Miracle-dz/UniFAR-FTUs huggingface dataset:
Kv1.3 induced hyperpolarisation and Cav3.2-mediated calcium entry are required for efficient Kaposi’s sarcoma-associated herpesvirus lytic replication

Understanding the host factors critical for Kaposi’s sarcoma-associated herpesvirus (KSHV) lytic replication can identify new targets for therapeutic intervention. Using pharmacological and genetic silencing approaches, we reveal for the first time that KSHV requires a B cell expressed voltage-gated K+ channel, Kv1.3, to enhance lytic replication. We show that the KSHV replication and transcription activator (RTA) protein upregulates Kv1.3 expression, leading to enhanced K+ channel activity and hyperpolarisation of the B cell membrane. Enhanced Kv1.3 activity then promotes intracellular Ca2+ influx through Cav3.2, a T-type Ca2+ channel, leading to the Ca2+ driven nuclear localisation of NFAT and the subsequent NFAT1-responsive gene expression. Importantly, KSHV lytic replication and infectious virion production could be inhibited by both Kv1.3 and Cav3.2 blockers or through Kv1.3 silencing. These findings provide new mechanistic insight into the essential role of host ion channels during KSHV infection and highlight Kv1.3 and Cav3.2 as new druggable host factors that are key to the successful completion of KSHV lytic replication.
Deep-Learning-Based Accelerated and Noise-Suppressed Estimation (DANSE) of quantitative Gradient Recalled Echo (qGRE) MRI metrics associated with Human Brain Neuronal Structure and Hemodynamic Properties

Purpose To introduce a Deep-Learning-Based Accelerated and Noise-Suppressed Estimation (DANSE) method for reconstructing quantitative maps of biological tissue cellular-specific, R2t* and hemodynamic-specific, R2′ from Gradient-Recalled-Echo (GRE) MRI data with multiple gradient-recalled echoes. Methods DANSE method adapts supervised learning paradigm to train a convolutional neural network for robust estimation of R2t* and R2′ maps free from the adverse effects of macroscopic (B0) magnetic field inhomogeneities directly from the GRE magnitude images without utilizing phase images. The corresponding ground-truth maps were generated by means of a voxel-by-voxel fitting of a previously-developed biophysical quantitative GRE (qGRE) model accounting for tissue, hemodynamic and B0-inhomogeneities contributions to GRE signal with multiple gradient echoes using nonlinear least square (NLLS) algorithm. Results We show that the DANSE model efficiently estimates the aforementioned brain maps and preserves all features of NLLS approach with significant improvements including noise-suppression and computation speed (from many hours to seconds). The noise-suppression feature of DANSE is especially prominent for data with SNR characteristic for typical GRE data (SNR~50), where DANSE-generated R2t* and R2′ maps had three times smaller errors than that of NLLS method. Conclusions DANSE method enables fast reconstruction of magnetic-field-inhomogeneity-free and noise-suppressed quantitative qGRE brain maps. DANSE method does not require any information about field inhomogeneities during application. It exploits spatial patterns in the qGRE MRI data and previously-gained knowledge from the biophysical model, thus producing clean brain maps even in the environments with high noise levels. These features along with fast computational speed can lead to broad qGRE clinical and research applications.
A Frame of Mind: Frame-based vs. Text-based Editing

Block-based programming has become popular for children and young school students, but at university level almost all programming is still text-based. A third intermediate option is the use of frame-based editors that combine elements of both block- and text-based systems. However, there have been few evaluations of the efficacy of frame-based editing, so its suitability for school use is uncertain. This paper describes an experiment comparing the use of frame-based and text-based editing in a UK school setting. A total of 85 teenage students from five different schools each completed three sessions of object-oriented programming tasks and a programming quiz, with each school assigned to use either a text-based editor or frame-based editor. We found no difference in understanding of object-oriented concepts between the two editors, and no difference in task completion times. This provides some evidence to suggest that frame-based editing is a viable option for use in a school setting, in place of text-based editing.
Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia, and solid tumor metastasis

The bone marrow microenvironment provides indispensable factors to sustain blood production throughout life. It is also a hotspot for the progression of hematologic disorders and the most frequent site of solid tumor metastasis. Preclinical research relies on xenograft mouse models, but these models preclude the human-specific functional interactions of stem cells with their bone marrow microenvironment. Instead, human mesenchymal cells can be exploited for the in vivo engineering of humanized niches, which confer robust engraftment of human healthy and malignant blood samples. However, mesenchymal cells are associated with major reproducibility issues in tissue formation. Here, we report the fast and standardized generation of human mini-bones by a custom-designed human mesenchymal cell line. These resulting humanized ossicles (hOss) consist of fully mature bone and bone marrow structures hosting a human mesenchymal niche with retained stem cell properties. As compared to mouse bones, we demonstrate superior engraftment of human cord blood hematopoietic cells and primary acute myeloid leukemia samples and also validate hOss as a metastatic site for breast cancer cells. We further report the engraftment of neuroblastoma patient-derived xenograft cells in a humanized model, recapitulating clinically described osteolytic lesions. Collectively, our human mini-bones constitute a powerful preclinical platform to model bone-developing tumors using patient-derived materials. Description Human mini-bones provide an advanced platform for the in vivo modeling of bone-developing cancers. Observations in ossicles Studying the interaction of cells with the bone marrow microenvironment is important for understanding cancer metastasis, but human-mouse mismatch in xenograft mouse models makes this difficult. Here, Grigoryan et al. generated mini-bones (ossicles, hOss) in mice by culturing a human mesenchymal cell line engineered to express bone morphogenetic protein 2 under Cho or Ost conditions and then implanting the cells subcutaneously. Transplanted human cord blood hematopoietic stem/progenitor cells engrafted in the hOss, and acute myeloid leukemia cells also engrafted in hOss. The authors further demonstrated that human breast and neuroblastoma cancer cells metastasized to the hOss and formed osteolytic lesions, respectively. This engineered bone model could be useful for investigating cell interactions in the bone marrow niche.
Optimal strategies to protect a sub-population at risk due to an established epidemic

Epidemics can particularly threaten certain sub-populations. For example, for SARS-CoV-2, the elderly are often preferentially protected. For diseases of plants and animals, certain sub-populations can drive mitigation because they are intrinsically more valuable for ecological, economic, socio-cultural or political reasons. Here we use optimal control theory to identify strategies to optimally protect a “high value” sub-population when there is a limited budget and epidemiological uncertainty. We use protection of the Redwood National Park in California in the face of the large ongoing state-wide epidemic of sudden oak death (caused by Phytophthora ramorum) as a case study. We concentrate on whether control should be focused entirely within the National Park itself, or whether treatment of the growing epidemic in the surrounding “buffer region” can instead be more profitable. We find that, depending on rates of infection and the size of the ongoing epidemic, focusing control on the high value region is often optimal. However, priority should sometimes switch from the buffer region to the high value region only as the local outbreak grows. We characterise how the timing of any switch depends on epidemiological and logistic parameters, and test robustness to systematic misspecification of these factors due to imperfect prior knowledge.
Behavioral and Neurostructural changes associated with Chronic Amygdala Hyperactivation

Background The amygdala (AMY) is a key brain region of the limbic system that plays a critical role in emotion processing and stress response. Functional magnetic resonance imaging (fMRI) studies identified abnormal AMY activation in psychiatric illnesses including major depressive disorder (MDD). Stress exposure is a major precipitating factor of MDD episodes which are associated with AMY hyperactivity. Preclinical studies using of pharmacologic, opto- and chemogenetic approaches to activate AMY neurons have consistently demonstrated that acute AMY hyperactivation induces anxiety-like behaviors in mice. However, it remains unknown if chronic hyperactivation of the amygdala (cHOA) is sufficient to induce chronic stress-like deficits or is a susceptibility factor for chronic stress-induced behavioral, volumetric and synaptic deficits. Methods Using designer receptor exclusively activated by designer drug (DREADD) approach, basolateral amygdala (BLA) neurons of Camk2a-cre mice infected with a virus driving the expression of the Gq-coupled DREADD were activated with clozapine-N-oxide (in drink water for 5 weeks). Mice were then exposed to chronic restraint stress (CRS; 1X/day for 1hr) for 2 weeks. All mice were behaviorally assessed in the Phenotyper (PT), and sucrose consumption tests (SCT) each week and in the novelty supressed feeding (NSF, once at the end of the experiment). Animals were then perfused for ex vivo-MRI and puncta density analysis. Results We found that mice with cHOA displayed a progressive increase in baseline anxiety-like deficits in the PT test and slightly more marked deficits following CRS compared to controls, but not statistically different from animals subjected to CRS alone. Also, cHOA did not exacerbate CRS effect in the NSF. No significant cAH effect was found in the SCT before or after CRS. MRI analysis revealed no statistical charges between groups, while increased synaptic puncta density was found in cHOA mice subjected to CRS compared to cHOA or CRS alone. Conclusion We demonstrate that cAH is sufficient to induce anxiety and may exacerbate CRS effects on anxiety and synaptic measures. Results also suggest that cHOA was not sufficient to induce depressive-like behavior and was not a vulnerability factor for stress-induced depressive-like behavior in mice. Altogether, our findings imply that a strong causal link between AMY hyperactivity and elevated anxiety, but not depressive-like behaviors and provide critical information to clinical research focused on using AMY activity level as a biomarker in stress-related illnesses.
Vestibular CCK signaling drives motion-induced malaise

Travel can induce motion sickness (MS) in susceptible individuals. MS is an evolutionary conserved mechanism caused by mismatches between motion-related sensory information and past visual and motion memory, triggering a malaise accompanied by hypolocomotion, hypothermia, hypophagia and nausea. Vestibular nuclei (VN) are critical for the processing of movement input from the inner ear. Motion-induced activation of VN neurons recapitulates MS-related signs. However, the genetic identity of VN neurons mediating MS- related autonomic and aversive responses remains unknown. Here, we identify a central role of cholecystokinin (CCK)-expressing VN neurons in motion-induced malaise. Moreover, we show that CCK VN inputs onto the parabrachial nucleus activate Calca- expressing neurons and are sufficient to establish avoidance to novel food, which is prevented by CCK-A receptor antagonism. These observations provide greater insight into the neurobiological regulation of MS by identifying the neural substrates of MS and providing potential targets for treatment. SIGNIFICANCE STATEMENT We live in an age where travel is paramount. However, one of the most disabling conditions inherent to traveling is motion sickness (MS). While studies have underscored the role of the vestibular system in the development of MS, the neuronal populations involved in motion-induced malaise remain largely unknown. Here, we describe the vestibular pathways eliciting MS responses, and identify a key role for cholecystokinin (CCK)-expressing vestibular neurons. We reveal that a vestibulo-parabrachial (PBN) CCKergic projection is sufficient to induce conditioned taste aversion, likely through the activation of calcitonin gene-related peptide-expressing PBN neurons. Finally, we underscore the role of CCK-A receptor signaling as a novel druggable target to treat MS, providing novel insight on the neurobiological substrates of MS.
Weight Pulling: A Novel Mouse Model of Human Progressive Resistance Exercise

This study describes a mouse model of progressive resistance exercise that utilizes a full-body/multi-joint exercise (weight pulling) along with a training protocol that mimics a traditional human paradigm (3 training sessions per week, ∼8-12 repetitions per set, 2 minutes of rest between sets, ∼2 maximal-intensity sets per session, last set taken to failure, and a progressive increase in loading that is based on the individual’s performance). We demonstrate that weight pulling can induce an increase in the mass of numerous muscles throughout the body. The relative increase in muscle mass is similar to what has been observed in human studies, and it is associated with the same type of long-term adaptations that occur in humans (e.g., fiber hypertrophy, myonuclear accretion, and in some instances a fast-to-slow transition in Type II fiber composition). Moreover, we demonstrate that weight pulling can induce the same type of acute responses that are thought to drive these long-term adaptations (e.g., the activation of signaling through mTORC1 and the induction of protein synthesis at 1 hr post-exercise). Collectively, the results of this study indicate that weight pulling can serve as a highly translatable mouse model of progressive resistance exercise.
Osteoblast-osteoclast co-cultures: A systematic review and map of available literature

Drug research with animal models is expensive, time-consuming and translation to clinical trials is often poor, resulting in a desire to replace, reduce, and refine the use of animal models. One approach to replace and reduce the use of animal models in research is using in vitro cell-culture models. To study bone physiology, bone diseases and drugs, many studies have been published using osteoblast-osteoclast co-cultures. The use of osteoblast-osteoclast co-cultures is usually not clearly mentioned in the title and abstract, making it difficult to identify these studies without a systematic search and thorough review. As a result, researchers are all developing their own methods from the ground up, leading to conceptually similar studies with many methodological differences and, as a direct consequence, incomparable results. The aim of this study was to systematically review existing osteoblast-osteoclast co-culture studies published up to 6 January 2020, and to give an overview of their methods, predetermined outcome measures (formation and resorption, and ALP and TRAP quantification as surrogate markers for formation and resorption, respectively), and other useful parameters for analysis. Information regarding these outcome measures was extracted and collected in a database, and each study was further evaluated on whether both the osteoblasts and osteoclasts were analyzed using relevant outcome measures. From these studies, additional details on methods, cells and culture conditions were extracted into a second database to allow searching on more characteristics. The two databases presented in this publication provide an unprecedented amount of information on cells, culture conditions and analytical techniques for using and studying osteoblast-osteoclast co-cultures. They allow researchers to identify publications relevant to their specific needs and allow easy validation and comparison with existing literature. Finally, we provide the information and tools necessary for others to use, manipulate and expand the databases for their needs.
Favorable clinical response and drug retention of anti-IL-6 receptor inhibitor in rheumatoid arthritis with high CRP levels: the ANSWER cohort study

Objective Currently, biological disease-modifying anti-rheumatic drugs (bDMARDs) with different modes of action [tumour necrosis factor inhibitor (TNFi), interleukin-6 receptor inhibitor (IL-6Ri), or cytotoxic T-lymphocyte antigen 4–immunoglobulin (CTLA4-Ig)] are used in clinical practice to treat rheumatoid arthritis (RA). However, it is unclear which type of bDMARD is the most efficacious for a specific clinical situation. C-reactive protein (CRP) is an acute-phase reactant driven by IL-6 signalling. Here, we aimed to establish whether therapeutic efficacy differs between IL-6Ri and other bDMARDs with alternative modes of action in RA patients according to their CRP level. Method RA patients treated with bDMARDs were enrolled from an observational multicentre registry in Japan. Patients were classified into three groups according to baseline CRP tertiles. The overall 3 year retention rates of each bDMARD category were assessed. The Clinical Disease Activity Index (CDAI) was also assessed before and 3, 6, and 12 months after bDMARD initiation. Results A total of 1438 RA patients were included and classified into three groups according to tertiles of baseline CRP levels (CRP1, 0–0.3; CRP2, 0.3–1.8; CRP3, 1.8–18.4 mg/dL). In CRP3, the overall 3 year drug retention rates were significantly higher for IL-6Ri than for TNFi and CTLA4-Ig (77.5 vs 48.2 vs 67.3, respectively). No significant difference was evident in terms of CDAI 12 months after bDMARD initiation in CRP1–CRP3. Conclusion IL-6Ri may be a favourable therapeutic option over TNFi and CTLA4-Ig in RA patients with high CRP levels.
Kif11 overexpression rescues cognition, long-term potentiation, and spine defects in mouse and cell models of Alzheimer’s disease

Competitive inhibition of kinesin motor proteins by amyloid-beta (Aβ) may contribute to alterations in the neuronal microtubule cytoskeleton that can disrupt plasticity mechanisms required for learning and memory, such as long-term potentiation (LTP), thus contributing to synaptic dysfunction and cognitive impairments associated with Alzheimer’s disease (AD). Here, we tested the hypothesis that overexpression of the microtubule motor protein KIF11 (Kinesin-5/Eg5) will rescue Aβ-mediated synaptic dysfunction and cognitive impairments. We found that overexpression of Kif11 prevented spatial learning and LTP deficits in the 5xFAD mouse model of AD and rescued Aβ-mediated decreases in postsynaptic dendritic spine density in neuronal cultures. Together, these data suggest that KIF11 function is important for preserving synaptic structures and functions that are critical for learning and memory and for protection against Aβ-mediated loss of cognition in AD. Highlights Deficits in cognition and long-term potentiation in the 5xFAD mouse model of Alzheimer’s disease are prevented by Kif11 overexpression. Aβ-mediated dendritic spine loss is blocked by Kif11 overexpression.
Drug Repurposing for Targeting Acute Leukemia With KMT2A (MLL)—Gene Rearrangements

The treatment failure rates of acute leukemia with rearrangements of the Mixed Lineage Leukemia (MLL) gene highlight the need for novel therapeutic approaches. Taking into consideration the limitations of the current therapies and the advantages of novel strategies for drug discovery, drug repurposing offers valuable opportunities to identify treatments and develop therapeutic approaches quickly and effectively for acute leukemia with MLL-rearrangements. These approaches are complimentary to de novo drug discovery and have taken advantage of increased knowledge of the mechanistic basis of MLL-fusion protein complex function as well as refined drug repurposing screens. Despite the vast number of different leukemia associated MLL-rearrangements, the existence of common core oncogenic pathways holds the promise that many such therapies will be broadly applicable to MLL-rearranged leukemia as a whole.
Urgency disrupts cognitive control of human action

Intelligent behavior requires cognitive control, the ability to act directed by goals despite competing action tendencies triggered by stimuli in the environment. For eye movements, it has recently been discovered that cognitive control is briefly disrupted in urgent situations (Salinas et al., 2019). In a time-window before an urgent response, participants could not help but look at a suddenly appearing visual stimulus, even though their goal was to look away from it. Urgency seemed to provoke a new visual-oculomotor phenomenon: A period in which saccadic eye movements are dominated by external stimuli, and uncontrollable by current goals. This period was assumed to arise from brain mechanisms controlling eye movements and spatial attention, such as those of the frontal eye field. Here, we show that the phenomenon is more general than previously thought. We found that urgency disrupted cognitive control also in well-investigated manual tasks, so that responses were dominated by goal-conflicting stimulus features. This dominance of behavior followed established trial-to-trial signatures of cognitive control that replicate across a variety of tasks. Thus together, these findings reveal that urgency temporarily impairs cognitive control in general, not only at brain mechanisms controlling eye movements.
Finding a Balance: Characterizing Teaching and Research Anxieties in Biology Graduate Teaching Assistants (GTAs)

Graduate students in the United States are reporting increased anxiety, affecting their mental health and attrition in graduate programs. Yet we are only beginning to understand what contributes to graduate student anxiety. Biology Graduate Teaching Assistants (GTAs) have simultaneous roles as teachers, researchers, students, and employees, and factors associated with these tasks may contribute to anxieties in graduate school, particularly in relation to teaching and research responsibilities. To explore factors related to GTA teaching and research anxieties, and guided by social cognitive career theory, we interviewed 23 Biology GTAs at a research-intensive southeastern university. Thematic analysis of interview transcripts revealed five major factors related to GTA anxieties: negative impact on self, negative impact on others, lack of self-efficacy, role tension, and personal anxieties. Lack of self-efficacy was most prevalent for research anxieties, compared to teaching anxieties, where the impact on others (e.g. students) was most prevalent. In research contexts, GTAs with academic career aspirations expressed less anxiety about role tensions compared to GTAs with non-academic career goals. By investigating GTA anxieties, this work can inform professional development or mental health interventions for GTAs and encourage greater awareness and dialogue about mental health issues in academia.