Miracle-dz/UniFAR-FTUs huggingface dataset:
Interfacial viscosities via stress autocorrelation functions

Transport properties of simple liquids (the Lennard-Jones model) have been determined, from stress correlation functions, for both the homogeneous liquid and in narrow pores of molecular dimensions. Viscosity profiles are defined by means of a resolution of the total stress tensor and its autocorrelation function into auto- and cross-components of single molecules. This enables a precise definition of viscosity profiles and provides a method of determination from molecular dynamics (MD) simulations of the interfacial regions. Preliminary shear viscosity profiles for liquids in periodic rectangular cavities (between two semi-infinite walls) have been obtained for both the transverse and longitudinal components. Profiles of these transport coefficients have no direct experimentally accessible counterparts, but could be useful for bulk fluid mechanics predictions. Results are presented for (i) a hard, elastic wall–molecule interaction and (ii) a Lennard-Jones (10–4) cohesive wall. Elongational viscosities, which have not previously been investigated via MD correlation functions have also been computed for the homogeneous fluid and the interfacial system. The results are discussed in relation to current experimentation on interfacial viscosities (including recent non-equilibrium molecular dynamics studies).
Role of the Ipsilateral Primary Motor Cortex in the Visuo-Motor Network During Fine Contractions and Accurate Performance

It is widely recognized that continuous sensory feedback plays a crucial role in accurate motor control in everyday life. Feedback information is used to adapt force output and to correct errors. While primary motor cortex contralateral to the movement (cM1) plays a dominant role in this control, converging evidence supports the idea that ipsilateral primary motor cortex (iM1) also directly contributes to hand and finger movements. Similarly, when visual feedback is available, primary visual cortex (V1) and its interactions with the motor network also become important for accurate motor performance. To elucidate this issue, we performed and integrated behavioral and electroencephalography (EEG) measurements during isometric compression of a compliant rubber bulb, at 10% and 30% of maximum voluntary contraction, both with and without visual feedback. We used a semi-blind approach (functional source separation (FSS)) to identify separate functional sources of mu-frequency (8-13[Formula: see text]Hz) EEG responses in cM1, iM1 and V1. Here for the first time, we have used orthogonal FSS to extract multiple sources, by using the same functional constraint, providing the ability to extract different sources that oscillate in the same frequency range but that have different topographic distributions. We analyzed the single-trial timecourses of mu power event-related desynchronization (ERD) in these sources and linked them with force measurements to understand which aspects are most important for good task performance. Whilst the amplitude of mu power was not related to contraction force in any of the sources, it was able to provide information on performance quality. We observed stronger ERDs in both contralateral and ipsilateral motor sources during trials where contraction force was most consistently maintained. This effect was most prominent in the ipsilateral source, suggesting the importance of iM1 to accurate performance. This ERD effect was sustained throughout the duration of visual feedback trials, but only present at the start of no feedback trials, consistent with more variable performance in the absence of feedback. Overall, we found that the behavior of the ERD in iM1 was the most informative aspect concerning the accuracy of the contraction performance, and the ability to maintain a steady level of contraction. This new approach of using FSS to extract multiple orthogonal sources provides the ability to investigate both contralateral and ipsilateral nodes of the motor network without the need for additional information (e.g. electromyography). The enhanced signal-to-noise ratio provided by FSS opens the possibility of extracting complex EEG features on an individual trial basis, which is crucial for a more nuanced understanding of fine motor performance, as well as for applications in brain-computer interfacing.
Examining factors related to the age of diagnosis of children with autism spectrum disorder from immigrant and non‐immigrant backgrounds in a diverse clinical sample

A timely diagnosis of autism spectrum disorder (ASD) is important for children as that may help inform the best services and supports needed for optimal outcomes. However, disparities in the identification of ASD have been consistently documented for racial/ethnic minority and immigrant populations. The majority of studies of immigrant populations have focused on the qualitative experience of ASD, however, greater knowledge about the predictors of the age of initial ASD diagnosis is needed. This study examined the child, maternal, and family‐level factors that predicted the age of initial ASD diagnosis in a diverse clinical sample through a retrospective medical record review. Medical records of clinical evaluations conducted between 2004 and 2014 were reviewed for children with ASD born to immigrant and non‐immigrant mothers. Regression analyses found that for both groups of children with ASD, using verbal language to communicate and having another diagnosis (attention‐deficit/hyperactivity disorder or another condition) predicted an older age of initial ASD diagnosis. For children with ASD born to immigrant mothers, residing in a multilingual household was associated with a younger age of diagnosis. These results highlight the complexities of an ASD diagnosis among diverse children and families, particularly among immigrant communities.
Association Between Hemoglobin and Growth Hormone Peak in Chinese Children and Adolescents with Short Stature: A Cross-Sectional Study

Objective This research aimed to investigate the relationship between hemoglobin (Hb) and growth hormone (GH) peak in children and adolescents with short stature. Design This cross-sectional study included a total of 787 children and adolescents with short stature. Anthropometric and biochemical indicators were measured at baseline. All patients underwent GH provocation tests with L-dopa and insulin to assess GH peak levels. Results The univariate analysis results showed that Hb was positively associated with GH peak (β 0.07, P=0.001). Furthermore, a non-linear relationship was detected between Hb and GH peaks through smooth curve fitting, and the inflection point was 123 g/L after multivariate piecewise linear regression analysis. GH peak increased with Hb elevation when the Hb level was greater than 123 g/L (β 0.08, 95% CI 0.01, 0.14; P=0.0207). Conclusion In children and adolescents with short stature, we found GH peak was positively associated with the Hb level when the Hb level reached the inflection point.
Outcomes in CLL patients with NOTCH1 regulatory pathway mutations

All authors made substantial contributions to the (a) conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; and (b) drafting the work or revising it critically for important intellectual content; and (c) final approval of the version to be published. All authors (d) agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
Polyamide 6 composite nano-fiber/net functionalized by polyethyleneimine on quartz crystal microbalance for highly sensitive formaldehyde sensors

A nanostructured complex, polyethyleneimine (PEI) functionalized polyamide 6 (PA 6) (PEI-PA 6) nano-fiber/net (NFN), is developed as a novel sensing coating on quartz crystal microbalance (QCM) for highly sensitive formaldehyde detection. The NFN structured substrate comprising common electrospun nanofibers and two-dimensional (2D) spider-web-like nano-nets fabricated by a facile electro-spinning/netting (ESN) process, exhibit large specific surface area, high porosity and large stacking density, which make them optimal candidates for sensing applications. The responses of the sensors in response to formaldehyde were analyzed in terms of PA 6 NFN membranes morphologies, PA 6 substrate and sensing PEI coating loads, and the comparison with nanoporous fibers. Experimental results show that this new PEI-PA 6 NFN nanostructure based QCM sensor exhibits excellent formaldehyde sensing performances in terms of remarkably low detection limit (50 ppb), rapid response, superior selectivity and good reproducibility. We expect the highly sensitive and robust NFN-based QCM sensor may serve as a practical and powerful tool for gas sensing and chemical analysis.
Engineering and optimization of the 2-phenylethylglucosinolate production in Nicotiana benthamiana by combining biosynthetic genes from Barbarea vulgaris and Arabidopsis thaliana

Among the glucosinolate (GLS) defense compounds characteristic of the Brassicales order, several have been shown to promote human health. This includes 2-phenylethylglucosinolate (2PE) derived from homophenylalanine (HPhe). In this study, we used transient expression in Nicotiana benthamiana to validate and characterize previously predicted key genes in the 2PE biosynthetic pathway from Barbarea vulgaris and demonstrate the feasibility of engineering 2PE production. We used genes from B. vulgaris and Arabidopsis thaliana, in which the biosynthesis of GLSs is predominantly derived from HPhe and dihomomethionine, respectively. The resulting GLS profiles partially mirrored GLS profiles in the gene donor plant, but in both cases the profiles in N. benthamiana were wider than in the native plants. We found that BvBCAT4 is a more efficient entry enzyme for biosynthesis of both HPhe and dihomomethionine and that MAM1 enzymes determine the chain-elongated profile. Co-expression of the chain elongation pathway and CYP79F6 from B. vulgaris with the remaining aliphatic GLS core pathway genes from A. thaliana, demonstrated the feasibility of engineering production of 2PE in N. benthamiana. Noticeably, the HPhe-converting enzyme BvCYP79F6 in the core GLS pathway belongs to the CYP79F subfamily, a family believed to have substrate specificity towards chain-elongated methionine derivatives. Replacing the B. vulgaris chain elongation pathway with a chimeric pathway consisting of BvBCAT4, BvMAM1, AtIPMI and AtIPMDH1 resulted in an additional 2-fold increase in 2PE production, demonstrating that chimeric pathway with genes from different species can increase flux and boost production in an engineered pathway. Our study provides a novel approach to produce the important HPhe and 2PE in a heterologous host. Chimeric engineering of a complex biosynthetic pathway enabled detailed understanding of catalytic properties of individual enzymes - a prerequisite for understanding biochemical evolution - and with biotechnological and plant breeding potentials of new-to-nature gene combinations.
Deletion of Calponin 2 Reduces the Formation of Postoperative Peritoneal Adhesions

Abstract Aim of the study: Postoperative peritoneal adhesions are a common cause of morbidity after surgery, resulting in multiple complications. Macrophage-mediated inflammation and myofibroblast differentiation after tissue injury play central roles in the pathogenesis and progression of adhesion formation. Calponin 2 is an actin cytoskeleton regulatory protein in endothelial cells, macrophages and fibroblasts that are key players in the development of fibrosis. Deletion of calponin 2 has been shown to attenuate inflammatory arthritis, atherosclerosis and fibrocalcification of the aortic valves. The present study investigated the effect of calponin 2 deletion on attenuating the formation of peritoneal adhesions in a mouse model for potential use as a new therapeutic target. Materials and methods: Sterile surgical procedures under general anesthesia were used on paired wild type (WT) and calponin 2 knockout (KO) mice to generate mild injury on the cecal and abdominal wall peritonea. Three and seven days post-operation, the mice were compared postmortem for the formation of peritoneal adhesions. Tissues at the adhesion sites were examined with histology and immunofluorescent studies for macrophage and myofibroblast activations. Results: Quantitative scoring demonstrated that calponin 2 KO mice developed significantly less postoperative peritoneal adhesions than that in WT mice. Calponin 2 deletion resulted in less infiltration of F4/80+ macrophages at the adhesion sites with less myofibroblast differentiation and collagen deposition than WT controls. Conclusions: The data show that deletion of calponin 2 effectively reduces postoperative peritoneal adhesion, presenting a novel molecular target for clinical prevention.
Electroactive biofilms: Current status and future research needs

Electroactive biofilms (EABFs) generated by electrochemically active microorganisms have many potential applications in bioenergy and chemicals production. Biofilm electroactivity can have a significant impact on the yield and efficiency of the conversion processes. This review assesses the effects of process and design parameters on the growth and activity of biofilms in bioelectrochemical systems (BESs). First we compare the role of planktonic and biofilm-forming microorganisms in BESs. The effect of physical, chemical, and electrochemical operating parameters such as flow rate, temperature, pH, ionic strength, substrate concentration and loading, external resistance, and redox potential on EABF attributes such as growth rate, exoelectrogen population, formation of extracellular polymeric substances, mediator synthesis, and rate of electron transfer are discussed. The relationship between electrochemical performance and operating parameters is also examined to identify gaps in assessment and the potential role of future modeling efforts. Similarly, we review what is currently known about the mechanisms that enable electroactive biofilms to transfer electrons and also the contribution of the electrical conductivity of the biofilms' exopolymeric components to BES performance. The current status of cathodic biofilms is also reviewed. Complementary approaches that use process control to optimize EABF composition and biomass density, while minimizing mass transfer effects and changes to system design parameters, are likely necessary to improve BES performance to a level needed for commercial consideration. Finally, future research needs that enable better understanding and optimization of the performance of EABFs are outlined.
Electron Beam Sterilization of Poly(Methyl Methacrylate)-Physicochemical and Biological Aspects.

Electron beam (E-beam) irradiation is an attractive and efficient method for sterilizing clinically implantable medical devices made of natural and/or synthetic materials such as poly(methyl methacrylate) (PMMA). As ionizing irradiation can affect the physicochemical properties of PMMA, understanding the consequences of E-beam sterilization on the intrinsic properties of PMMA is vital for clinical implementation. A detailed assessment of the chemical, optical, mechanical, morphological, and biological properties of medical-grade PMMA after E-beam sterilization at 25 and 50 kiloGray (kGy) is reported. Fourier transform infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry studies indicate that E-beam irradiation has minimal effect on the chemical properties of the PMMA at these doses. While 25 kGy irradiation does not alter the mechanical and optical properties of the PMMA, 50 kGy reduces the flexural strength and transparency by 10% and 2%, respectively. Atomic force microscopy demonstrates that E-beam irradiation reduces the surface roughness of PMMA in a dose dependent manner. Live-Dead, AlamarBlue, immunocytochemistry, and complement activation studies show that E-beam irradiation up to 50 kGy has no adverse effect on the biocompatibility of the PMMA. These findings suggest that E-beam irradiation at 25 kGy may be a safe and efficient alternative for PMMA sterilization.
Chrysophanol inhibits the osteoglycin/mTOR and activats NF2 signaling pathways to reduce viability and proliferation of malignant meningioma cells

ABSTRACT Chrysophanol shows promising antitumor activity, but how it may work against malignant meningioma is poorly understood. In addition, osteoglycin (OGN) may help mediate the antitumor effects of chrysophanol; thus, this study investigated the potential antitumor mechanism of chrysophanol in malignant meningioma cultures. Meningioma cell line HBL-52 were incubated with varying doses of chrysophanol (0–90 μM) for different time points, and osteoglycin (OGN) was overexpressed or inhibited in some cell cultures to assess its roles. Cell viability was quantified using the CCK8 assay and colony formation assays, while effects on cell cycle distribution and apoptotic rates were examined by flow cytometry and enzyme-linked immunosorbent assays (ELISA) to detect histone DNA levels. Caspase-3 and −9 activities were detected by related commercial kits. Protein expression was assessed using Western blotting. Chrysophanol significantly reduced HBL-52 cell viability, based on reduced colony formation, and proliferation, based on low levels of bromodeoxyuridine incorporation. Annexin V/propidium iodide staining revealed a 30% increase in apoptotic cells at 90 μM chrysophanol (33.7% vs 3.3% in control cultures). Chrysophanol treatment greatly decreased the Bcl-2/Bax expression ratio and increased the expressions of cleaved caspase-3 and −9, and the activities of caspase-3 and −9. Chrysophanol blocked cells in G1 phase and inhibited the OGN/mTOR signaling cascade, but activated neurofibromatosis 2 (NF2) cascade. OGN overexpression activated mTOR, down-regulated NF2, and partially reversed growth inhibition by chrysophanol. Chrysophanol may be useful as a treatment against malignant meningioma by inhibiting OGN/mTOR signaling and activating NF2 signaling. Graphical Abstract
Heavy Alcohol Use Is Associated With Gastric Cancer: Analysis of the National Health and Nutrition Examination Survey From 1999 to 2010

INTRODUCTION: Evidence regarding the association between alcohol use and gastric cancer (GC) has been inconsistent. METHODS: Adults who participated in the National Health and Nutrition Examination Survey (NHANES) from 1999 to 2010 were included. Multivariable regression was used to assess the association between GC and heavy alcohol use (≥5 alcoholic drinks daily). RESULTS: Of 470,168 individuals surveyed, 342 had a history of GC. Heavy alcohol use was associated with GC (odds ratio 3.13, 95% confidence interval 1.15–8.64) on multivariable analysis. DISCUSSION: This is the largest study to our knowledge to demonstrate an association between heavy alcohol use and GC in the United States.
Monopolar versus bipolar transurethral resection of lateral wall-located bladder cancer under obturator nerve block: a single center prospective randomized study

ABSTRACT Introduction: The aim of the present prospective-randomized study was to compare perioperative outcomes and complications of bipolar and monopolar TURBT for lateral wall-located non-muscle invasive bladder cancers (NMIBC) under obturator nerve block (ONB). Patients and Methods: 80 patients who underwent TURBT for lateral wall-located primary bladder tumors under ONB from March, 2016 to November, 2019 were included in the present study. The patients were randomized equally into two groups; monopolar TUR (M-TURBT) and bipolar TUR (B-TURBT). The primary and secondary outcomes were safety (obturator jerk and bladder perforation) and efficacy (complete tumor resection and sampling of the deep muscle tissue). Results: Obturator jerk was detected in 2 patients (5%) in M-TURBT while obturator jerk was not observed during B-TURBT (p=0.494). Bladder perforation was not observed in both groups. All of the patients underwent complete tumor resection. There was no significant difference in muscle tissue sampling (67.5% vs. 72.5%, p=0.626) and thermal tissue damage rates (12.5% vs. 25%, p=0.201). The majority of complications were low-grade and the differences in Clavien grade 1-3 complications between groups were not statistically significant. Conclusion: In the treatment of lateral-wall located NMIBCs, either M-TURBT or B-TURBT can be safely and effectively performed by combining spinal anesthesia with ONB. Even so, it should be taken into consideration that low-grade postoperative hemorrhagic complications may occur in patients who undergo M-TURBT.
[Carotid artery wall imaging using 7.0T magnetic resonance imaging with threedimensional DANTE-prepared FLASH in ApoE-/- mice].

OBJECTIVE To explore the feasibility of three-dimensional (3D) vessel wall imaging of carotid atherosclerotic plaques in ApoE-/- mice using 7.0T magnetic resonance imaging (MRI) with delays alternating with nutations for tailored excitation (DANTE)-prepared fast low-angle shot (DANTE-FLASH) technique. OBJECTIVE Numerical simulations were performed for optimizing imaging parameters to maximize the wall-lumen contrast. Six ApoE-/- and three wild-type mice were scanned using a 7.0T MRI scanner with DANTE-FLASH and multi-slice 2D RARE coupled with inflow outflow saturation bands (2D-IOSBRARE). The wall signal-to-noise ratio (SNRwall), lumen SNR (SNRlumen), wall-lumen contrast-to-noise ratio (CNR), lumen area (LA), and wall area (WA) were compared between DANTE- FLASH and 2D-IOSB-RARE sequences. Linear regression analysis was performed to assess the correlation between the MRI measurements and histopathological measurements of LA and WA. OBJECTIVE Based on the simulation results, a flip angle of 15° and a train length of 150 were implemented in the live imaging study. Compared with 2D-IOSB-RARE, DANTE-FLASH provided a slightly reduced CNR (P < 0.001) but much improved slice resolution. The LA and WA measurements from the DANTE-FLASH and 2D-IOSB- RARE showed excellent agreement based on ICC analysis (LA: ICC=0.94, P < 0.001; WA: ICC=0.93, P < 0.001) and Bland-Altman plots. Strong correlations were observed between the MRI and histopathological measurements for both LA (P < 0.0001) and WA (P < 0.0001). OBJECTIVE As a 3D black-blood MR sequence, DANTE-FLASH provides isotropic high spatial resolution to allow reliable visualization and quantitative evaluation of the arteriosclerotic lesions within the carotid artery of ApoE-/- mice using a 7.0T MRI scanner.
Development of a platform process for the production and purification of single‐domain antibodies

Single‐domain antibodies (sdAbs) offer the affinity and therapeutic value of conventional antibodies, with increased stability and solubility. Unlike conventional antibodies, however, sdAbs do not benefit from a platform manufacturing process. While successful production of a variety of sdAbs has been shown in numerous hosts, purification methods are often molecule specific or require affinity tags, which generally cannot be used in clinical manufacturing due to regulatory concerns. Here, we have developed a broadly applicable production and purification process for sdAbs in Komagataella phaffii (Pichia pastoris) and demonstrated the production of eight different sdAbs at a quality appropriate for nonclinical studies. We developed a two‐step, integrated purification process without the use of affinity resins and showed that modification of a single process parameter, pH of the bridging buffer, was required for the successful purification of a variety of sdAbs. Further, we determined that this parameter can be predicted based only on the biophysical characteristics of the target molecule. Using these methods, we produced nonclinical quality sdAbs as few as 5 weeks after identifying the product sequence. Nonclinical studies of three different sdAbs showed that molecules produced using our platform process conferred protection against viral shedding of rotavirus or H1N1 influenza and were equivalent to similar molecules produced in Escherichia coli and purified using affinity tags.