Miracle-dz/UniFAR-FTUs huggingface dataset:
HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics

Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165E indicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
Cross-linking of T cell to B cell lymphoma by the T cell bispecific antibody CD20-TCB induces IFNγ/CXCL10-dependent peripheral T cell recruitment in humanized murine model

Diffuse large B cell lymphomas (DLBCL) are a highly heterogeneous subtype of Non Hodgkin Lymphoma (NHL), accounting for about 25% of NHL [1]. Despite an increased progression-free survival upon therapy, 40-50% of patients develop relapse/refractory disease, therefore there remains an important medical need [2]. T cell recruiting therapies, such as the CD20xCD3 T cell bi-specific antibody CD20-TCB (RG6026 or glofitamab), represent a novel approach to target all stages of DLBCL, especially those that fail to respond to multiple lines of treatment [3, 4]. We aimed for a better understanding of the molecular features related to the mode of action (MoA) of CD20-TCB in inducing Target/T cell synapse formation and human T cell recruitment to the tumor. To directly evaluate the correlation between synapse, cytokine production and anti-tumor efficacy using CD20-TCB, we developed an innovative preclinical human DLBCL in vivo model that allowed tracking in vivo human T cell dynamics by multiphoton intravital microscopy (MP-IVM). By ex vivo and in vivo approaches, we revealed that CD20-TCB is inducing strong and stable synapses between human T cell and tumor cells, which are dependent on the dose of CD20-TCB and on LFA-1 activity but not on FAS-L. Moreover, despite CD20-TCB being a large molecule (194.342 kDa), we observed that intra-tumor CD20-TCB-mediated human T cell-tumor cell synapses occur within 1 hour upon CD20-TCB administration. These tight interactions, observed for at least 72 hours post TCB administration, result in tumor cell cytotoxicity, resident T cell proliferation and peripheral blood T cell recruitment into tumor. By blocking the IFNγ-CXCL10 axis, the recruitment of peripheral T cells was abrogated, partially affecting the efficacy of CD20-TCB treatment which rely only on resident T cell proliferation. Altogether these data reveal that CD20-TCB’s anti-tumor activity relies on a triple effect: i) fast formation of stable T cell-tumor cell synapses which induce tumor cytotoxicity and cytokine production, ii) resident T cell proliferation and iii) recruitment of fresh peripheral T cells to the tumor core to allow a positive enhancement of the anti-tumor effect.
Evaluation of the Direct and Enrichment Iso 10272 Methods for the Detection of Campylobacter Spp. in Chicken Meat

In 2006, the International Organization for Standardization (ISO) published two standard protocols for the detection and enumeration of Campylobacter spp. in foods: the ISO 10272-2(direct method) and the ISO 10272-1 (enrichment method). The aim of this study was to compare the efficiency of these two methods in the detection of Campylobacter spp. and propose a modification in the enrichment method. Compared with the enrichment method, the direct method yielded a higher number of positive results for Campylobacter spp. and, consequently, presented higher sensitivity percentage. The isolation of Campylobacter spp. was more difficult when 10 mL of rinse was used in the enrichment method, which is currently recommended by the ISO protocol. Therefore, different rinse volumes were tested (2.5 and 5 mL). The most efficient recovery of Campylobacter spp. occurred when 2.5 mL of rinse were used in the enrichment method, most likely due to a lower number of microbial contaminants than that present in the 5 or 10 mL rinses. The proposed modification of the enrichment method will contribute to the food analysis by improving the detection of Campylobacter spp. in chicken carcass.
Aging alters the mediating effect of endogenous GABA on the interaction between functional connectivity and motor-state transitions

Previous links endogenous gamma-aminobutyric acid (GABA) with behavioral efficiency across perceptual and cognitive domains but with potentially strongest impact on those types of behavior that require a high level of dynamic control. Using a Bayesian moderated mediation analysis, we modeled the age-associated interactions between electroencephalography- and electromyography-derived connectivity metrics and behavior and investigated the specificity of the indirect effect of GABA concentration as measured with magnetic resonance spectroscopy. Only the integrated analysis of all three modalities revealed marked differences between the two age groups. Specifically, relatively lower GABA was more beneficial for the connectivity-behavior association in the young, whereas the older showed a beneficial behavioral effect in the presence of higher GABA given their generally elevated task-related connectivity. Age-related alteration of the preferred state of endogenous GABA concentration may reflect a generic compensatory mechanism allowing for higher temporal precision in neural tuning and maintaining a higher behavioral functioning level.
Natural Oil Blend Formulation (NOBF) as an anti- African Swine Fever Virus (ASFV) agent in Primary Porcine Alveolar Macrophases (PAM) cells of Swine

African swine fever is one of the severe pathogens of swine. It has a significant impact on production and on economics. So far, there are no known remedies, such as vaccines or drugs, reported. The natural oil blend formulation (NOBF) successfully tested against the African swine fever virus (ASFV) in in vitro conditions. The natural oil blend formulation (NOBF) combines Eucalyptus globulus, Pinus sylvestris, and Lavandula latifolia. We used a two-fold serial dilution to test the NOBF formulation dose. The in vitro trial results demonstrated that NOBF up to dilution 13 or 0.000625 ml deactivates the lethal dose 105HAD50 of ASFV. There was no hemadsorption (Rosetta formation) up to dilution 12 or 0.00125 ml of NOBF. The Ct value of the NOBF group at 96 hours post-infection was the same as the initial value or lower (25), whereas the Ct value of positive controls increased several folds (17.84). The in vitro trial demonstrated that NOBF can deactivate the African swine fever virus. HIGHLIGHTS The natural oil blend formulation (NOBF) was formulated using three natural oils, i.e., Eucalyptus globulus, Pinus sylvestris, and Lavandula latifolia. The in vitro trial was conducted using porcine alveolar macrophages (PAMs) and further passaged in the PAMs; the stock used in the present study was that obtained after the 15th passage. The natural oil blend formulation (NOBF) showed protection against ASF virus up to a dilution of 13 or 0.000625 of a dilution of 16 or 0.000078 ml that was tried. The real-time PCR analysis showed that the virus did not replicate in the NOBF group, which implies that either ASFV growth was inhibited in the presence of NOBF or that it was inactivated. The in vitro trial outcome showed that NOBF has anti-ASFV properties.
LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes

Porphyromonas gingivalis (P. gingivalis), one of the most important pathogens of periodontitis, is closely associated with the aggravation and recurrence of periodontitis and systemic diseases. Antibacterial peptide LL-37, transcribed from the cathelicidin antimicrobial peptide (CAMP) gene, exhibits a broad spectrum of antibacterial activity and regulates the immune system. In this study, we demonstrated that LL-37 reduced the number of live P. gingivalis (ATCC 33277) in HaCaT cells in a dose-dependent manner via an antibiotic-protection assay. LL-37 promoted autophagy of HaCaT cells internalized with P. gingivalis. Inhibition of autophagy with 3-methyladenine (3-MA) weakened the inhibitory effect of LL-37 on the number of intracellular P. gingivalis. A cluster of orthologous groups (COGs) and a gene ontology (GO) functional analysis were used to individually assign 65 (10%) differentially expressed genes (DEGs) to an “Intracellular trafficking, secretion, and vesicular transport” cluster and 306 (47.08%) DEGs to metabolic processes including autophagy. Autophagy-related genes, a tripartite motif-containing 22 (TRIM22), and lysosomal-associated membrane protein 3 (LAMP3) were identified as potentially involved in LL-37-induced autophagy. Finally, bioinformatics software was utilized to construct and predict the protein–protein interaction (PPI) network of CAMP-TRIM22/LAMP3-Autophagy. The findings indicated that LL-37 can reduce the quantity of live P. gingivalis internalized in HaCaT cells by promoting autophagy in these cells. The transcriptome sequencing and analysis also revealed the potential molecular pathway of LL-37-induced autophagy.
Action potential-coupled Rho GTPase signaling drives presynaptic plasticity

In contrast to their postsynaptic counterparts, the contributions of activity-dependent cytoskeletal signaling to presynaptic plasticity remain controversial and poorly understood. To identify and evaluate these signaling pathways, we conducted a proteomic analysis of the presynaptic cytomatrix using in vivo biotin identification (iBioID). The resultant proteome was heavily enriched for actin cytoskeleton regulators, including Rac1, a Rho GTPase that activates the Arp2/3 complex to nucleate branched actin filaments. Strikingly, we find Rac1 and Arp2/3 are closely associated with presynaptic vesicle membranes and negatively regulate synaptic vesicle replenishment at both excitatory and inhibitory synapses. Using optogenetics and fluorescence lifetime imaging, we show this pathway bidirectionally sculpts short-term synaptic depression and that its presynaptic activation is coupled to action potentials by voltage-gated calcium influx. Thus, this study provides a new proteomic framework for understanding presynaptic physiology and uncovers a previously unrecognized mechanism of actin-regulated short-term presynaptic plasticity that is conserved across cell types.
Elevational Gradients as a Model for Understanding Associations Among Temperature, Breeding Phenology and Success

Climate change is associated with advancing phenology of seasonal traits in many taxa, but shifts by higher trophic levels are generally reduced compared with those of lower trophic levels. For example, the eclosion date of caterpillars and the lay date of insectivorous passerine birds have both advanced recently, but the former has done so more than the latter. While the ensuring phenological mismatch between predator and prey is well-documented, our understanding of the origins of this mismatch is more limited. Here we shed light on the interplay between ambient temperature, breeding phenology and reproductive success in a single population of blue tits (Cyanistes caeruleus) nesting over a 1,000 m (∼5°C) elevational gradient in the French Pyrenees. During the 6 years of this study, we found that average breeding phenology varied by 2–9 days among years, but was on average 11 days earlier at low versus high elevation. Despite the delay, breeding at high elevation was associated with lower and more variable temperatures during breeding. Early breeders within a given year generally had larger clutch sizes than late breeders, which led to more offspring fledged as typically found in other studies. However, in three of the 6 years, the probability of producing fledglings was actually lower among early layers. Additionally, birds breeding at high elevations who experience conditions typical of early breeders in other populations had reduced hatching success and were significantly less likely to fledge any young compared with those breeding at lower elevation. Reduced success at high elevation was not obviously driven by higher nest predation, which was exceptionally low, or reduced food availability because high elevation birds laid clutches of comparable size and fledged the same number of offspring of comparable mass as those breeding at low elevation. Our study reveals the capacity for substantial variation in breeding phenology within a population, but that the success of early breeders varies across years and temperature gradients. We suggest that the evolution of phenological advancements by small endotherms might be curtailed by increased probability of experiencing, and failure under, challenging meteorological conditions in late winter or very early spring.
Phenotyping severity of patient‐centered outcomes using clinical notes: A prostate cancer use case

A learning health system (LHS) must improve care in ways that are meaningful to patients, integrating patient‐centered outcomes (PCOs) into core infrastructure. PCOs are common following cancer treatment, such as urinary incontinence (UI) following prostatectomy. However, PCOs are not systematically recorded because they can only be described by the patient, are subjective and captured as unstructured text in the electronic health record (EHR). Therefore, PCOs pose significant challenges for phenotyping patients. Here, we present a natural language processing (NLP) approach for phenotyping patients with UI to classify their disease into severity subtypes, which can increase opportunities to provide precision‐based therapy and promote a value‐based delivery system.
Predicting Poor Outcome Before Endovascular Treatment in Patients With Acute Ischemic Stroke

Background: Although endovascular treatment (EVT) has greatly improved outcomes in acute ischemic stroke, still one third of patients die or remain severely disabled after stroke. If we could select patients with poor clinical outcome despite EVT, we could prevent futile treatment, avoid treatment complications, and further improve stroke care. We aimed to determine the accuracy of poor functional outcome prediction, defined as 90-day modified Rankin Scale (mRS) score ≥5, despite EVT treatment. Methods: We included 1,526 patients from the MR CLEAN Registry, a prospective, observational, multicenter registry of ischemic stroke patients treated with EVT. We developed machine learning prediction models using all variables available at baseline before treatment. We optimized the models for both maximizing the area under the curve (AUC), reducing the number of false positives. Results: From 1,526 patients included, 480 (31%) of patients showed poor outcome. The highest AUC was 0.81 for random forest. The highest area under the precision recall curve was 0.69 for the support vector machine. The highest achieved specificity was 95% with a sensitivity of 34% for neural networks, indicating that all models contained false positives in their predictions. From 921 mRS 0–4 patients, 27–61 (3–6%) were incorrectly classified as poor outcome. From 480 poor outcome patients in the registry, 99–163 (21–34%) were correctly identified by the models. Conclusions: All prediction models showed a high AUC. The best-performing models correctly identified 34% of the poor outcome patients at a cost of misclassifying 4% of non-poor outcome patients. Further studies are necessary to determine whether these accuracies are reproducible before implementation in clinical practice.
The Effect of Analytic Cognitive Style on Credulity

Belief in astrology remains strong even today, and one of the explanations why some people endorse paranormal explanations is the individual differences in analytical thinking. Therefore, the main aim of this paper was to determine the effects of priming an analytical or intuitive thinking style on the credulity of participants. In two experiments (N = 965), analytic thinking was induced and the source of fake profile (astrological reading vs. psychological testing) was manipulated and participants’ prior paranormal beliefs, anomalous explanation, cognitive reflection, and depression were measured. Although analytic thinking was proved to be hard to induce experimentally, the results showed that analytic thinking predicts credulity and belief in the paranormal was linked with experiencing more anomalous experiences and more paranormal explanations. The more people were able to think analytically, the less credulous they were as reflected in the lower acceptance of fake profile as accurate.
Metabolic Pattern of Systemic Sclerosis: Association of Changes in Plasma Concentrations of Amino Acid-Related Compounds With Disease Presentation

Objective Amino acids (AA) and their derivatives play an integral role in the synthesis of structural and regulatory elements in human organisms and therefore pathologies such as systemic sclerosis that may alter the blood pattern of these compounds. This study aimed to evaluate changes in plasma concentrations of amino acid-related metabolites in systemic sclerosis in a search for potential biomarkers and mechanisms of the disease. Methods Plasma samples from 42 patients diagnosed with systemic sclerosis (SSc) according to the 2013 American College of Rheumatology and European League Against Rheumatism ACR/EULAR classification criteria were compared to 27 matched healthy controls. Liquid chromatography/mass spectrometry was applied for the analysis of 36 amino acid-related metabolites. Results The analysis of plasma AA metabolite patterns revealed the number of changes including an increase (20%) in concentrations of NO synthase (NOS) inhibitor asymmetric dimethylarginine (ADMA) in SSc vs. healthy subjects. Furthermore, SSc patients had higher glutamine, proline, betaine, 1-methylhistidine, and methylnicotinamide levels, while the concentration of tryptophan was lower. The specific metabolic pattern was identified for several aspects of disease presentation. Most interestingly NOS inhibitor L-NAME was elevated in patients with diffuse systemic sclerosis or telangiectasia. Conclusions These results provide further evidence for the involvement of endothelium-dependent pathways in the mechanisms and presentation of SSc. Endothelial dysfunction biomarkers may be useful in the assessment of presentation and prognosis in SSc.
Emerging Roles of Disabled Homolog 2 (DAB2) in Immune Regulation

Disabled-2 (DAB2) is a clathrin and cargo binding endocytic adaptor protein recognized for its multifaceted roles in signaling pathways involved in cellular differentiation, proliferation, migration, tumor suppression, and other fundamental homeostatic cellular mechanisms. The requirement for DAB2 in the canonical TGFβ signaling in fibroblasts suggested that a similar mechanism may exist in immune cells and that DAB2 may contribute to immunological tolerance and suppression of inflammatory responses. In this review, we synthesize the current state of knowledge on the roles of DAB2 in the cells of the innate and adaptive immune system, with particular focus on antigen presenting cells (APCs; macrophages and dendritic cells) and regulatory T cells (Tregs). The emerging role of DAB2 in the immune system is that of an immunoregulatory molecule with significant roles in Treg-mediated immunosuppression, and suppression of TLR signaling in APC. DAB2 itself is downregulated by inflammatory stimuli, an event that likely contributes to the immunogenic function of APC. However, contrary findings have been described in neuroinflammatory disorders, thus suggesting a highly context-specific roles for DAB2 in immune cell regulation. There is need for better understanding of DAB2 regulation and its roles in different immune cells, their specialized sub-populations, and their responses under specific inflammatory conditions.
Lipid Accumulation and Injury in Primary Calf Hepatocytes Challenged With Different Long-Chain Fatty Acids

Fatty liver disease is one of the most common disorders afflicting dairy cows during the postpartum period, and is associated with increased blood non-esterified fatty acid (NEFA) uptake by the liver. Major long-chain fatty acids (LCFA) in NEFA are palmitic (PA), palmitoleic (POA), stearic (SA), oleic (OA), and linoleic (LA) acid. In order to investigate the characteristics of lipid accumulation and injury caused by these NEFA, primary calf hepatocytes were isolated and challenged for 12 h with 1.2 mmol/L PA, POA, SA, OA, LA, or a mixture of these LCFA (NEFA). Compared with POA, OA, and LA, culture with PA and SA led to greater abundance of CCAAT-enhancer binding protein, glucose-regulated protein 78 mRNA, and stearoyl-CoA desaturase 1 mRNA along with greater concentrations of H2O2, malondialdehyde and reactive oxygen species (ROS). Although culture with POA, OA, and LA led to lower very low density lipoprotein (VLDL) concentration in cell culture medium, POA and OA led to greater concentrations of triacylglycerol, protein abundance of sterol regulatory element-binding protein 1c, fatty acid synthase, acetyl coenzyme A carboxylase 1, ApoB100, and sortilin 1 (SORT1). Compared with individual fatty acids, culture with NEFA led to an intermediate degree of lipid accumulation and hepatocytes damage. Overall, the data suggest that saturated fatty acids cause more severe oxidative and ER stress. However, unsaturated fatty acids cause serious lipid accumulation. Furthermore, a fatty acid balanced nutrient regulation was suggested useful improve liver health of transition period dairy cows.
α2-Adrenergic Disruption of β Cell BDNF-TrkB Receptor Tyrosine Kinase Signaling

Adrenergic signaling is a well-known input into pancreatic islet function. Specifically, the insulin-secreting islet β cell expresses the Gi/o-linked α2-adrenergic receptor, which upon activation suppresses insulin secretion. The use of the adrenergic agonist epinephrine at micromolar doses may have supraphysiological effects. We found that pretreating β cells with micromolar concentrations of epinephrine differentially inhibited activation of receptor tyrosine kinases. We chose TrkB as an example because of its relative sensitivity to the effects of epinephrine and due to its potential regulatory role in the β cell. Our characterization of brain-derived neurotrophic factor (BDNF)-TrkB signaling in MIN6 β cells showed that TrkB is activated by BDNF as expected, leading to canonical TrkB autophosphorylation and subsequent downstream signaling, as well as chronic effects on β cell growth. Micromolar, but not nanomolar, concentrations of epinephrine blocked BDNF-induced TrkB autophosphorylation and downstream mitogen-activated protein kinase pathway activation, suggesting an inhibitory phenomenon at the receptor level. We determined epinephrine-mediated inhibition of TrkB activation to be Gi/o-dependent using pertussis toxin, arguing against an off-target effect of high-dose epinephrine. Published data suggested that inhibition of potassium channels or phosphoinositide-3-kinase signaling may abrogate the negative effects of epinephrine; however, these did not rescue TrkB signaling in our experiments. Taken together, these results show that (1) TrkB kinase signaling occurs in β cells and (2) use of epinephrine in studies of insulin secretion requires careful consideration of concentration-dependent effects. BDNF-TrkB signaling in β cells may underlie pro-survival or growth signaling and warrants further study.