Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient activity of the florigen complex during the floral transition in Arabidopsis thaliana

ABSTRACT FLOWERING LOCUS T (FT) is an essential component of florigen in Arabidopsis thaliana. Transcription of FT is induced in leaves, and the resulting FT protein is transported to the shoot apex, in which it initiates floral development. Previous analyses suggest that, together with the b-ZIP transcription factor FD, FT regulates the transcription of downstream targets such as APETALA1 (AP1) in floral anlagen. However, conclusive in vivo evidence that FT is transported to the shoot apex to form an FT–FD complex is lacking. Here, using an innovative in vivo imaging technique, we show that the FT–FD complex and AP1 colocalise in floral anlagen. In addition, the FT–FD complex disappears soon after the floral transition owing to a reduction in FD transcripts in the shoot apex. We further show that misinduction of FD activity after the transition leads to defective reproductive development. Taken together, our results indicate that the FT–FD complex functions as a transient stimulus and imply that a regulatory mechanism exists during the floral transition that reduces FT–FD complex levels via modulation of FD expression. Highlighted Article: In vivo imaging analysis shows reduced levels of the florigen complex in the shoot apical meristem soon after the floral transition owing to the decreased level of FD expression.
Cryogenic free-form extrusion bioprinting of decellularized small intestinal submucosa for potential applications in skin tissue engineering

A novel strategy of cryogenic 3D bioprinting assisted by free-from extrusion printing has been developed and applied to printing of a decellularized small intestinal submucosa (dSIS) slurry. The rheological properties, including kinetic viscosity, storage modulus (G′), and loss modulus (G″), were appropriate for free-from extrusion printing of dSIS slurry. Three different groups of scaffolds, including P500, P600, and P700, with filament distances of 500, 600, and 700 μm, respectively were fabricated at a 5 mm s−1 working velocity of the platform (Vxy) and 25 kPa air pressure of the dispensing system (P) at −20 °C. The fabricated scaffolds were crosslinked via 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) which resulted in a polyporous microstructure. The variations in the filament diameter and pore size were evaluated in the initial frozen state after printing, the lyophilized state, and after immersion in a PBS solution. The Young’s modulus of the P500, P600, and P700 scaffolds was measured in wet and dry states for EDC-crosslinked scaffolds. The cell experiment results showed improved cell adhesion, viability, and proliferation both on the surface and within the scaffold, indicating the biocompatibility and suitability of the scaffold for 3D cell models. Further, gene and protein expression of normal skin fibroblasts on dSIS scaffolds demonstrated their ability to promote the production of some extracellular matrix proteins (i.e. collagen I, collagen III, and fibronectin) in vitro. Overall, this study presents a new potential strategy, by combining cryogenic 3D bioprinting with decellularized extracellular matrix materials, to manufacture ideal scaffolds for skin tissue engineering applications.
The three cytokines IL-1β, IL-18, and IL-1α share related but distinct secretory routes

Interleukin (IL)-1 family cytokines potently regulate inflammation, with the majority of the IL-1 family proteins being secreted from immune cells via unconventional pathways. In many cases, secretion of IL-1 cytokines appears to be closely coupled to cell death, yet the secretory mechanisms involved remain poorly understood. Here, we studied the secretion of the three best-characterized members of the IL-1 superfamily, IL-1α, IL-1β, and IL-18, in a range of conditions and cell types, including murine bone marrow–derived and peritoneal macrophages, human monocyte–derived macrophages, HeLa cells, and mouse embryonic fibroblasts. We discovered that IL-1β and IL-18 share a common secretory pathway that depends upon membrane permeability and can operate in the absence of complete cell lysis and cell death. We also found that the pathway regulating the trafficking of IL-1α is distinct from the pathway regulating IL-1β and IL-18. Although the release of IL-1α could also be dissociated from cell death, it was independent of the effects of the membrane-stabilizing agent punicalagin, which inhibited both IL-1β and IL-18 release. These results reveal that in addition to their role as danger signals released from dead cells, IL-1 family cytokines can be secreted in the absence of cell death. We propose that models used in the study of IL-1 release should be considered context-dependently.
Distinct gut microbiota profile in ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.

OBJECTIVE Persistent inflammation and higher risk to develop cardiovascular diseases (CVDs) still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota (GM) profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART. DESIGN Cross-sectional study including sixty-one ART-treated PHIV (age range 3-30 years old) and seventy-one age-matched healthy controls (CTRL). Blood and stool sample were collected at the same time and analyzed for GM composition and plasma biomarkers. METHODS GM composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, SI and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4+ and CD8+T-cells. RESULTS We identified two distinct GM profiles (group A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila (A.muciniphila), whereas GM of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of sE-selectin (p = 0.0296), ICAM-1 (p = 0.0028), VCAM-1 (p = 0.0230), IL-6 (p = 0.0247) and sCD14 (p = 0.0142) in group A compared to group B. CONCLUSIONS Distinctive GM profiles are differently associated with inflammation, MT and VEA. Future studies are needed in order to understand the role of A.muciniphila and risk to develop CVDs in PHIV.
Non-calcific aortic tissue quantified from computed tomography angiography improves diagnosis and prognostication of patients referred for transcatheter aortic valve implantation.

AIMS We aimed to investigate the role of aortic valve tissue composition from quantitative cardiac computed tomography angiography (CTA) in patients with severe aortic stenosis (AS) for the differentiation of disease subtypes and prognostication after transcatheter aortic valve implantation (TAVI). METHODS AND RESULTS Our study included 447 consecutive AS patients from six high-volume centres reporting to a prospective nationwide registry of TAVI procedures (POL-TAVI), who underwent cardiac CTA before TAVI, and 224 matched controls with normal aortic valves. Components of aortic valve tissue were identified using semi-automated software as calcific and non-calcific. Volumes of each tissue component and composition [(tissue component volume/total tissue volume) × 100%] were quantified. Relationship of aortic valve composition with clinical outcomes post-TAVI was evaluated using Valve Academic Research Consortium (VARC)-2 definitions.High-gradient (HG) AS patients had significantly higher aortic tissue volume compared to low-flow low-gradient (LFLG)-AS (1672.7 vs. 1395.3 mm3, P < 0.001) as well as controls (509.9 mm3, P < 0.001), but increased non-calcific tissue was observed in LFLG compared to HG patients (1063.6 vs. 860.2 mm3, P < 0.001). Predictive value of aortic valve calcium score [area under the curve (AUC) 0.989, 95% confidence interval (CI): 0.981-0.996] for severe AS was improved after addition of non-calcific tissue volume (AUC 0.995, 95% CI: 0.991-0.999, P = 0.011). In the multivariable analysis of clinical and quantitative computed tomography parameters of aortic valve tissue, non-calcific tissue volume [odds ratio (OR) 5.2, 95% CI 1.8-15.4, P = 0.003] and history of stroke (OR 2.6, 95% CI 1.1-6.5, P = 0.037) were independent predictors of 30-day major adverse cardiovascular event (MACE). CONCLUSION Quantitative CTA assessment of aortic valve tissue volume and composition can improve detection of severe AS, differentiation between HG and LFLG-AS in patients referred for TAVI as well as prediction of 30-day MACEs post-TAVI, over the current clinical standard.
Dynamic modelling of cold-hardiness in tea buds by imitating past temperature memory

Abstract Background and Aims Most perennial plants memorize cold stress for a certain period and retrieve the memories for cold acclimation and deacclimation, which leads to seasonal changes in cold-hardiness. Therefore, a model for evaluating cold stress memories is required for predicting cold-hardiness and for future frost risk assessments under warming climates. In this study we develop a new dynamic model of cold-hardiness by introducing a function imitating past temperature memory in the processes of cold acclimation and deacclimation. Methods We formulated the past temperature memory for plants using thermal time weighted by a forgetting function, and thereby proposed a dynamic model of cold-hardiness. We used the buds of tea plants (Camellia sinensis) from two cultivars, ‘Yabukita’ and ‘Yutakamidori’, to calibrate and validate this model based on 10 years of observed cold-hardiness data. Key Results The model captured more than 90 % of the observed variation in cold-hardiness and predicted accurate values for both cultivars, with root mean square errors of ~1.0 °C. The optimized forgetting function indicated that the tea buds memorized both short-term (recent days) and long-term (previous months) temperatures. The memories can drive short-term processes such as increasing/decreasing the content of carbohydrates, proteins and antioxidants in the buds, as well as long-term processes such as determining the bud phenological stage, both of which vary with cold-hardiness. Conclusions The use of a forgetting function is an effective means of understanding temperature memories in plants and will aid in developing reliable predictions of cold-hardiness for various plant species under global climate warming.
A Hybrid Information Extraction Approach Exploiting Structured Data Within a Text Mining Process

Many data sets encompass structured data fields with embedded free text fields. The text fields allow customers and workers to input information which cannot be encoded in structured fields. Several approaches use structured and unstructured data in isolated analyses. The result of isolated mining of structured data fields misses crucial information encoded in free text. The result of isolated text mining often mainly repeats information already available from structured data. The actual information gain of isolated text mining is thus limited. The main drawback of both isolated approaches is that they may miss crucial information. The hybrid information extraction approach suggested in this paper adresses this issue. Instead of extracting information that in large parts was already available beforehand, it extracts new, valuable information from free texts. Our solution exploits results of analyzing structured data within the text mining process, i.e., structured information guides and improves the information extraction process on textual data. Our main contributions comprise the description of the concept of hybrid information extraction as well as a prototypical implementation and an evaluation with two real-world data sets from aftersales and production with English and German free text fields.
Myocardial perfusion scintigraphy for risk stratification of patients with coronary artery disease: the AMICO registry.

AIMS We assessed the prognostic value of myocardial perfusion scintigraphy (MPS) with cadmium-zinc-telluride in addition to clinical and coronary anatomy analysis. METHODS AND RESULTS We prospectively enrolled 1464 patients (26% females, 69.5 ± 10.4 years) referred for stress-rest MPS. All the patients underwent invasive coronary angiography (1171, 80%) or coronary computed tomography angiography (293, 20%). We defined a composite endpoint of cardiovascular death and non-fatal MI. After an 8-year follow-up, summed stress score (SSS) had the highest accuracy in predicting primary endpoint with a ROC-derived cut-off of SSS >8 (>10% myocardium). SSS >8 portended the lowest survival probability at Kaplan-Meier analysis (P < 0.0001 for the composite endpoint and individual components). The Cox-regression analysis indicated SSS as an independent predictor of the composite endpoint, along with fasting blood glucose and total cholesterol and contrary to coronary anatomy parameters. Patients with SSS >8 treated with optimal medical therapy (OMT) had the largest area of necrosis, the lower ischaemic burden, the most compromised LV systo-diastolic function and the highest LV mass, but received a less aggressive treatment in comparison to early revascularized patients. Survival analysis revealed patients with SSS ≤8 had the greater freedom from events, irrespective of the treatment strategy, while the group with SSS >8 and OMT had the worst outcome, followed by patients with SSS >8 and early revascularization (log-rank test: all P < 0.0001). CONCLUSION MPS-SSS constitutes a strong independent predictor of future adverse events after adjustment for multiple clinical parameters and coronary angiography. In particular, MPS could help risk stratification of patients who did not undergo early revascularization.
Importance of modelling decisions on estimating trajectories of depressive symptoms and co-morbid conditions in older adults: Longitudinal studies from ten European countries

Background International comparisons of trajectories of depressive symptoms in older adults are scarce and longitudinal associations with co-morbid conditions not fully understood. Objective To compare trajectories of depressive symptoms from participants living in 10 European Countries and identify ages at which the associations of co-morbid conditions with these trajectories become more relevant. Methods Latent growth curve models were fitted to depressive symptoms scores from participants of the Survey of Health and Retirement in Europe (SHARE) initiative (combined n = 21,253) and co-morbid conditions modelled as time varying covariates. To identify the ages at which the association between co-morbid conditions and depressive symptoms was significant the Johnson-Neyman (JN) technique was used. Results The shape of depressive symptoms trajectories varied between countries, and was highly dependent on modelling decisions. The association between the average number of co-morbidities reported over time and depressive symptoms was consistent and positive across countries and ages. Conclusion International differences in ageing-related trajectories of depressive symptoms emerged. The longitudinal association of co-morbid conditions with trajectories of depressive symptoms was found, but the results overall suggest that modelling decisions could greatly influence the outcomes, and should thus be interpreted with caution.
Establishment of vestibular function multimodality platform

Background: The technology of using inertial measurement units (IMUs) to detect motions in different body segments has drawn enormous attention to research and industry. In our previous research, we have applied IMUs in evaluating and treating patients with vestibular hypofunction. Furthermore, according to the research, when a person’s head rotates over 60° on either side in the horizontal plane, and desires to focus vision on any targets, then the function of gaze shift comes in to operation. Herein, we aimed to use IMUs to build up a system to evaluate vestibular ocular reflex (VOR) during gaze shifting maneuver. Methods: In this study, we developed a platform, which combines the features of gaze shift and computerized dynamic visual acuity (cDVA), called the gaze shift DVA (gsDVA) platform. The gsDVA platform measures the orientations of the subject’s head by IMU, and executed the evaluation according to the algorithm that was developed by us. Finally, we used the VICON system to validate the performance of gsDVA platform. Results: The performance of the accuracy was 2.41° ± 1.08°, the maximal sensor error was within 4.25°, and highly correlated between our platform and VICON (p < 0.05, R = 0.99). The intraclass correlation coefficient (ICC) of between-day and within-day was 0.984 and 0.999, respectively. Furthermore, the platform not only executed the evaluation automatically but also recorded other information besides the head orientation, such as rotation speed, rotation time, reaction time, and visual acuity. Conclusion: In this study, we demonstrated the utility of vestibular evaluation, and this platform can help to clarify the relationship between gaze shift and VOR. This methodology is useful and can be applied efficiently to different disease groups for interactive evaluation and rehabilitation programs.
Elastocapillary self-assembled neurotassels for stable neural activity recordings

Neurotassels self-assemble into thin fibers through elastocapillary interactions and enable stable neural activity recordings. Implantable neural probes that are mechanically compliant with brain tissue offer important opportunities for stable neural interfaces in both basic neuroscience and clinical applications. Here, we developed a Neurotassel consisting of an array of flexible and high–aspect ratio microelectrode filaments. A Neurotassel can spontaneously assemble into a thin and implantable fiber through elastocapillary interactions when withdrawn from a molten, tissue-dissolvable polymer. Chronically implanted Neurotassels elicited minimal neuronal cell loss in the brain and enabled stable activity recordings of the same population of neurons in mice learning to perform a task. Moreover, Neurotassels can be readily scaled up to 1024 microelectrode filaments, each with a neurite-scale cross-sectional footprint of 3 × 1.5 μm2, to form implantable fibers with a total diameter of ~100 μm. With their ultrasmall sizes, high flexibility, and scalability, Neurotassels offer a new approach for stable neural activity recording and neuroprosthetics.
QSAR analysis of immune recognition for triazine herbicides based on immunoassay data for polyclonal and monoclonal antibodies

A common task in the immunodetection of structurally close compounds is to analyze the selectivity of immune recognition; it is required to understand the regularities of immune recognition and to elucidate the basic structural elements which provide it. Triazines are compounds of particular interest for such research due to their high variability and the necessity of their monitoring to provide safety for agricultural products and foodstuffs. We evaluated the binding of 20 triazines with polyclonal (pAb) and monoclonal (mAb) antibodies obtained using atrazine as the immunogenic hapten. A total of over 3000 descriptors were used in the quantitative structure-activity relationship (QSAR) analysis of binding activities (pIC50). A comparison of the two enzyme immunoassay systems showed that the system with pAb is much easier to describe using 2D QSAR methodology, while the system with mAb can be described using the 3D QSAR CoMFA. Thus, for the 3D QSAR model of the polyclonal antibodies, the main statistical parameter q2 (‘leave-many-out’) is equal to 0.498, and for monoclonal antibodies, q2 is equal to 0.566. Obviously, in the case of pAb, we deal with several targets, while in the case of mAb the target is one, and therefore it is easier to describe it using specific fields of molecular interactions distributed in space.
Voltage‐gated sodium channel‐dependent retroaxonal modulation of photoreceptor function during post‐natal development in mice

Juvenile (postnatal day 16) mice lacking Nav1.6 channels (null‐mutant Scn8admu) have reduced photoreceptor function, which is unexpected given that Nav channels have not been detected in mouse photoreceptors and do not contribute appreciably to photoreceptor function in adults. We demonstrate that acute block of Nav channels with intravitreal TTX in juvenile (P16) wild‐type mice has no effect on photoreceptor function. However, reduced light activity by prolonged dark adaptation from P8 caused significant reduction in photoreceptor function at P16. Injecting TTX into the retrobulbar space at P16 to specifically block Nav channels in the optic nerve also caused a reduction in photoreceptor function comparable to that seen at P16 in null‐mutant Scn8a mice. In both P16 null‐mutant Scn8admu and retrobulbar TTX‐injected wild‐type mice, photoreceptor function was restored following intravitreal injection of the TrkB receptor agonist 7,8‐dihydroxyflavone, linking Nav‐dependent retrograde transport to TrkB‐dependent neurotrophic factor production pathways as a modulatory influence of photoreceptor function at P16. We also found that in Scn8admu mice, photoreceptor function recovers by P22‐25 despite more precarious general health of the animal. Retrobulbar injection of TTX in the wild type still reduced the photoreceptor response at this age but to a lesser extent, suggesting that Nav‐dependent modulation of photoreceptor function is largely transient, peaking soon after eye opening. Together, these results suggest that the general photosensitivity of the retina is modulated following eye opening by retrograde transport through activity‐dependent retinal ganglion cell axonal signaling targeting TrkB receptors.
Building resilience by challenging social norms: integrating a transformative approach within the BRACED consortia

Resilience is a complex phenomenon whereby a multitude of social and environmental factors, including gender, combine to shape the ways that shocks affect people. Looking at two BRACED (Building Resilience and Adaptation to Climate Extremes and Disasters) projects, in Burkina Faso and in Ethiopia, this article uses a desk review and primary data from partners and people at risk to explore how a gender‐transformative approach can be an integral part of resilience‐building projects, particularly those implemented by multi‐stakeholder consortia. It also suggests ways to incorporate a stronger gender component in similar future projects. The article argues that donors and programme managers must provide clear principles and guidelines for achieving gender equity within resilience‐building efforts. However, these must allow flexibility to adapt to norms, needs and resources as determined by implementing partners. The right balance can be achieved by facilitating spaces for individual and collective goal‐setting; assessing current capacity and trajectories; and lesson‐sharing as an iterative process for institutional learning.