Miracle-dz/UniFAR-FTUs huggingface dataset:
Segmentation and inpainting for stereoscopic videos

Nowadays, video processing technology is ubiquitous. It has found numerous applications from cinema post-production to television sets. Recent developments of digital stereoscopic videography call for new tools to help carry out post-production tasks for this medium. The flexibility offered by digital video is a key factor to the recent success of stereoscopic cinema, as most artifacts can be corrected or attenuated during post-production so as to deliver a pleasant 3D experience throughout. In this thesis, we study two difficult fundamental aspects of stereo-video post-production, for which existing tools are far from matching the abilities of artists: segmentation and inpainting. Both algorithms need temporal stability as well as view consistency. We investigate the adaptation and extension of existing techniques for monoscopic videos so as to process stereoscopic sequences. Our work exploits stereo-disparity information from a stereo scene in conjunction with long-term trajectories to improve on state-of-the-art approaches. Automatic video segmentation techniques are aimed at creating masks to delineate coherent regions in a video. The far reaching goal is that these segments correspond to semantically meaningful video objects. Current state-of-the-art techniques cannot replace semi-automatic rotoscoping, but they alleviate the work of artists by limiting the amount of required interaction. In this thesis, we present a novel sparse stereo-video segmentation technique that builds on existing 2D sparse segmentation frameworks. Our technique is based on the computation of an affinity measure between feature tracks, designed to process stereo videos. Our approach leads to greater temporal coherence and yields a more consistent segmentation across views, compared to existing techniques. Instead of requiring user interaction on a frame-to-frame basis to correct the segmentation output, we employ user interaction at the shot level, and on both views jointly. Video inpainting is particularly important during post-production to create clean plates or remove rig attached to actors or objects, so as to create convincing visual effects. The goal of research in this domain is to create a fully automated approach. However, existing techniques need user intervention both during the creation of the mask delimiting the object to inpaint, and often to correct artifacts in the inpainted region. In this thesis, we focus on improving the quality of the results to reduce the need for user-driven retouching. Our main contribution is to present a hybrid method that combines an exemplar-based approach, which fills in the missing area via sampling, and a motion/disparity-based approach, which reconstructs the missing region by pulling the available data from other parts of the sequence. Our idea is to guide the selection of candidate pixel samples by using long-term motion and inter-view disparity information.
LQR Suppression of Hopf Bifurcation in Hodgkin- Huxley Neurons

The work of Hodgkin and Huxley on nerve conduction has long been recognized as an outstanding scientific achievement. The Hodgkin-Huxley equations are modeled by a number of parameters and perform diverse behaviors depending on the various parameters. The purpose of this research is to solve the bifurcation control problem in the Hodgkin-Huxley nerve fibers. In this study, we focus on the Hopf bifurcation in the HH model, which arises by the external current injection. We present a feedback controlled approach to control the bifurcation phenomenon in the Hodgkin-Huxley nerve fibers via washout filter which can stop the repetitive firing in a particular region of the nervous system validly. A washout filter is augmented to the HH dynamics and the output of the filter is fed to an external controller generator through a linear gain. The linear projective control theory is applied to compute the control gain. The stable controller is performed by two similar control rules that are designed by the integration of the washout filters and static projective control theory. The first case of the control rule filters all the dynamic variables including the membrane potential and the channel activation, while the second case of the control rule filters merely the membrane potential. The MATCONT software package is used for analysis of the bifurcation points in conjunction with MATLAB.
Reward Expectation Reduces Representational Drift in the Hippocampus

Spatial memory in the hippocampus involves dynamic neural patterns that change over days, termed representational drift. While drift may aid memory updating, excessive drift could impede retrieval. Memory retrieval is influenced by reward expectation during encoding, so we hypothesized that diminished reward expectation would exacerbate representational drift. We found that high reward expectation limited drift, with CA1 representations on one day gradually re-emerging over successive trials the following day. Conversely, the absence of reward expectation resulted in increased drift, as the gradual re-emergence of the previous day’s representation did not occur. At the single cell level, lowering reward expectation caused an immediate increase in the proportion of place-fields with low trial-to-trial reliability. These place fields were less likely to be reinstated the following day, underlying increased drift in this condition. In conclusion, heightened reward expectation improves memory encoding and retrieval by maintaining reliable place fields that are gradually reinstated across days, thereby minimizing representational drift.
Clustering of RNA co-expression network identifies novel long non-coding RNA biomarkers in squamous cell carcinoma

Long non-coding RNAs (lncRNAs) have been shown to play an important role in cancer progression. Cutaneous squamous cell carcinoma is the most common metastatic skin cancer with increasing incidence worldwide. The prognosis of the metastatic cSCC is poor, and currently there are no established biomarkers to predict metastatic risk nor specific therapeutic targets for advanced or metastatic cSCC. To elucidate the role of lncRNAs in cSCC, RNA sequencing of patient derived cSCC cell lines and normal human epidermal keratinocytes was performed. The correlation analysis of differentially expressed lncRNA and protein-coding genes revealed six distinct clusters. One of the upregulated clusters involved genes related to cell motility. Upregulation of the expression of lncRNAs involved in cSCC cell motility in cSCC and head and neck SCC (HNSCC) cells was confirmed by qRT-PCR. Upregulation of HOTTIP and LINC00543 was also noted in SCC tumors in vivo and was associated with worse prognosis in HNSCC and lung SCC cohorts in the TCGA data, respectively. Altogether, these results reveal a novel set of lncRNAs involved in cSCC cell locomotion. These lncRNAs may serve as potential novel biomarkers or a biomarker panel and as putative therapeutic targets in locally advanced and metastatic cSCC.
“Non-viral CRISPR/Cas9 Mutagenesis for Streamlined Generation of Mouse Lung Cancer Models.”

Functional analysis in mouse models is necessary to establish the involvement of a set of genetic variations in tumor development. Many lung cancer models have been developed using genetic techniques to create gain- or loss-of-function alleles in genes involved in tumorigenesis; however, because of their labor- and time-intensive nature, these models are not suitable for quick and flexible hypothesis testing. Here we introduce a lung mutagenesis platform that utilizes CRISPR/Cas9 RNPs delivered via cationic polymers. This approach allows for the simultaneous inactivation of multiple genes. We validate the effectiveness of this system by targeting a group of tumor suppressor genes, specifically Rb1, Rbl1, Pten, and Trp53, which were chosen for their potential to cause lung tumors, namely Small Cell Lung Carcinoma (SCLC). This polymer-based delivery platform enables the modeling of lung tumorigenesis independently of the genetic background, thus simplifying and expediting the process without the need for modifying the mouse germline or creating custom viral vectors. Significance The development of models to rapidly introduce gene mutations into lung tissue to study their impact on tumor growth is critical for advancing the functional genomics of lung cancer. While previous methods using viral vectors and genetic manipulation in mice have been time-consuming and expensive, here we describe a new technique using cationic polymers as non-viral carriers for CRISPR/Cas9 delivery to induce cancer driving mutations that streamlines this process. This approach mimics natural mutations in lung cancer and accelerates the generation of accurate tumor models. Our study demonstrates the effectiveness of this method in generating small cell lung cancer (SCLC) by modifying four tumor suppressor genes in different mouse genetic backgrounds. This innovative strategy holds promise for faster and more cost-effective cancer modeling. Graphical Abstrac Small Cell Lung Cancer (SCLC) tumors are rapidly generated in any mouse genetic background by using cationic polymers to simultaneously deliver Cas9 and gRNAs targeting the Rb1, Rbl1, Pten and Trp53 tumor-suppressor genes to the adult airway respiratory system in vivo. Addition of the frt guide in the RC::FLTG mice provides a tdTomato gene editing reporter. This study shows the feasibility of rapidly generating lung cancer mouse models via somatic genome engineering through delivery of all CRISPR components in the form of nanoparticles.
Seasonal variation in D2/3 dopamine receptor availability in the human brain

Brain functional and physiological plasticity is essential to combat dynamic environmental challenges. The rhythmic in vivo dopamine signaling pathway, which regulates emotion, reward and learning, shows seasonal patterns with higher capacity of dopamine synthesis and lower number of dopamine transporters during dark seasons. However, seasonal variation of the dopamine receptor signaling remains to be characterized. Here, based on historical database of healthy human brain [11C]raclopride PET scans (n = 291, 224 males and 67 females), we investigated the seasonal patterns of D2/3 dopamine receptor signaling. We found that daylength at the time of scanning was negatively correlated with availability of this type of receptors in the striatum. Likely, seasonally varying D2/3 receptor signaling also underlies the seasonality of mood, feeding, and motivational processes. Significance of the study Brain in vivo neurotransmitter signaling demonstrates seasonal patterns. The dopamine D2/3 receptor, with both pre- and postsynaptic expressions, has been targeted by major antipsychotic and antiparkinsonian pharmaceuticals. The current study, based on a large dataset of healthy brain PET images quantifying these receptors, shows that dark seasons are associated with increased receptor availability in the striatum. Considering the previous findings of increased dopamine synthesis and lowered number of transporters, findings may suggest elevated presynaptic control of dopamine release and increased dopamine receptor sensitivity during dark seasons. The rhythmic D2/3 receptor availability may be a mechanism underlying seasonality in mood, feeding, and motivational processes.
Insights into the complex formation of a trimeric autotransporter adhesin with a peptidoglycan-binding periplasmic protein

Trimeric autotransporter adhesin (TAA) is an outer membrane (OM) protein that is widely distributed in gram-negative bacteria and is involved primarily in adhesion to biotic and abiotic surfaces, cell agglutination, and biofilm formation. TAAs are secreted onto the OM by the type Vc secretion system (SS). Because the interactions between TAAs and chaperones or special assistant proteins during secretion are short-lived, it is thought that TAAs reside on the OM without forming complexes with other proteins after secretion. In this study, we aimed to clarify the interactions between an Acinetobacter TAA, AtaA, and a peptidoglycan (PG)-binding periplasmic protein, TpgA, and to identify additional roles of TpgA based on these interactions. Pull-down assays using recombinant proteins identified the interacting domains. X-ray crystallography revealed the A3B3 heterohexameric complex structure of the N-terminal domain of TpgA with the transmembrane domain of AtaA and showed that both electrostatic and hydrophobic interactions contribute to stable complex formation. Bioinformatic analysis suggested that the TAA-TpgA complex is formed in a wide range of species that harbor the taa-tpgA gene cassette in their genome. Furthermore, the absence of TpgA increased the release of AtaA from the cell surface, suggesting that TpgA prevents the release of TAA from the cell surface via its anchoring to the PG. We propose that the TAAs that form a complex with TpgA be assigned to type Vc2 SS, a new subtype of type Vc SS. Significance Gram-negative bacteria have specialized secretion systems (SSs) that translocate molecules from the cytoplasm to the extracellular space. This is the first report directly demonstrating that the transmembrane domain of a trimeric autotransporter adhesin (TAA), which is secreted by the type Vc SS, forms a stable complex with a peptidoglycan-binding periplasmic protein. This complex prevents the release of TAA from the cell surface. These results suggest that the secretion and architecture of some TAAs are more complex than was previously understood. Our work provides structural and functional insights into bacterial SSs that are important not only in microbiology but also for medical and bioengineering applications.
Metabolite Fingerprinting for Phenotypic Screening by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry

The adoption of mass spectrometry for high-throughput screening in drug discovery has become increasingly prevalent and has enabled label-free screening against diverse targets. Cellular assays for phenotypic screening, however, are primarily conducted by microscopy as there remain many challenges associated with conducting phenotypic screens via ultra-high throughput mass spectrometry. Following a simple on-plate extraction, infrared matrix assisted laser desorption electrospray ionization (IR-MALDESI) was employed to directly sample the cell lysate at a speed of one second per sample. A549 cells were treated with compounds identified as hits in literature including a recently reported glutaminase cellular screen. Among the test compounds, there were confirmed glutaminase inhibitors, proposed nuisance compounds, and cell-active but enzyme-inactive compounds. Filtered data were further processed in R for dimensionality reduction and unsupervised clustering. Though it was observed that all compounds affected the intracellular conversion of glutamine to glutamate, there were clear metabolic differences between the biochemically active compounds and the off-target hits. Moreover, two nuisance compounds were observed to cluster separately from the confirmed glutaminase inhibitors in the observed metabolite fingerprints. This proof-of-concept work establishes a complete workflow that enables highthroughput mass spectrometry-based phenotypic screening. The methods proposed herein, at the throughput enabled by IR-MALDESI, could offer a new avenue for discovery of novel drugs.
Cyclin A/Cdk1 promotes chromosome alignment and timely mitotic progression

To ensure genomic fidelity a series of spatially and temporally coordinated events are executed during prometaphase of mitosis, including bipolar spindle formation, chromosome attachment to spindle microtubules at kinetochores, the correction of erroneous kinetochore-microtubule (k-MT) attachments, and chromosome congression to the spindle equator. Cyclin A/Cdk1 kinase plays a key role in destabilizing k-MT attachments during prometaphase to promote correction of erroneous k-MT attachments. However, it is unknown if Cyclin A/Cdk1 kinase regulates other events during prometaphase. Here, we investigate additional roles of Cyclin A/Cdk1 in prometaphase by using an siRNA knockdown strategy to deplete endogenous Cyclin A from human cells. We find that depleting Cyclin A significantly extends mitotic duration, specifically prometaphase, because chromosome alignment is delayed. Unaligned chromosomes display erroneous monotelic, syntelic, or lateral k-MT attachments suggesting that bioriented k-MT attachment formation is delayed in the absence of Cyclin A. Mechanistically, chromosome alignment is likely impaired because the localization of the kinetochore proteins BUB1 kinase, KNL1, and MPS1 kinase are reduced in Cyclin A-depleted cells. Moreover, we find that Cyclin A promotes BUB1 kinetochore localization independently of its role in destabilizing k-MT attachments. Thus, Cyclin A/Cdk1 facilitates chromosome alignment during prometaphase to support timely mitotic progression.
STAT3 regulates the generation of astroglia in human brain organoids with high mTORC1 activity

During brain development, neural progenitor cells first produce neurons, then astrocytes and other glial cell types, which provide important trophic support and shape neuronal development and function. Intrinsic genetic programs interact with extracellular signals to control progenitor fate, resulting in temporally segregated periods of neurogenesis and gliogenesis. Animal models have implicated STAT3 as an important driver of astrogenesis; however, the signaling pathways that control glial differentiation during human brain development are less well understood. Prior work demonstrated that constitutive activation of mTORC1 signaling in human brain organoid models resulted in the precocious generation of glial-lineage cells. In this study, we tested whether mTORC1 acts via STAT3 to control astrogenesis in brain organoids. We show that knockdown of STAT3 reduces astrogenesis in wild-type organoids and in organoids with constitutively high mTORC1 signaling caused by deletion of the negative regulator TSC2. However, mTORC1 is not required for cytokine-induced activation of STAT3 and expression of the astrocytic protein GFAP. Together, these results show that mTORC1 acts through STAT3 to control astroglia production in human brain organoid models, but that mTOR signaling is dispensable for STAT3-driven astrogenesis. Summary statement Deb et al, use human brain organoid models to show a requirement for STAT3 downstream of mTORC1 in regulating astrogliogenesis during early human brain development.
Structure and methyl-lysine binding selectivity of the HUSH complex subunit MPP8

The Human Silencing Hub (HUSH) guards the genome from the pathogenic effects of retroelement expression. Composed of MPP8, TASOR, and Periphilin-1, HUSH recognizes actively transcribed retrotransposed sequences by the presence of long (>1.5-kb) nascent transcripts without introns. HUSH recruits effectors that alter chromatin structure, degrade transcripts, and deposit transcriptionally repressive epigenetic marks. Structural and biochemical data for the three HUSH subunits are sparse. Here, we report the crystal structure of the C-terminal domain (CTD) of MPP8 necessary for HUSH activity. The MPP8 CTD consists of five ankyrin repeats followed by a domain with structural homology to the PINIT domains of Siz/PIAS-family SUMO E3 ligases. AlphaFold-Multimer modeling predicts that the MPP8 CTD forms extended interaction interfaces with a SPOC domain and a domain with a novel fold, DomI, in TASOR. The chromodomain of MPP8, known to bind the repressive mark H3K9me3, binds with similar or higher affinity to H3K9-like sequences in the mammalian H3K9 methyltransferase subunits SETDB1, ATF7IP, G9a, and GLP. Hence, MPP8 promotes heterochromatinization by recruiting H3K9 methyltransferases. Our work identifies novel structural elements in MPP8 that are required for HUSH complex assembly and silencing, thereby fulfilling vital functions in controlling the transcription of retrotransposons of endogenous and viral origin. Key Points Structure of MPP8 CTD reveals ankyrin repeats and PINIT-like domain required for HUSH activity AlphaFold predicts a large interaction interface between MPP8 CTD and TASOR SPOC and DomI domains The MPP8 chromodomain binds trimethyl-lysines in ATF7IP and GLP with higher affinity than H3K9me3
Model-Based Closed-Loop Control of Thalamic Deep Brain Stimulation

Closed-loop control of deep brain stimulation (DBS) is crucial for effective and automatic treatments of various neurological disorders like Parkinson’s disease (PD) and essential tremor (ET). Manual (open-loop) DBS programming solely based on clinical observations relies on neurologists’ expertise and patients’ experience. The continuous stimulation in open-loop DBS may decrease battery life and cause side effects. On the contrary, a closed-loop DBS system utilizes a feedback biomarker/signal to track worsening (or improving) patient’s symptoms and offers several advantages compared to open-loop DBS. Existing closed-loop DBS control systems do not incorporate physiological mechanisms underlying the DBS or symptoms, for example how DBS modulates dynamics of synaptic plasticity. In this work, we proposed a computational framework for development of a model-based DBS controller where a biophysically-reasonable model can describe the relationship between DBS and neural activity, and a polynomial-based approximation can estimate the relationship between the neural and behavioral activity. A controller is utilized in our model in a quasi-real-time manner to find DBS patterns that significantly reduce the worsening of symptoms. These DBS patterns can be tested clinically by predicting the effect of DBS before delivering it to the patient. We applied this framework to the problem of finding optimal DBS frequencies for essential tremor given EMG recordings solely. Building on our recent network model of ventral intermediate nuclei (Vim), the main surgical target of the tremor, in response to DBS, we developed a biophysically-reasonable simulation in which physiological mechanisms underlying Vim-DBS are linked to symptomatic changes in EMG signals. By utilizing a PID controller, we showed that a closed-loop system can track EMG signals and adjusts the stimulation frequency of Vim-DBS so that the power of EMG in [2, 200] Hz reaches a desired target. We demonstrated that our model-based closed-loop control system of Vim-DBS finds an appropriate DBS frequency that aligns well with clinical studies. Our model-based closed-loop system is adaptable to different control targets, highlighting its potential usability for different diseases and personalized systems.