Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Electric Fields Induced by Transcranial Magnetic Stimulation in the Brain using a Deep Encoder-Decoder Convolutional Neural Network

Transcranial magnetic stimulation (TMS) is a non-invasive, effective, and safe neuromodulation technique to diagnose and treat neurological and psychiatric disorders. However, the complexity and heterogeneity of the brain composition and structure pose a challenge in accurately determining whether critical brain regions have received the right level of induced electric field. Numerical computation methods, like finite element analysis (FEA), can be used to estimate electric field distribution. However, these methods need exceedingly high computational resources and are time-consuming. In this work, we developed a deep convolutional neural network (DCNN) encoder-decoder model to predict induced electric fields, in real-time, from T1-weighted and T2-weighted magnetic resonance imaging (MRI) based anatomical slices. We recruited 11 healthy subjects and applied TMS to the primary motor cortex to measure resting motor thresholds. Head models were developed from MRIs of the subjects using the SimNIBS pipeline. Head model overall size was scaled to 20 new size scales for each subject to form a total of 231 head models. Scaling was done to increase the number of input data representing different head model sizes. Sim4Life, a FEA software, was used to compute the induced electric fields, which served as the DCNN training data. For the trained network, the peak signal to noise ratios of the training and testing data were 32.83dB and 28.01dB, respectively. The key contribution of our model is the ability to predict the induced electric fields in real-time and thereby accurately and efficiently predict the TMS strength needed in targeted brain regions.
Theta phase specific modulation of hippocampal memory neurons

The theta rhythm, a quasi-periodic 4-10 Hz oscillation, is observed during memory processing in the hippocampus, with different phases of theta hypothesized to separate independent streams of information related to the encoding and recall of memories. At the cellular level, the discovery of hippocampal memory cells (engram neurons), as well as the modulation of memory recall through optogenetic activation of these cells, has provided evidence that certain memories are stored, in part, in a sparse ensemble of neurons in the hippocampus. In previous research, however, engram reactivation has been carried out using open loop stimulation at fixed frequencies; the relationship between engram neuron reactivation and ongoing network oscillations has not been taken into consideration. To address this concern, we implemented a closed-loop reactivation of engram neurons that enabled phase-specific stimulation relative to theta oscillations in the local field potential. Using this real-time approach, we tested the impact of activating engram neurons during the peak (encoding phase) and trough (recall phase) of theta oscillations. Consistent with previously hypothesized functions of theta oscillations in memory function, we show that stimulating engram neurons at the trough of theta is more effective in eliciting behavioral recall than either fixed frequency stimulation or stimulation at the peak of theta. Moreover, phase-specific trough stimulation is accompanied by an increase in the coupling between gamma and theta oscillations in CA1 hippocampus. Oure results provide a causal link between phase-specific activation of engram cells and the behavioral expression of memory.
Randomly incorporated genomic 6mA delays zygotic transcription initiation

N6-methyldeoxyadenosine (6mA) is a chemical alteration of DNA, observed across all realms of life. The functions of 6mA are well understood in bacteria but its roles in animal genomes have been controversial. We show that 6mA randomly accumulates in early embryos of the cnidarian Hydractinia symbiolongicarpus, with a peak at the 16-cell stage followed by clearance to background levels two cell cycles later, at the 64-cell stage – the embryonic stage at which zygotic genome activation occurs in this animal. Knocking down Alkbh1, a putative initiator of animal 6mA clearance, resulted in higher levels of 6mA at the 64-cell stage and a delay in the commencement of zygotic transcription. Our data are consistent with 6mA originating from recycled nucleotides of degraded m6A-marked maternal RNA post-fertilization. Therefore, while 6mA does not function as an epigenetic mark in Hydractinia, its random incorporation into the early embryonic genome inhibits transcription. Alkbh1 functions as a genomic 6mA ‘cleaner’, facilitating timely zygotic genome activation. Given the random nature of genomic 6mA accumulation and its ability to interfere with gene expression, defects in 6mA clearance may represent a hitherto unknown cause of various pathologies.
Sur La Classification Des Espaces Fibrés Vectoriels Holomorphes Sur Un Tore Complexe Admettant Des Connexions Holomorphes

Dans ce travail nous étudierons le problème de classifier les espaces fibres principaux holomorphes de groupe GL(m, C) sur un tore complexe admettant des connexions holomorphes i.e. la classification des espaces fibres vectoriels holomorphes sur un tore complexe admettant des connexions holomorphes. Récemment M. Matsushima [6] a démontré qu’un espace fibré vectoriel holomorphe sur un tore complexe admettant une connexion holomorphe de fibre de dimension 2 possède nécessairement une connexion holomorphe intégrable c. à. d. une connexion holomorphe dont la forme de courbure est nulle. D’autre part d’après Atiyah [1] on sait qu’un espace fibré holomorphe de base M et de groupe structural G admettant une connexion holomorphe intégrable est uu espace fibré principal associé au revêtement universel de la base M par une représentation du groupe fondamental de M dans G et vice versa.
Cell-specific expression of key mitochondrial enzymes precludes OXPHOS in astrocytes of the adult human neocortex and hippocampal formation

The astrocyte-to-neuron lactate shuttle hypothesis entails that glycolytically derived pyruvate in astrocytes is converted to lactate instead of being catabolized in mitochondria. The mechanism of this metabolic rewiring is unclear. Here we show that astrocytes of the adult human neocortex and hippocampal formation do not express mitochondrial proteins critical for performing oxidative phosphorylation (OXPHOS) to a detectable degree, including cytochrome c and complex IV. Without OXPHOS, human brain astrocytes are bound to produce lactate to avoid interruption of glycolysis.
An Inducible T7 Polymerase System for High-Level Protein Expression in Diverse Gram-Negative Bacteria

A broad host range (BHR)-inducible T7 RNA polymerase system was developed, enabling induction with isopropyl-β-d-thiogalactopyranoside (IPTG), similar to the Escherichia coli strain BL21(DE3) protocol, but it is now applicable in a wide range of bacteria. This system allows for high protein yields and purification from diverse Gram-negative bacteria, including the native host. ABSTRACT A broad host range (BHR)-inducible T7 RNA polymerase system was developed, enabling induction with isopropyl-β-d-thiogalactopyranoside (IPTG), similar to the Escherichia coli strain BL21(DE3) protocol, but it is now applicable in a wide range of bacteria. This system allows for high protein yields and purification from diverse Gram-negative bacteria, including the native host.
Gait speed and individual characteristics can be used to predict specific gait metric magnitudes in neurotypical adults

Background Gait biofeedback is commonly used to reduce gait dysfunction in a variety of clinical conditions. In these studies, participants alter their walking to reach the desired magnitude of a specific gait parameter (the biofeedback target) with each step. Biofeedback of parameters such as anterior ground reaction force and step length have been well-studied. Yet, there is no standardized methodology to set the target magnitude of these parameters. Here we present an approach to predict the anterior ground reaction force and step length of neurotypical adults walking at different speeds as a potential method for personalized gait biofeedback. Research question To determine if anterior ground reaction force and step lengths achieved during neurotypical walking could be predicted using gait speed and participants’ demographic and anthropomorphic characteristics. Methods We analyzed kinetic and kinematic data from 51 neurotypical adults who walked on a treadmill at up to eight speeds. We calculated the average peak anterior ground reaction force and step length of the right lower extremity at each speed. We used linear mixed-effects models to evaluate the effect of speed, leg length, mass, and age on anterior ground reaction force and step length. We fit the model to data from 37 participants and validated predictions from the final models on an independent dataset from 23 participants. Results Final prediction models for anterior ground reaction force and step length both included speed, speed squared, age, mass, and leg length. The models both showed strong agreement between predicted and actual values on an independent dataset. Significance Anterior ground reaction force and step length for neurotypical adults can be predicted given an individual’s gait speed, age, leg length, and mass. This may provide a standardized method to personalize targets for individuals with gait dysfunction in future studies of gait biofeedback.
The Novel Role of Midbody-Associated mRNAs in Regulating Abscission

Midbodies (MBs) have been shown to function during telophase as a recruiting hub, especially for ESCRT-III complex subunits, to regulate the abscission step of cytokinesis. However, the molecular machinery governing specific protein targeting and activation at the MB remains poorly understood. Until recently, it was thought that abscission regulating proteins, such as ESCRT-III complex subunits, accumulate at the MB by directly or indirectly binding to the MB resident protein, CEP55. However, recent studies have shown that depletion of CEP55 does not fully block ESCRT-III targeting to the MB, and cells in CEP55 knock-out mice divide normally. Additionally, since MBs are microtubule-rich, proteinaceous structures, it is conceptually hard to imagine how large protein complexes, such as the ESCRT-III complex, can successfully diffuse into the MB from the cytosol in a rapid and highly regulated manner. Here, we show that MBs contain mRNAs and that these MB-associated mRNAs can be locally translated, resulting in the accumulation of abscission-regulating proteins. We also demonstrate that localized MB-associated translation of CHMP4B is required for its targeting to the abscission site and that 3′ UTR-dependent CHMP4B mRNA targeting to the MB is required for successful completion of cytokinesis. Finally, we identify regulatory cis-elements within RNAs that are necessary and sufficient for mRNA trafficking to the MB. Based on all this data, we propose a novel method of regulating cytokinesis and abscission by MB-associated targeting and localized translation of selective mRNAs.
Daily Artificial Gravity is Associated with Greater Neural Efficiency during Sensorimotor Adaptation

Altered vestibular signaling and body unloading in microgravity results in sensory reweighting and adaptation. Microgravity effects are well-replicated in head-down tilt bed rest (HDBR). Artificial gravity (AG) is a potential countermeasure to mitigate effects of microgravity. We examined the effectiveness of daily AG for mitigating brain and/or behavioral changes in 60 days of HDBR. One group received AG for 30 minutes daily (AG; n=16) and a control group spent the same time in HDBR but received no AG (CTRL; n=8). All participants performed a sensorimotor adaptation task 5 times during fMRI scanning: twice prior to HDBR twice during HDBR, and once following HDBR. The AG group showed similar behavioral adaptation effects compared with the CTRLs. We identified decreased brain activation in the AG group from pre to late HDBR in the cerebellum for the task baseline portion and in the thalamus, calcarine, cuneus, premotor cortices, and superior frontal gyrus in the AG group during the early adaptation phase. The two groups also exhibited differential brain-behavior correlations. Together, these results suggest that AG may result in a reduced recruitment of brain activity for basic motor processes and sensorimotor adaptation. These effects may stem from somatosensory and vestibular stimulation from AG.
Wnt signaling regulates passive cell competition in the retina by inducing differential cell adhesion

Self-assortation of progenitor cells during development is essential for establishment of distinct tissue identity. This is exemplified in the eye, where the early optic cup is divided into the neural retina (NR) in the center and the ciliary margin (CM) in the periphery. Previous studies have demonstrated that Wnt signaling is required for specification of the CM, but here we show that genetic ablation of Wnt signaling mediator β-catenin in the peripheral optic cup failed to prevent the formation of the CM-derived ciliary body and iris in adult animals. Mosaic analysis revealed that this was only partially due to loss of adherens junctions among β-catenin deficient cells, which were preferentially excluded from the CM. Even in β-catenin mutant cells that can maintain adherens junctions, their inability to mediate Wnt signaling resulted in a change from P-cadherin to N-cadherin expression. We showed that this cadherin switch was sufficient to segregate otherwise identical cells into separate clusters. As a result, the ciliary body and iris were still formed after inactivation of Wnt signaling in the peripheral retina. These results showed that the dual functions of β-catenin in adherens junction and Wnt signaling are required for the passive cell competition to constitute retinal compartments.
Linearly Convergent First-Order Algorithms for Semi-definite Programming

In this paper, we consider two formulations for Linear Matrix Inequalities (LMIs) under Slater type constraint qualification assumption, namely, SDP smooth and non-smooth formulations. We also propose two first-order linearly convergent algorithms for solving these formulations. Moreover, we introduce a bundle-level method which converges linearly uniformly for both smooth and non-smooth problems and does not require any smoothness information. The convergence properties of these algorithms are also discussed. Finally, we consider a special case of LMIs, linear system of inequalities, and show that a linearly convergent algorithm can be obtained under a weaker assumption.
Laser pulse-length effects in trident pair production

Laser pulses facilitate multiphoton contributions to the trident pair production e L − → e L − + e L + + e L − , where the label L indicates a laser field dressed electron (e−) or positron (e+ ). We isolate the impact of the pulse envelope in the trident S matrix element, formulated within the Furry picture, in leading order of a series expansion in the classical nonlinearity parameter a0. Generally, the Fourier transform of the envelope carries the information on the pulse length, which becomes an easily tractable function in the case of a cos 2 pulse envelope. The transition to a monochromatic laser wave can be handled in a transparent manner, as also the onset of bandwidth effects for short pulses can be factorized out and studied separately.
Lipid-mRNA nanoparticles landscape for cancer therapy

Intracellular delivery of message RNA (mRNA) technique has ushered in a hopeful era with the successive authorization of two mRNA vaccines for the Coronavirus disease-19 (COVID-19) pandemic. A wide range of clinical studies are proceeding and will be initiated in the foreseeable future to treat and prevent cancers. However, efficient and non-toxic delivery of therapeutic mRNAs maintains the key limited step for their widespread applications in human beings. mRNA delivery systems are in urgent demand to resolve this difficulty. Recently lipid nanoparticles (LNPs) vehicles have prospered as powerful mRNA delivery tools, enabling their potential applications in malignant tumors via cancer immunotherapy and CRISPR/Cas9-based gene editing technique. This review discusses formulation components of mRNA-LNPs, summarizes the latest findings of mRNA cancer therapy, highlights challenges, and offers directions for more effective nanotherapeutics for cancer patients.
Subversion of host cell signaling: The arsenal of Rickettsial species

Rickettsia is a genus of nonmotile, Gram-negative, non-spore-forming, highly pleomorphic bacteria that cause severe epidemic rickettsioses. The spotted fever group and typhi group are major members of the genus Rickettsia. Rickettsial species from the two groups subvert diverse host cellular processes, including membrane dynamics, actin cytoskeleton dynamics, phosphoinositide metabolism, intracellular trafficking, and immune defense, to promote their host colonization and intercellular transmission through secreted effectors (virulence factors). However, lineage-specific rickettsiae have exploited divergent strategies to accomplish such challenging tasks and these elaborated strategies focus on distinct host cell processes. In the present review, we summarized current understandings of how different rickettsial species employ their effectors’ arsenal to affect host cellular processes in order to promote their own replication or to avoid destruction.
Correlation between Hashimoto’s thyroiditis and polycystic ovary syndrome: A systematic review and meta-analysis

Objective A growing body of research suggests that patients with polycystic ovary syndrome (PCOS) may be at increased risk of developing Hashimoto’s thyroiditis (HT), and having both conditions can make the condition worse. However, current research views are not uniform. Therefore, to explore the link between PCOS and HT, we conducted this study. Methods From the establishment of the database to August 2022, we searched 2 databases to study the correlation between Hashimoto’s and polycystic ovary syndrome. Two authors independently screened the articles for eligibility, and three authors extracted relevant data. Statistical analysis was performed using STATA16.0 software. Results A total of 20 studies were included, including 7 case-control studies and 13 cross-sectional studies. A total of 13 countries and 7857 participants were embraced. Studies have demonstrated that both PCOS patients have an increased risk of HT, and meanwhile, HT patients also have an increased risk of PCOS compared with controls. The study also incorporated that the prevalence of HT in PCOS patients in India and Turkey was higher than in other countries, and the prevalence of HT in PCOS patients in South America was higher than in Asia and Europe. Conclusions In conclusion, our study illustrates that there is a correlation between PCOS and HT, and it is necessary to further study the underlying mechanism between PCOS and HT. At the same time, it is of great significance to regularly screen PCOS patients for HT risk and HT patients for PCOS risk. Systematic Review Registration https://www.crd. york.ac. uk/prospero/, identifier CRD 42022351168.
Sepsis causes neutrophil infiltration in muscle leading to muscle atrophy and weakness in mice

Background Sepsis-induced muscle atrophy leads to prolonged physical dysfunction. Although the interaction of muscle atrophy and macrophage has been reported in sepsis, the role of neutrophils in muscle atrophy has not been thoroughly investigated. This study sought to investigate the long-term changes in muscle-localized neutrophils after sepsis induction and their possible role in sepsis. Methods Sepsis was induced in seven-week-old male C57BL/6J mice 8-12 (cecal slurry [CS] model) via intraperitoneal injection of 1 mg/g cecal slurry. The percentage change in body weight and grip strength was evaluated. The tibialis anterior muscles were dissected for microscopic examination of the cross-sectional area of myofibers or Fluorescence-activated cell sorting (FACS) analysis of immune cells. These changes were evaluated in the following conditions: (1) Longitudinal change until day 61, (2) CS concentration-dependent change on day 14 at the low (0.3 mg/g), middle (1.0 mg/g), and high (2.0 mg/g) concentrations, and (3) CS mice on day 14 treated with an anti-Ly6G antibody that depletes neutrophils. Results Body weight and grip strength were significantly lower in the CS model until day 61 (body weight: 123.1% ± 1.8% vs. 130.3% ± 2.5%, p = 0.04; grip strength: 104.5% ± 3.8% vs. 119.3% ± 5.3%, p = 0.04). Likewise, cross-sectional muscle area gradually decreased until day 61 from the CS induction (895.6 [606.0–1304.9] μm2 vs. 718.8 [536.2–937.0] μm2, p < 0.01). The number of muscle-localized neutrophils increased from 2.3 ± 0.6 cell/mg on day 0 to 22.2 ± 13.0 cell/mg on day 14, and decreased thereafter. In terms of CS concentration–dependent change, cross-sectional area was smaller (484.4 ± 221.2 vs. 825.8 ± 436.2 μm2 [p < 0.001]) and grip strength was lower (71.4% ± 12.8% vs. 116.3% ± 7.4%, p = 0.01) in the CS High group compared with the control, with increased neutrophils (p = 0.03). Ly6G-depleted mice demonstrated significant increase of muscle cross-sectional area and grip strength compared with control mice (p < 0.01). Conclusions Sepsis causes infiltration of neutrophils in muscles, leading to muscle atrophy and weakness. Depletion of neutrophils in muscle reverses sepsis-induced muscle atrophy and weakness. These results suggest that neutrophils may play a critical role in sepsis-induced muscle atrophy and weakness.
The outbursting protostar 2MASS 22352345 + 7517076 and its environment

We studied the Class I protostar 2MASS 22352345+7517076 whose dramatic brightening between the IRAS, Akari, and WISE surveys was reported by Onozato et al. (2015). 2MASS 22352345+7517076 is a member of a small group of low-mass young stellar objects, associated with IRAS 22343+7501 in the molecular cloud Lynds 1251. The IRAS, ISO, Spitzer, Akari, Herschel, and WISE missions observed different stages of its outburst. Supplemented these data with archival and our own near-infrared observations, and considering the contributions of neighbouring sources to the mid-infrared fluxes we studied the nature and environment of the outbursting object, and its photometric variations from 1983 to 2017. The low-state bolometric luminosity Lbol ~ 32 Lsun is indicative of a 100000-200000 years old protostar of 1.6-1.8 solar masses. Its 2-micron brightness started rising between 1993 and 1998, reached a peak in 2009-2011, and started declining in 2015. Changes in the spectral energy distribution suggest that the outburst was preceded by a decade-long, slow brightening in the near-infrared. The actual accretion burst occurred between 2004 and 2007. We fitted the spectral energy distribution in the bright phases with simple accretion disc models. The modelling suggested an increase of the disc accretion rate from some 3.5\times 10^{-7} Msun yr^{-1} to 1.1 \times 10^{-4} Msun yr^{-1}. The central star accreted nearly 10^{-3} solar masses, about a Jupiter mass during the ten years of the outburst. We observed H_2 emission lines in the K-band spectrum during the fading phase in 2017. The associated optical nebulosity RNO 144 and the Herbig-Haro object HH 149 have not exhibited significant variation in shape and brightness during the outburst.