Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal change in neural response to vocal emotion in adolescence

Abstract Adolescence is associated with maturation of function within neural networks supporting the processing of social information. Previous longitudinal studies have established developmental influences on youth’s neural response to facial displays of emotion. Given the increasing recognition of the importance of non-facial cues to social communication, we build on existing work by examining longitudinal change in neural response to vocal expressions of emotion in 8- to 19-year-old youth. Participants completed a vocal emotion recognition task at two timepoints (1 year apart) while undergoing functional magnetic resonance imaging. The right inferior frontal gyrus, right dorsal striatum and right precentral gyrus showed decreases in activation to emotional voices across timepoints, which may reflect focalization of response in these areas. Activation in the dorsomedial prefrontal cortex was positively associated with age but was stable across timepoints. In addition, the slope of change across visits varied as a function of participants’ age in the right temporo-parietal junction (TPJ): this pattern of activation across timepoints and age may reflect ongoing specialization of function across childhood and adolescence. Decreased activation in the striatum and TPJ across timepoints was associated with better emotion recognition accuracy. Findings suggest that specialization of function in social cognitive networks may support the growth of vocal emotion recognition skills across adolescence.
Influence of Temperature and Polymer Concentration on the Nonlinear Response of Highly Acetylated Chitosan–Genipin Hydrogels

Strain hardening, i.e., the nonlinear elastic response of materials under load, is a physiological response of biological tissues to mechanical stimulation. It has recently been shown to play a central role in regulating cell fate. In this paper, we investigate the effect of temperature and polymer concentrations on the strain hardening of covalent hydrogels composed of pH-neutral soluble chitosans crosslinked with genipin. A series of highly acetylated chitosans with a fraction of acetylated units, FA, in the range of 0.4–0.6 was synthesized by the homogeneous re-N-acetylation of a partially acetylated chitosan or the heterogeneous deacetylation of chitin. A chitosan sample with an FA = 0.44 was used to prepare hydrogels with genipin as a crosslinker at a neutral pH. Time and frequency sweep experiments were then performed to obtain information on the gelling kinetics and mechanical response of the resulting hydrogels under small amplitude oscillatory shear. While the shear modulus depends on the chitosan concentration and is almost independent of the gel temperature, we show that the extent of hardening can be modulated when the gelling temperature is varied and is almost independent of the experimental conditions used to build the hydrogels (ex situ or in situ gelation). The overall effect is attributed to a subtle balance between the physical (weak) entanglements and covalent (strong) crosslinks that determine the mechanical response of highly acetylated chitosan hydrogels at large deformations.
Towards improved FAIRness of the ThermoML Archive

The ThermoML Archive is a subset of Thermodynamics Research Center (TRC) data holdings corresponding to cooperation between NIST TRC and five journals: Journal of Chemical Engineering and Data (ISSN: 1520‐5134), The Journal of Chemical Thermodynamics (ISSN: 1096‐3626), Fluid Phase Equilibria (ISSN: 0378‐3812), Thermochimica Acta (ISSN: 0040‐6031), and International Journal of Thermophysics (ISSN: 1572‐9567). Data from initial cooperation (around 2003) through the 2019 calendar year are included. The archive has undergone a major update with the goal of improving the FAIRness and user experience of the data provided by the service. The web application provides comprehensive property browsing and searching capabilities; searching relies on a RESTful API provided by the Cordra software for managing digital objects. JSON files with a schema derived from ThermoML are provided as an additional serialization to lower the barrier to programmatic consumption of the information, for stakeholders who may have a preference of JSON over XML. The ThermoML and JSON files for all available entries can be downloaded from data.nist. gov (https://data.nist.gov/od/id/mds2-2422).
Dasiglucagon Effectively Mitigates Postbariatric Postprandial Hypoglycemia: A Randomized, Double-Blind, Placebo-Controlled, Crossover Trial.

OBJECTIVE To investigate the efficacy and safety of dasiglucagon, a novel stable glucagon analog in a liquid formulation, in Roux-en-Y gastric bypass (RYGB)-operated individuals suffering from postbariatric hypoglycemia (PBH). RESEARCH DESIGN AND METHODS In a randomized, double-blind, placebo-controlled, crossover trial, 10 RYGB-operated participants with continuous glucose monitoring-verified PBH were randomly assigned to 3 trial days, each consisting of a 240-min standardized liquid mixed-meal test with the subcutaneous injection of placebo or 80 μg or 200 μg dasiglucagon. RESULTS Compared with placebo, treatment with both 80 and 200 µg dasiglucagon raised nadir plasma glucose (PG) (placebo: 3.0 ± 0.2 mmol/L [mean ± SEM]; 80 μg dasiglucagon: 3.9 ± 0.3 mmol/L, P = 0.002; 200 μg dasiglucagon: 4.5 ± 0.2 mmol/L, P = 0.0002) and reduced time in hypoglycemia (PG <3.9 mmol/L) by 70.0 min (P = 0.030 and P = 0.008). CONCLUSIONS Single-dose administration of dasiglucagon effectively mitigated postprandial hypoglycemia.
Long‐term manipulation of mean climatic conditions alters drought effects on C‐ and N‐cycling in an arable soil

Climate is changing and predicted future scenarios include both changes in long‐term mean climatic conditions and intensification of extreme events such as drought. Drought can have a major impact on soil functional processes; soil microorganisms, key to these processes, depend on water and temperature dynamics. Consequently, feedback mechanisms regarding microbially mediated carbon and nitrogen cycling in soils may be affected. There are indications that microbial exposure to increasingly unfavorable environmental conditions influences their stress responses. Here, the long‐term field experiment Hohenheim Climate Change (HoCC) provided a research platform to explore how microbial exposure to long‐term reduced water availability and soil warming modifies microbially driven soil processes, especially gas fluxes from soil, both during drought and after rewetting. The HoCC experiment is an agroecosystem in which the soil microbiome has been exposed to reduced annual mean precipitation and elevated temperature since 2008. Treatment levels were chosen based on a realistic future climate scenario. In June 2019, we exposed this system to a drought period of four weeks. We found that even after 11 years, warming remained a driver of CO2 and N2O fluxes across the different soil moisture conditions in our drought experiment. Importantly, however, microbial exposure to long‐term reduced water availability limited the stimulatory effect of warming on gas fluxes during drought and after rewetting. Our results were neither related to a legacy effect within overall microbial biomass carbon levels nor a shift towards enhanced fungal abundance. We found no indications that extracellular enzyme activities or microbial substrate availability explained the gas flux dynamics observed in our drought experiment. Our study indicates that soil warming promotes gaseous C and N loss even under extreme drought conditions. We suspect, however, that a shift in microbial function following long‐term water limitation can hamper the enhancing effect of warming on soil gas fluxes.
Multi-Modal Imaging Genetics Data Fusion via a Hypergraph-Based Manifold Regularization: Application to Schizophrenia Study

Recent studies show that multi-modal data fusion techniques combine information from diverse sources for comprehensive diagnosis and prognosis of complex brain disorder, often resulting in improved accuracy compared to single-modality approaches. However, many existing data fusion methods extract features from homogeneous networs, ignoring heterogeneous structural information among multiple modalities. To this end, we propose a Hypergraph-based Multi-modal data Fusion algorithm, namely HMF. Specifically, we first generate a hypergraph similarity matrix to represent the high-order relationships among subjects, and then enforce the regularization term based upon both the inter- and intra-modality relationships of the subjects. Finally, we apply HMF to integrate imaging and genetics datasets. Validation of the proposed method is performed on both synthetic data and real samples from schizophrenia study. Results show that our algorithm outperforms several competing methods, and reveals significant interactions among risk genes, environmental factors and abnormal brain regions.
Telomerase RNA TERC and the PI3K-AKT pathway form a positive feedback loop to regulate cell proliferation independent of telomerase activity

Abstract The core catalytic unit of telomerase comprises telomerase reverse transcriptase (TERT) and telomerase RNA (TERC). Unlike TERT, which is predominantly expressed in cancer and stem cells, TERC is ubiquitously expressed in normal somatic cells without telomerase activity. However, the functions of TERC in these telomerase-negative cells remain elusive. Here, we reported positive feedback regulation between TERC and the PI3K-AKT pathway that controlled cell proliferation independent of telomerase activity in human fibroblasts. Mechanistically, we revealed that TERC activated the transcription of target genes from the PI3K-AKT pathway, such as PDPK1, by targeting their promoters. Overexpression of PDPK1 partially rescued the deficiency of AKT activation caused by TERC depletion. Furthermore, we found that FOXO1, a transcription factor negatively regulated by the PI3K-AKT pathway, bound to TERC promoter and suppressed its expression. Intriguingly, TERC-induced activation of the PI3K-AKT pathway also played a critical role in the proliferation of activated CD4+ T cells. Collectively, our findings identify a novel function of TERC that regulates the PI3K-AKT pathway via positive feedback to elevate cell proliferation independent of telomerase activity and provide a potential strategy to promote CD4+ T cells expansion that is responsible for enhancing adaptive immune reactions to defend against pathogens and tumor cells.
In vitro activity of honey, total alkaloids of Sophora alopecuroides and matrine alone and in combination with antibiotics against multidrug‐resistant Pseudomonas aeruginosa isolates

Natural products, including honey, total alkaloids of Sophora alopecuroides (TASA) and matrine have been used in combination with antibiotics against various pathogenic bacteria. However, there are limited data on the antibacterial activity of these natural products in combination against multidrug‐resistant Pseudomonas aeruginosa strains. The in vitro activity of honey, TASA and matrine alone and in combination with antibiotics against P. aeruginosa isolates was investigated. In this study, four biofilm‐producing P. aeruginosa isolates, which were resistant to multiple antibiotics, were used. These natural products were not the most effective single agent against four isolates. The fractional inhibitory concentration index method revealed the synergistic effect of matrine and TASA‐honey in combination with ciprofloxacin (Cip) against all tested isolates. When these combinations were used, the resistance of isolates to Cip was decreased significantly (six to eightfold reduction in the minimum inhibitory concentration of Cip. The disk diffusion method showed that all isolates were resistant to β‐lactams. Combinations of these antibiotics with TASA and matrine changed slightly the activity of either antibiotic used as a single agent. All isolates produced metallo‐β‐lactamase enzymes (MBL). Pretreatment isolates with Cip‐matrine and Cip‐TASA‐honey resulted in a statistically downregulated expression of the mexA gene. These natural products can be used against overactivating MexAB‐OprM but not MBL‐producing P. aeruginosa isolates.
Study on Techniques Simulation of Production System

The rationality of programming and layout for production system and operability of its scheduling scheme can be verified with simulating production system. On the base of simulation and optimization technique, applied objects, class library and simulation models were established. And materials circulation and production scheduling was simulated, key equipment and fault was analyzed and the ability of production system was evaluated. Reliable scientific gist was provided for establishing production programming and production scheduling plan.
Cotranscriptionally encoded RNA strand displacement circuits

Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions have demonstrated the largest and most computationally powerful molecular circuits to date but are limited in biological systems due to the difficulty in genetically encoding components. Here, we develop scalable cotranscriptionally encoded RNA strand displacement (ctRSD) circuits that are rationally programmed via base pairing interactions. ctRSD circuits address the limitations of DNA-based strand displacement circuits by isothermally producing circuit components via transcription. We demonstrate circuit programmability in vitro by implementing logic and amplification elements, as well as multilayer cascades. Furthermore, we show that circuit kinetics are accurately predicted by a simple model of coupled transcription and strand displacement, enabling model-driven design. We envision ctRSD circuits will enable the rational design of powerful molecular circuits that operate in biological systems, including living cells.
HiCuT: An efficient and low input method to identify protein-directed chromatin interactions

3D genome organization regulates gene expression, and disruption of these long-range (>20kB) DNA-protein interactions results in pathogenic phenotypes. Chromosome conformation methods in conjunction with chromatin immunoprecipitation were used to decipher protein-directed chromatin interactions. However, these methods required abundant starting material (>500,000 cells), sizable number of sequencing reads (>100 million reads), and elaborate data processing methods to reduce background noise, which limited their use in primary cells. Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT) is a new transposase-assisted tagmentation method that generates high-resolution protein directed long-range chromatin interactions as efficiently as existing methods, HiChIP and ChIA-PET, despite using 100,000 cells (5-fold less) and 12 million sequencing reads (8-fold fewer). Moreover, HiCuT generates high resolution fragment libraries with low background signal that are easily interpreted with minimal computational processing. We used HiCuT in human primary skin cells to link previously identified single nucleotide polymorphisms (SNPs) in skin disease to candidate genes and to identify functionally relevant transcription factors in an unbiased manner. HiCuT broadens the capacity for genomic profiling in systems previously unmeasurable, including primary cells, human tissue samples, and rare cell populations, and may be a useful tool for all investigators studying human genetics and personalized epigenomics.
Effect of Bis‐Dimethylamine Substitution on DNA Binding Property and Cytotoxic Activity of Polyhydroxyxanthone

A bis‐dimethylamine substituted xanthone (Xan‐2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6‐trihydroxyxanthone (Xan‐1) which was isolated from Polygala hongkongensis Hemsl. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan‐1 and Xan‐2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan‐2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan‐2 exhibited higher DNA binding affinity than Xan‐1. Further study showed that Xan‐2 could inhibit the proliferation of HeLa, SGC‐7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan‐2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.
Involvement of Urm1, a Ubiquitin-Like Protein, in the Regulation of Oxidative Stress Response of Toxoplasma gondii

T. gondii has an intricate life cycle which involves multiple morphologically and physiologically distinct stages, and posttranslational modifications (PTMs) may be key regulators of protein expression at relevant life cycle stages. In recent years, ubiquitin-like proteins with modification functions have been discovered and studied, including Sumo, Rub1, ATG8, and ATG12. ABSTRACT Ubiquitin-related modifier 1 (Urm1) is a ubiquitin-like molecule (UBL) with the ability to act as a posttranslational protein modifier. Here, we characterized the Toxoplasma gondii homolog of URM1 located in the tachyzoite cytoplasm. The total loss of the TgURM1 resulted in a significant reduction in parasite invasion, replication, and virulence in mice, revealing that TgURM1 plays a pivotal role in T. gondii survival. For TgURM1, urmylation was significantly induced by oxidative stress, and mutations of the C-terminal glycine-glycine motif of TgURM1 blocked the urmylation process. Furthermore, the TgURM1 knockout strain was intolerant to oxidative stress, suggesting that TgURM1 is involved in the oxidative stress process. TgAHP1, an alkyl hydroperoxide reductase, was screened via proximity-based protein labeling techniques and proteomics and was shown to interact with TgURM1 under oxidative stress conditions. In conclusion, TgURM1 is a UBL protein involved in the response of Toxoplasma to oxidative stress. IMPORTANCE T. gondii has an intricate life cycle which involves multiple morphologically and physiologically distinct stages, and posttranslational modifications (PTMs) may be key regulators of protein expression at relevant life cycle stages. In recent years, ubiquitin-like proteins with modification functions have been discovered and studied, including Sumo, Rub1, ATG8, and ATG12. Ubiquitin-related modifier 1 (Urm1) is a ubiquitin-like molecule (UBL), which is considered to be the oldest ubiquitin-like system. In this study, we identified the Urm1 gene in Toxoplasma and explored that the urmylation of Urm1 was significantly induced by oxidative stress. Fewer studies have been conducted on ubiquitin-like proteins of parasites, and our results provide theoretical support for the research of metabolic regulation and antioxidative stress processes in T. gondii.
An Application of Kane's Validity Framework to Evaluate Formative and Summative Assessment Instruments for Telesimulations in Clinical Lactation

Introduction Health professional learners have limited exposure to breastfeeding patients from diverse backgrounds in clinical rotations. Instead, simulation-based training is used for lactation skills training. There are no validated or standardized simulations and assessment rubrics for lactation. In this pilot, breastfeeding telesimulations with standardized patients (SPs) wearing a high-fidelity breast model matching their skin tone were developed. The validity of Formative and Summative Assessment Rubrics (FAR, SAR) were assessed following Kane's validity framework. The objective was to provide initial evidence for the validity of the FAR and SAR as constructs of competence in lactation support at the entry to practice or practice level. Methods Three breastfeeding case scenarios, FAR, and SAR were developed and evaluated with clinical lactation specialists (evaluators, n = 17) and SPs. The FAR was used in practice telesimulations where SPs' (n = 14) performance and telesimulation feasibility were assessed. The FAR was updated in preparation for a pilot study where medical students (n = 13) completed the 3 telesimulations. In the pilot, the updated FAR was used by SPs (n = 6) to assess medical students' performance of clinical skills. After the pilot, rubrics were updated after focus groups with SPs and discussions with evaluators. Evaluators (n = 3) graded students' posttelesimulation documentations using the SAR. Cronbach ɑ level and the intraclass correlation coefficient were assessed iteratively to collect evidence for the scoring, generalizability, and extrapolation of the FAR and SAR according to Kane's framework. Results The FAR and SAR were found to have acceptable internal consistency and moderate to high interrater reliability (intraclass correlation coefficient, 0.55–0.94), which provided evidence for scoring and generalizability of the instruments. Evaluators agreed that SPs' performances were realistic (5.6/6), and SPs' feedback was organized (5.5/6) and helpful (5.6/6), which provided evidence for extrapolation. Conclusions Initial evidence for validity of scoring, generalization, and extrapolation FAR and SAR (according to Kane's framework) in assessing health professional learner's performance of clinical lactation skills has been presented. These results from a pilot study suggest that the FAR and SAR are reliable instruments for assessing learners' clinical performance in a breastfeeding-focused telesimulation where the SP wears a high-fidelity breast model matching their skin tone. Additional studies will be required to collect evidence according to all 4 categories of Kane's framework for the validity of the FAR and SAR.
What are the visuo-motor tendencies of omnidirectional scene free-viewing in virtual reality?

Abstract Central and peripheral vision during visual tasks have been extensively studied on two-dimensional screens, highlighting their perceptual and functional disparities. This study has two objectives: replicating on-screen gaze-contingent experiments removing central or peripheral field of view in virtual reality, and identifying visuo-motor biases specific to the exploration of 360 scenes with a wide field of view. Our results are useful for vision modelling, with applications in gaze position prediction (e.g., content compression and streaming). We ask how previous on-screen findings translate to conditions where observers can use their head to explore stimuli. We implemented a gaze-contingent paradigm to simulate loss of vision in virtual reality, participants could freely view omnidirectional natural scenes. This protocol allows the simulation of vision loss with an extended field of view (>80°) and studying the head's contributions to visual attention. The time-course of visuo-motor variables in our pure free-viewing task reveals long fixations and short saccades during first seconds of exploration, contrary to literature in visual tasks guided by instructions. We show that the effect of vision loss is reflected primarily on eye movements, in a manner consistent with two-dimensional screens literature. We hypothesize that head movements mainly serve to explore the scenes during free-viewing, the presence of masks did not significantly impact head scanning behaviours. We present new fixational and saccadic visuo-motor tendencies in a 360° context that we hope will help in the creation of gaze prediction models dedicated to virtual reality.