Miracle-dz/UniFAR-FTUs huggingface dataset:
OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow

For refining and designing protein structures, it is essential to have an efficient protein folding and docking framework that generates a protein 3D structure based on given constraints. In this study, we introduce OPUS-Fold3 as a gradient-based, all-atom protein folding and docking framework, which accurately generates 3D protein structures in compliance with specified constraints, such as a potential function as long as it can be expressed as a function of positions of heavy atoms. Our tests show that, for example, OPUS-Fold3 achieves performance comparable to pyRosetta in backbone folding, and significantly better in side-chain modeling. Developed using Python and TensorFlow 2.4, OPUS-Fold3 is user-friendly for any source-code level modifications and can be seamlessly combined with other deep learning models, thus facilitating collaboration between the biology and AI communities. The source code of OPUS-Fold3 can be downloaded from http://github.com/OPUS-MaLab/opus_fold3. It is freely available for academic usage.
Low forces push the maturation of neural precursors into neurons

Mechanical stimulation modulates neural development and neuronal activity. In a previous study, we proposed magnetic “nano-pulling” as a tool to generate active forces. By loading neural cells with magnetic nanoparticles (MNPs), a precise force vector is remotely generated through static magnetic fields. In the present study, human neural stem cells (NSCs) were subjected to a standard differentiation protocol, in the presence or absence of nano-pulling. Under mechanical stimulation, we found an increase in the length of the neural processes which showed an enrichment in microtubules, endoplasmic reticulum, and mitochondria. A stimulation lasting up to 52 days induced a strong remodelling at the level of synapse density and a re-organization of the neuronal network, halving the time required for the maturation of neural precursors into neurons. We then injected the MNP-loaded NSCs into mouse spinal cord slices, demonstrating that nano-pulling stimulates the elongation of the NPC processes and modulates their orientation even in an ex vivo model system. To the best of our knowledge, this is the first evidence showing that active mechanical stimuli can guide the outgrowth of NSCs transplanted into the spinal cord tissue. Our findings suggest that MNPs play an important role in neuronal maturation which could be applied in regenerative medicine.
Coronary artery established through amniote evolution

Coronary arteries are part of the vascular system that nourishes the heart; they are generally considered a synapomorphy of jawed vertebrates. However, the so-called coronary arteries originated from different body parts in amniotes and other groups, and the evolution of these arteries remains unclear. Here we propose that the amniote coronary arteries were newly obtained, overriding the ancestral arterial systems. In mouse (Mus musculus) and quail (Coturnix japonica) embryos, the amniote-type coronary arteries are established by the reconstitution of the transient vascular plexus (aortic subepicardial vessels; ASVs) on the outflow tract and the primitive coronary plexus during the development. In contrast, amphibians (Xenopus laevis, Hyla japonica, Lithobates catesbeianus, and Cynops pyrrhogaster) retain the ASV-like vasculature as extrinsic cardiac arteries throughout their lives and have no primitive coronary plexus. A comparison of zebrafish (Danio rerio) and chondrichthyans (Lamna sp., Narke japonica, and Deania calcea) suggested that their hypobranchial arteries correspond morphologically to the ASVs and also serve as heart-feeding arteries throughout their lives. Thus, the coronary artery of adult amniotes is an evolutionary novelty that has acquired new anatomical connections through the addition of a new developmental process to the ancestral pattern. This change is probably related to the modification of branchial arteries, highlights the drastic morphological changes underlying the physiological transition in amniote evolution.
Conceptual Associations Generate Sensory Predictions

A crucial ability of the human brain is to learn and exploit probabilistic associations between stimuli to facilitate perception and behavior by predicting future events. Although studies have shown how perceptual relationships are used to predict sensory inputs, relational knowledge is often between concepts rather than percepts (e.g., we learned to associate cats with dogs, rather than specific images of cats and dogs). Here, we asked if and how sensory responses to visual input may be modulated by predictions derived from conceptual associations. To this end we exposed participants of both sexes to arbitrary word–word pairs (e.g., car–dog) repeatedly, creating an expectation of the second word, conditional on the occurrence of the first. In a subsequent session, we exposed participants to novel word–picture pairs, while measuring fMRI BOLD responses. All word–picture pairs were equally likely, but half of the pairs conformed to the previously formed conceptual (word–word) associations, whereas the other half violated this association. Results showed suppressed sensory responses throughout the ventral visual stream, including early visual cortex, to pictures that corresponded to the previously expected words compared with unexpected words. This suggests that the learned conceptual associations were used to generate sensory predictions that modulated processing of the picture stimuli. Moreover, these modulations were tuning specific, selectively suppressing neural populations tuned toward the expected input. Combined, our results suggest that recently acquired conceptual priors are generalized across domains and used by the sensory brain to generate category-specific predictions, facilitating processing of expected visual input. SIGNIFICANCE STATEMENT Perceptual predictions play a crucial role in facilitating perception and the integration of sensory information. However, little is known about whether and how the brain uses more abstract, conceptual priors to form sensory predictions. In our preregistered study, we show that priors derived from recently acquired arbitrary conceptual associations result in category-specific predictions that modulate perceptual processing throughout the ventral visual hierarchy, including early visual cortex. These results suggest that the predictive brain uses prior knowledge across various domains to modulate perception, thereby extending our understanding of the extensive role predictions play in perception.
Prefrontal representation of affective stimuli: importance of stress, sex, and context

Major depressive disorder diminishes health-related quality-of-life and disproportionality impacts females. Negative life events predict the onset of depressive symptoms including negative mood, anhedonia, and social withdrawal. While the neurobiology of affective illness is not completely understood, structural and functional changes in the ventromedial prefrontal cortex (vmPFC) associate with mood and anxiety disorders. Rodent studies have investigated the prefrontal impact of chronic stress, a preclinical model of mood disruption. However, ex vivo slice and postmortem histological studies have focused largely on males and yielded mixed results. Although genetically-defined recordings in behaving animals of both sexes have not been reported. Here, we hypothesized that chronic variable stress (CVS) would reduce the neural processing of affective stimuli in the infralimbic region of rodent vmPFC region. To test this hypothesis, we targeted expression of a fluorescent calcium indicator, GCaMP6s, to infralimbic pyramidal cells. In males, CVS reduced infralimbic responses to social interaction and restraint stress but increased responses to novel objects and food reward. In contrast, females did not have CVS-induced changes in infralimbic activity, which was partially dependent on ovarian status. Collectively, these results indicate that both male and female vmPFC pyramidal cells encode social, stress, and reward stimuli. However, chronic stress effects are sex-dependent and behavior-specific. Ultimately, these findings extend the understanding of chronic stress-induced prefrontal dysfunction and indicate that sex is a critical factor for cortical processing of affective stimuli. Significance Mood disorders are often preceded by stressful experiences and exhibit sex differences in prevalence. Further, affective illness is frequently accompanied by changes in prefrontal cortical function. However, the neurobiology that underlies sex-specific cortical processing of affective stimuli is poorly understood. Therefore, the current studies employ cell type-specific calcium photometry to determine the effects of chronic stress on ventromedial prefrontal cortex (vmPFC) activity in male and female rats. Our results indicate that chronic stress exposure differentially alters vmPFC encoding of social, stress, and reward stimuli. Moreover, the sex-specific effects of chronic stress are partially mediated by ovarian hormones. Ultimately, our results indicate that prolonged stress alters vmPFC function in a context-dependent and sex-specific manner, contributing to the biological bases for sex differences in emotional processing.
Plant production of high affinity nanobodies that block SARS-CoV-2 spike protein binding with its receptor, human angiotensin converting enzyme

Nanobodies® (VHH antibodies), are small peptides that represent the antigen binding domain, VHH of unique single domain antibodies (heavy chain only antibodies, HcAb) derived from camelids. Here, we demonstrate production of VHH nanobodies against the SARS-CoV-2 spike proteins in the solanaceous plant Nicotiana benthamiana through transient expression and their subsequent detection verified through western blot. We demonstrate that these nanobodies competitively inhibit binding between the SARS-CoV-2 spike protein receptor binding domain and its human receptor protein, angiotensin converting enzyme 2 (ACE2). We present plant production of nanobodies as an economical and scalable alternative to rapidly respond to therapeutic needs for emerging pathogens in human medicine and agriculture.
Msh2-Msh3 interferes with DNA metabolism in vivo

Mismatch repair (MMR) is a highly conserved DNA repair pathway that safeguards the genome from errors in DNA replication. In Saccharomyces cerevisiae, two MutS homolog (Msh) complexes, Msh2-Msh3 or Msh2-Msh6, initiate MMR. Msh2-Msh3, the focus of this study, recognizes and directs repair of insertion/deletion loops (IDLs) up to ~17 nucleotides. Msh2-Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR), and the DNA damage response. Msh2-Msh3 also promotes genome instability through trinucleotide repeat (TNR) expansions. This non-canonical activity is likely an unfortunate consequence of Msh2-Msh3’s intrinsic ability to bind a wide range of DNA structures, including those formed with single-stranded (ss) TNR sequences. We previously demonstrated that Msh2-Msh3 binding to 5’ ssDNA flap structures interfered with the in vitro binding and cleavage activities of the flap endonuclease Rad27 (Fen1 in mammals), which promotes 5’ ssDNA flap processing during Okazaki fragment maturation (OFM) and long-patch base excision repair (LP-BER). Here we demonstrate that elevated Msh2-Msh3 levels interfere with DNA replication and LP-BER in vivo, consistent with the hypothesis that protein abundance and Msh3 ATPase activities are key drivers of Msh2-Msh3-mediated genomic instability.
The spatiotemporal dynamics of semantic integration in the human brain

Language depends critically on the integration of lexical information to derive semantic concepts. The neurobiology of this fundamental aspect of human cognition remains mostly unknown. Limitations of spatiotemporal resolution have previously rendered it difficult to disentangle processes involved in semantic integration from independent computations such as tracking word meaning and establishing referents. We utilized intracranial recordings (n = 58) during the presentation of orthographic descriptions that were either referential or non-referential to a common object. Referential contexts enabled high frequency broadband gamma activation (70–150 Hz) of a distributed network including the inferior frontal sulcus (IFS), medial parietal cortex (MPC) and medial temporal lobe (MTL) in the left, language-dominant hemisphere. Components of this network (IFS, MPC), alongside posterior superior temporal sulcus, showed greater engagement for trials that did not progressively isolate a limited set of referents, relative to trials that did. IFS and posterior middle temporal gyrus activity was modulated by semantic coherence, regardless of whether the sentence picked out a common object. Centered around IFS and spreading out dorsally towards middle frontal gyrus and ventrally towards anterior/posterior inferior frontal gyrus, we uncovered a cortical mosaic of functional specialization for reference, coherence and semantic narrowing. Early processing windows implicated IFS in all aspects of semantics, and in later windows sub-portions of IFS exposed a clearer functional tessellation with some remaining overlap. This work unveils how lateral fronto-temporal regions make distinctly rich semantic contributions and are involved jointly in semantic integration and conflict resolution, depending on the sub-region and processing stage.
Behavior shapes retinal motion statistics during natural locomotion

Walking through an environment generates retinal motion, which humans rely on to perform a variety of visual tasks. Retinal motion patterns are determined by an interconnected set of factors, including gaze location, gaze stabilization, the structure of the environment, and the walker’s goals. The characteristics of these motion signals have important consequences for neural organization and behavior. However, to date, there are no empirical in situ measurements of how combined eye and body movements interact with real 3D environments to shape the statistics of retinal motion signals. Here, we collect measurements of the eyes, the body, and the 3D environment during locomotion. We describe properties of the resulting retinal motion patterns. We explain how these patterns are shaped by gaze location in the world, as well as by behavior, and how they may provide a template for the way motion sensitivity and receptive field properties vary across the visual field.
Acquisition of hybrid E/M phenotype associated with increased migration, drug resistance and stemness is mediated by reduced miR-18a levels in ER-negative breast cancer

The complexity of the ER-negative subtype of breast cancer arises due to the heterogeneous nature of the disease rendering them more aggressive and this poses a challenge to effective treatment and eventually the prognosis of the patients. We have explored the miRNA regulation of altered molecular signatures and the effect on tumour progression in ER-negative breast cancer. Using breast tumour specimens, gene expression data from public datasets and in-vitro and in-vivo model systems we have shown that low-levels of miR-18a in ER-negative tumours drives enrichment of hybrid Epithelial/Mesenchymal (E/M) cells with luminal attributes. On inhibition of miR-18a in ER-negative breast cancer cell lines, the cells showed traits of increased migration, stemness and drug-resistance. miR-18a/low tumours were also associated with increased expression of genes associated with EMT, stemness, drug resistance and immune-suppression. Further analysis of the miR-18a targets pointed out at a possible HIF-1α mediated signalling in these tumours. HIF-1α inhibition reduced the enrichment of the hybrid E/M cells and decreased the migratory ability of miR-18a/low cells. Our study reports for the first time a dual role of miR-18a in breast cancer that is subtype specific based on hormone receptor expression and a novel association of low miR-18a levels and enrichment of hybrid E/M cells. The results highlight the possibility of stratifying the ER-negative disease into clinically relevant groups by analysing epigenetic signatures.
A prediction on the impacts of China’s national emissions trading scheme on CO2 emissions from electricity generation

One of the government policies that can reduce CO2 emissions is the Emissions Trading Scheme (ETS), which was implemented in the Chinese economy on 16 July 2021. It is the largest ETS in the world, covering 12% of global CO2 emissions. Since this policy has not been experienced in China, it is necessary to predict its impact on CO2 emissions in this country. Furthermore, electricity and heat production is the major contributor to total CO2 emissions from fuel combustion. Therefore, this study attempts to predict the impact of the emissions trading scheme on CO2 emissions from the combustion of coal, oil and natural gas in electricity generation using annual data from 1985 to 2019. For this purpose, this study first predicts CO2 emissions from the combustion of coal, oil and natural gas for electricity generation in power plants using ARIMA and structural Vector Autoregression (SVAR) techniques over the 2020–2030 period. It then estimates the short- and long-run impact of the ETS policy on CO2 emissions from the combustion of coal, oil and natural gas in power plants over the projected period (2020–2030) by employing the ARDL methodology. The results suggest that the ETS policy is effective in reducing the CO2 emissions from the combustion of all fuels in electricity generation over the long-run. This is because of the increase in CO2 emissions from the combustion of these fuels in power plants in the long run, which exceed the threshold value. But in the short-run, it has a negative and statistically significant impact only on CO2 emissions from the natural gas power plants. These results suggest that improving the efficiency of all fuels can significantly reduce CO2 emissions in electricity generation from coal, oil and natural gas in the short- and long-run. They also enable China’s energy policymakers to update the ETS policy in its next phases.
Modifying the conductive properties of poly(3,4-ethylenedioxythiophene) thin films in green solvents

With the rapid development of flexible electronic devices, flexible transparent conductive materials acted as the charge transport layer or electrical interconnect in the devices are of great need. As one of the representative conductive materials, poly(3,4-ethylenedioxythiophene) (PEDOT) has received more and more attention due to its high transparency in the visible region, good flexibility, especially the tunable conductivity. In order to achieve high conductivities, various of effective approaches have been adopted to modify the PEDOT thin films. However, some strategies need to be carried out in hazardous solvents, which may pollute the environment and even hinder the application of PEDOT thin films in emerging bioelectronics. Therefore, in this mini review, we focus on the discussion about the modification methods for PEDOT thin films in green solvents. According to the source of PEDOT, the modification methods of PEDOT thin films are mainly described from two aspects: 1) modification of in-situ PEDOT, 2) modification of PEDOT complex with poly(styrenesulfonic acid) (PEDOT:PSS). Finally, we conclude with the remaining challenges for future development on the PEDOT thin films prepared by green methods.
A scientometric analysis of the 100 most cited articles on magnetic resonance guided focused ultrasound

Background Diagnostic ultrasound has long been a part of a physician’s armamentarium, but transcranial focused ultrasound (FUS) is an emerging treatment of neurological disorders. Consequently, the literature in this field is increasing at a rapid pace. Objective This analysis was aimed to identify the top-cited articles on FUS to discern their origin, spread, current trends highlighting future impact of this novel neurosurgical intervention. Methods We searched the Web of Science database on 28th May 2021 and identified the top 100 cited articles. These articles were analyzed with various scientometric parameters like the authors, corresponding authors, country of corresponding author, journal of publication, year of publication. Citation based parameters including total citations, mean citations per article and mean citations, citation count, and the citation per year, citations per year and co-authors per document were studied as well in addition to Hirsch h-index, g-index, m-index, Bradford’s Law, Lotka’s law and Collaboration index. Results The 100 top-cited articles were published between 1998 and 2019 in 45 different journals. The average citations per document and citations per document per year were 97.78 and 12.47, respectively. The most prolific authors were Hynynen K (Medical Biophysics—Toronto), Elias WJ (Neurosurgery—Virginia), Zadicario (InSightec). The Journal of Neurosurgery published the most top-cited articles (n = 11), and most articles originated from the United States, followed by Canada. Among individual institutions, the University of Toronto was the most productive. Conclusion FUS is an emerging treatment of neurological disorders. With its increasing application, the FUS literature is increasing rapidly. Eleven countries contributed to the top 100 cited articles, with the top 2 countries (the United States and Canada) contributing to more than half of these articles.