing astrocytes called the glial tube. So far, the origin of the glial tube astrocytes was attributed to differentiation of Type-B stem cells of the striatal SVZ. The true identity of these cells (Type-B stem cells versus immature/mature astrocytes) is also unclear. By analyzing a neocortex-specific conditional knockout of the transcriptional repressor Sip1 (Smad-interacting protein 1), we have now identified a novel pool of progenitors located within the dorsal SVZ (dSVZ) at early postnatal stages that differentiate into GFAP+ cells of the glial tube. We show that Sip1, expressed in postmitotic cortical neurons, controls the size of this dorsal progenitor pool possibly through cell-extrinsic mechanisms. Lack of Sip1 in the neocortex causes an expansion of this population leading to an increased production of GFAP+ astrocytes/Type-B stem cells in the glial tube, and a denser intercalation of these cells with Dcx+ neuroblasts of the RMS, the consequence of which is not yet clear. Neocortex-specific Sip1 deletion also led to an expansion of Dcx+ and Tbr2+ progenitor populations in the dSVZ. We show that the dSVZ progenitors (possibly remnants of embryonic radial glia) differentiate exclusively into BLBP+ cells which migrate into the RMS and mature into GFAP+ astrocytes/Type-B stem cells at around two weeks of postnatal development. In summary, our work shows that Sip1 controls the generation of GFAP+ cells of the RMS by regulating the size of a novel progenitor pool located in the postnatal dSVZ.

SummarySip1 is an important transcription factor that regulates several aspects of CNS development. Mutations in the human SIP1 gene have been implicated in Mowat-Wilson syndrome (MWS), characterized by severe mental retardation and agenesis of the corpus callosum. In this study we have shown that Sip1 is essential for the formation of intracortical, intercortical, and cortico-subcortical connections in the murine forebrain. Sip1 deletion from all postmitotic neurons in the neocortex results in lack of corpus callosum, anterior commissure, and corticospinal tract formation. Mosaic deletion of Sip1 in the neocortex reveals defects in axonal growth and in ipsilateral intracortical-collateral formation. Sip1 mediates these effects through its direct downstream effector ninein, a microtubule binding protein. Ninein in turn influences the rate of axonal growth and branching by affecting microtubule stability and dynamics.