Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbispora fusca sp. nov., a novel actinomycete isolated from the ear of wheat (Triticum aestivum L.).

A novel actinomycete, designated strain NEAU-HEGS1-5T, was isolated from the ear of wheat (Triticum aestivum L.) and characterized using a polyphasic approach. The morphological and chemotaxonomic characteristics of the strain coincided with those of members of the genus Microbispora. The results of 16S rRNA gene sequence analysis showed that the isolate was most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.3 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora amethystogenes JCM 3021T (99.1 %) and Microbispora rosea subsp. rosea JCM 3006T (98.5 %). However, two tree-making algorithms supported the position that strain NEAU-HEGS1-5T formed a distinct clade with M. bryophytorum NEAU-TX2-2T, M. camponoti 2C-HV3T and M. rosea subsp. rosea JCM 3006T. Furthermore, multilocus sequence analysis based on the 16S-gyr B-rpo B genes and a combination of DNA-DNA hybridization results and some physiological and biochemical properties demonstrated that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-HEGS1-5T should be classified as representative of a novel species of the genus Microbispora, for which the name Microbispora fusca sp. nov. is proposed. The type strain is NEAU-HEGS1-5T (=CCTCC AA 2019030T=DSM 104648T).
PIRIN2 suppresses S‐type lignin accumulation in a noncell‐autonomous manner in Arabidopsis xylem elements

Summary PIRIN (PRN) genes encode cupin domain‐containing proteins that function as transcriptional co‐regulators in humans but that are poorly described in plants. A previous study in xylogenic cell cultures of Zinnia elegans suggested a role for a PRN protein in lignification. This study aimed to identify the function of Arabidopsis (Arabidopsis thaliana) PRN proteins in lignification of xylem tissues. Chemical composition of the secondary cell walls was analysed in Arabidopsis stems and/or hypocotyls by pyrolysis–gas chromatography/mass spectrometry, 2D‐nuclear magnetic resonance and phenolic profiling. Secondary cell walls of individual xylem elements were chemotyped by Fourier transform infrared and Raman microspectroscopy. Arabidopsis PRN2 suppressed accumulation of S‐type lignin in Arabidopsis stems and hypocotyls. PRN2 promoter activity and PRN2:GFP fusion protein were localised specifically in cells next to the vessel elements, suggesting a role for PRN2 in noncell‐autonomous lignification of xylem vessels. Accordingly, PRN2 modulated lignin chemistry in the secondary cell walls of the neighbouring vessel elements. These results indicate that PRN2 suppresses S‐type lignin accumulation in the neighbourhood of xylem vessels to bestow G‐type enriched lignin composition on the secondary cell walls of the vessel elements. Gene expression analyses suggested that PRN2 function is mediated by regulation of the expression of the lignin‐biosynthetic genes.
Hippocampal gamma rhythms during Y‐maze navigation in the juvenile rat

The neurobiology of postnatal hippocampal development in rodents is receiving increased attention as a means to address neurodevelopmental questions and to better understand the neural code(s) for spatial navigation in adulthood. We previously showed that spontaneous alternation (SA) in a Y‐maze, which emerges at the end of the third postnatal week, was related to changes in fast glutamatergic synaptic transmission. In adults, oscillations in the hippocampal local field potential (LFP) (i.e., theta, 4–12 Hz; slow gamma, 25–55 Hz; and fast gamma, 65–100 Hz) have been shown to coordinate the activity of spatially tuned cell types in the hippocampus during route planning and execution. Other investigators have shown that theta activity matures during the first month of life. However, relationships between developmental alterations in gamma oscillations and cognitive function have not been investigated in juveniles, and the impact of developmental changes in excitatory synaptic transmission on network activity remains unclear. We implanted rats at postnatal day 14 to record LFPs from the synaptic layer of area CA1 during Y‐maze exploration at postnatal Days 18, 19, 23, and 24. The positive allosteric modulator of AMPA receptors, CX614, or vehicle was administered prior to each test. We found that slow gamma peak frequency, but not peak power, remained constant across this age range. Fast gamma event rate increased with increasing age, while peak frequency decreased. AMPA receptor modulation impacted slow and fast gamma differently at different ages. Furthermore, gamma events showed relationships with novelty and movement speed that differed based on gamma sub‐band (slow vs. fast). These results support the presence of environmentally‐driven gamma oscillations in hippocampal network activity prior to the end of the third postnatal week of development. Differential refinement of slow and fast gamma occurring across the subsequent week supports involvement in the emergence of spatial navigation ability.
When resolution does matter: Modelling indirect contacts in dairy farms at different levels of detail

Animal exchanges are considered the major pathway for between-farm transmission of many livestock infectious diseases. Yet, vehicles and operators visiting several farms during routine activities can also contribute to disease spread. Indeed, if contaminated, they can act as mechanical vectors of fomites, generating indirect contacts between visited farms. While data on animal exchanges is often available in national databases, information about the daily itineraries of trucks and operators is rare because difficult to obtain. Thus, some unavoidable approximations have been frequently introduced in the description of indirect contacts in epidemic models. Here, we showed that the level of detail in such description can significantly affect the predictions on disease dynamics. Our analyses focused on the potential spread of a disease in a dairy farm system subject of a comprehensive data collection campaign on calf transportations. We developed two temporal multilayer networks to model between-farm contacts generated by either animal exchanges (direct contacts) and connections operated by trucks moving calves (indirect contacts). The complete model used the full knowledge of the daily trucks’ itineraries, while the partial informed one used only a subset of such available information. To account for various conditions of pathogen survival ability and effectiveness of cleaning operations, we performed a sensitivity analysis on trucks’ contamination period. An accurate description of indirect contacts was crucial both to correctly predict the final size of epidemics and to identify the seed farms responsible for generating the most severe outbreaks. The importance of detailed information emerged even more clearly in the case of short contamination periods. Our conclusions could be extended to between-farm contacts generated by other vehicles and operators. Overcoming these information gaps would be decisive for a deeper understanding of epidemic spread in livestock and to develop effective control plans.
Comparative Docking to Distinct G Protein–Coupled Receptor Conformations Exclusively Yields Ligands with Agonist Efficacy

G protein–coupled receptors exist in a whole spectrum of conformations that are stabilized by the binding of ligands with different efficacy or intracellular effector proteins. Here, we investigate whether three-dimensional structures of receptor conformations in different states of activation can be used to enrich ligands with agonist behavior in prospective docking calculations. We focused on the β2-adrenergic receptor, as it is currently the receptor with the highest number of active-state crystal structures. Comparative docking calculations to distinct conformations of the receptor were used for the in silico prediction of ligands with agonist efficacy. The pharmacology of molecules selected based on these predictions was characterized experimentally, resulting in a hit rate of 37% ligands, all of which were agonists. The ligands furthermore contain a pyrazole moiety that has previously not been described for β2-adrenergic receptor ligands, and one of them shows an intrinsic efficacy comparable to salbutamol. SIGNIFICANCE STATEMENT Structure-based ligand design for G protein–coupled receptors crucially depends on receptor conformation and, hence, their activation state. We explored the influence of using multiple active-conformation X-ray structures on the hit rate of docking calculations to find novel agonists, and how to predict the most fruitful strategy to apply. The results suggest that aggregating the ranks of molecules across docking calculations to more than one active-state structure exclusively yields agonists.
A Somatostatin Receptor Subtype-3 (SST3) Peptide Agonist Shows Antitumor Effects in Experimental Models of Nonfunctioning Pituitary Tumors

Purpose: Somatostatin analogues (SSA) are efficacious and safe treatments for a variety of neuroendocrine tumors, especially pituitary neuroendocrine tumors (PitNET). Their therapeutic effects are mainly mediated by somatostatin receptors SST2 and SST5. Most SSAs, such as octreotide/lanreotide/pasireotide, are either nonselective or activate mainly SST2. However, nonfunctioning pituitary tumors (NFPTs), the most common PitNET type, mainly express SST3 and finding peptides that activate this particular somatostatin receptor has been very challenging. Therefore, the main objective of this study was to identify SST3-agonists and characterize their effects on experimental NFPT models. Experimental Design: Binding to SSTs and cAMP level determinations were used to screen a peptide library and identify SST3-agonists. Key functional parameters (cell viability/caspase activity/chromogranin-A secretion/mRNA expression/intracellular signaling pathways) were assessed on NFPT primary cell cultures in response to SST3-agonists. Tumor growth was assessed in a preclinical PitNET mouse model treated with a SST3-agonist. Results: We successfully identified the first SST3-agonist peptides. SST3-agonists lowered cell viability and chromogranin-A secretion, increased apoptosis in vitro, and reduced tumor growth in a preclinical PitNET model. As expected, inhibition of cell viability in response to SST3-agonists defined two NFPT populations: responsive and unresponsive, wherein responsive NFPTs expressed more SST3 than unresponsive NFPTs and exhibited a profound reduction of MAPK, PI3K-AKT/mTOR, and JAK/STAT signaling pathways upon SST3-agonist treatments. Concurrently, SSTR3 silencing increased cell viability in a subset of NFPTs. Conclusions: This study demonstrates that SST3-agonists activate signaling mechanisms that reduce NFPT cell viability and inhibit pituitary tumor growth in experimental models that expresses SST3, suggesting that targeting this receptor could be an efficacious treatment for NFPTs.
FEM Simulation and Verification of Brazing SiC Ceramic with Novel Zr-Cu Filler Metal

Zr-Cu filler metal is proposed for SiC ceramic under special working conditions, as a novel type of the active filler metal, the difference of physical and chemical properties between SiC ceramic and Zr-Cu filler metal leads to greater residual stress in the joint, which affects the mechanical properties of brazing SiC ceramic joint. Based on the finite element method (FEM) simulation, the residual stress of the joint is simulated to guide the design of Zr-based filler metal and formulation of brazing process. The residual stress distribution of SiC ceramic joints brazed at 1200 °C with different thickness of the filler metal and cooling rate is simulated by ANSYS software. The simulation results of the residual stress are verified by brazing experiments and XRD measurements. The results show that the simulated residual stress of the joint is mainly axial compressive stress. The axial compressive stresses are the lowest when the filler metal thickness is 0.1 mm and the cooling rate is 2 °C /min, and increase with the increase of the filler metal layer thickness and cooling rate. The shear strength of the brazed SiC ceramic joint that achieves the highest with 2 °C /min is about 72 MPa, and then decreases with the increase of cooling rate. The experimental test of residual stress in different locations of the brazed SiC ceramic joint basically coincide with the FEM simulation.
Gellan Gum-Based Hydrogel for the Transdermal Delivery of Nebivolol: Optimization and Evaluation

Poor solubility and appreciable first-pass metabolism have limited the oral bioavailability of nebivolol. The objective of the current investigation was to design, formulate, and optimize a hydrogel-based transdermal system for nebivolol using factorial design and compare its pharmacokinetics with oral suspension. Hydrogel formulations (F1–F8) were prepared by varying the amounts of gellan gum, carbopol, and polyethylene glycol. A 23 full factorial design was used to assess the effect of independent variables such as gellan gum, carbopol, and polyethylene glycol 400 on dependent variables like viscosity, in vitro release, and ex vivo permeation after 2 h at two levels. Optimized gel (F7), containing nebivolol hydrochloride (75 mg), gellan gum (300 mg), carbopol (150 mg), polyethylene glycol 400 (20 µL), tween 80 (1 mL), ethanol (10 mL), and water (up to 30 mL) was selected and evaluated in albino rats. The physicochemical properties of F7 (pH: 7.1 ± 0.15, viscosity: 8943 ± 116 centipoise, drug content: 98.81% ± 2.16%) seem ideal for transdermal application. It was noticed that the concentration of carbopol has a more significant role than gellan gum in gel viscosity. A biphasic release pattern was exhibited by gels, and the release rate was mainly influenced by the concentration of gellan gum. Greater transdermal flux (30.86 ± 4.08 µg/cm2/h) was observed in F7 as compared with other prepared gels. Noticeable enhancement in AUC0-α value (986.52 ± 382.63 ng.h/mL; p < 0.01) of transdermal therapy (~2-fold higher compared with oral administration) established the potential of F7 to improve the rate and extent of nebivolol delivery. The overall results demonstrated here signify that F7 could be a feasible alternative to oral therapy of nebivolol.
Patient Dossier: Healthcare queries over distributed resources

As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain greatly hinders these developments, including ethical and legal issues, fragmentation of the relevant data in different locations, and a level of (meta)data complexity that requires great expertise across technical, clinical, and biological domains. We propose the Patient Dossier paradigm as a way to organize new innovative healthcare services that sorts the current limitations. The Patient Dossier conceptual framework identifies the different issues and suggests how they can be tackled in a safe, efficient, and responsible way while opening options for independent development for different players in the healthcare sector. An initial implementation of the Patient Dossier concepts in the Rbbt framework is available as open-source at https://github.com/mikisvaz and https://github.com/Rbbt-Workflows.
Anorectal Function and Quality of Life in IBD Patients With A Perianal Complaint

Abstract Purpose Anorectal function of inflammatory bowel disease (IBD) patients is still poorly understood, with contradictory results. This prospective observational study aimed to analyze the effect of perianal disease on anorectal function and quality of life in IBD patients. Methods: Patient assessment included full clinical examination, validated scores, anorectal manometry, three-dimensional endoanal ultrasonography, and endoscopy. The Inflammatory Bowel Disease Questionnaire was adopted to evaluate patients’ quality of life. Results: From January to November 2016, 37 consecutive IBD patients (30 Crohn’s disease, 7 ulcerative colitis) and 20 controls were enrolled in the study. Twenty-five patients had a history of perianal fistula, 9 reported fecal incontinence, and 2 had anal fissure. Fecal incontinent patients were older, had a longer disease duration, and higher bowel movement number than continent patients. Endoanal ultrasound findings were normal in all volunteers, while pathological features were found in 31/37 patients. Rectal sensory testing and anal pressure did not differ between the IBD patients and controls. However, the rectoanal inhibitory reflex was normally elicited in all controls vs. 32/37 (86%) IBD patients; 25/37 (68%) IBD patients showed manometric features of dyssynergic defecation. Rectal inflammation and incontinence were associated with low maximum anal resting pressure. The quality of life score was lower in ulcerative colitis patients than in Crohn’s patients and significantly lower in fecal incontinent patients. Conclusions: Anorectal function is impaired in IBD patients with perianal disease. Fecal incontinence correlates with poorer quality of life. Anorectal manometry and ultrasonography are useful tools for evaluating IBD patients.
Evaluation of Gas Formation and Consumption Driven by Crossover Effect in High Voltage Lithium-Ion Batteries with Ni-Rich NMC Cathodes.

Gas formation during lithium ion battery (LIB) cycling impacts the stability and safety of these batteries, especially for those containing Ni-rich NMC cathodes. In this paper, the cycling performance and gassing behavior of NMC811/graphite full cells with 4.2 V and 4.4 V upper cut-off voltages was first compared. Cells with 4.2 V upper cut-off voltage had good cycling stability exhibiting a capacity retention of 96.8 % after 100 cycles and generated little gas. On the other hand, cells with 4.4 V upper cut-off voltage lost over 25% of initial capacity after 100 cycles and generated large amounts of gas in the first 10 cycles. Electrochemical cycling of anode and cathode symmetric cells were implemented to isolate gases formed at electrode. GC-MS, FTIR, XPS, and STEM was used to characterize the gas formation and associated materials surfaces and structural properties. It was found that CO2 and fluorinated alkanes were the dominant gases evolved on the cathode side during cycling to 4.4 V. Gas crossover to the anode led to the depletion of gaseous products, which stabilized the cell performance to some extent. However, the growing surface reconstruction layer at the cathode, the thickening of the SEI layer at the anode, and the gradual depletion of lithium inventory collectively contributed to the continuous capacity loss of full cells cycled to 4.4 V.
The In Vivo Net Energy Content of Resistant Starch and Its Effect on Macronutrient Oxidation in Healthy Adults

The in vivo net energy content of resistant starch (RS) has not been measured in humans so it has not been possible to account for the contribution of RS to dietary energy intake. We aimed to determine the in vivo net energy content of RS and examine its effect on macronutrient oxidation. This was a randomized, double-blind cross-over study. Eighteen healthy adults spent 24 h in a whole room indirect calorimeter to measure total energy expenditure (TEE), substrate oxidation, and postprandial metabolites in response to three diets: 1) digestible starch (DS), 2) RS (33% dietary fiber; RS), or 3) RS with high fiber (RSF, 56% fiber). The in vivo net energy content of RS and RSF are 2.74 ± 0.41 and 3.16 ± 0.27 kcal/g, respectively. There was no difference in TEE or protein oxidation between DS, RS, and RSF. However, RS and RSF consumption caused a 32% increase in fat oxidation (p = 0.04) with a concomitant 18% decrease in carbohydrate oxidation (p = 0.03) versus DS. Insulin responses were unaltered after breakfast but lower in RS and RSF after lunch, at equivalent glucose concentrations, indicating improved insulin sensitivity. The average in vivo net energy content of RS is 2.95 kcal/g, regardless of dietary fiber content. RS and RSF consumption increase fat and decrease carbohydrate oxidation with postprandial insulin responses lowered after lunch, suggesting improved insulin sensitivity at subsequent meals.
Advanced Estimation Techniques for Vehicle System Dynamic State: A Survey

In order to improve handling stability performance and active safety of a ground vehicle, a large number of advanced vehicle dynamics control systems—such as the direct yaw control system and active front steering system, and in particular the advanced driver assistance systems—towards connected and automated driving vehicles have recently been developed and applied. However, the practical effects and potential performance of vehicle active safety dynamics control systems heavily depend on real-time knowledge of fundamental vehicle state information, which is difficult to measure directly in a standard car because of both technical and economic reasons. This paper presents a comprehensive technical survey of the development and recent research advances in vehicle system dynamic state estimation. Different aspects of estimation strategies and methodologies in recent literature are classified into two main categories—the model-based estimation approach and the data-driven-based estimation approach. Each category is further divided into several sub-categories from the perspectives of estimation-oriented vehicle models, estimations, sensor configurations, and involved estimation techniques. The principal features of the most popular methodologies are summarized, and the pros and cons of these methodologies are also highlighted and discussed. Finally, future research directions in this field are provided.
Clinical value of haptoglobin and soluble CD163 testing for the differential diagnosis of tuberculous and malignant pleural effusions

Abstract This study aims to evaluate the clinical value of haptoglobin (Hp) and sCD163 testing for the differential diagnosis of pleural effusion, and investigate the correlation of Hp and sCD163 with the inflammatory response of the body. Pleural effusion samples were collected from 78 patients (38 tuberculous pleural effusions [TPE] and 40 malignant pleural effusions [MPE]). The concentrations of Hp and sCD163 in the pleural effusion were measured by enzyme-linked immunosorbent assay (ELISA). The concentrations of Hp and sCD163 were significantly higher in the TPE group than in the MPE group (P < .05). The sensitivity and specificity of the Hp test for the differential diagnosis of TPE and MPE was 82.4% and 86.1%, respectively (P < .01), while the cut off value was 779.05 ug/mL. Furthermore, the sensitivity and specificity of the sCD163 test for the differential diagnosis of TPE and MPE was 76.3% and 85.0%, respectively (P < .01), while the cut off value was 16,401.11 ng/mL. Moreover, the sensitivity and specificity of the combination of Hp and sCD163 tests for diagnosing TPE was 90.0% and 87.5%, respectively. Hp and IL-1β, TNF-α, CRP and ESR were positively correlated in both the TPE group and MPE group (P < .05). Hp and sCD163 were positively correlated in the TPE group (r = 0.3735, P = .0209), but not in the MPE group (r = 0.22, P = .1684). However, there was no correlation between sCD163 and TNF-α, CRP and ESR in either the TPE group, or the MPE group (P > .05). Furthermore, sCD163 and IL-1β were weakly correlated in the TPE group (r = 0.49, P = .0018), but these had no correlation in the MPE group (r = 0.068, P = .6767). Hp and sCD163 can be used as biological markers for the differential diagnosis of pleural effusion in clinic, and the level of Hp in pleural effusion may reflect the intensity of inflammation in the body to some extent.