Miracle-dz/UniFAR-FTUs huggingface dataset:
Attenuation of obesity related inflammation in RAW 264.7 macrophages and 3T3-L1 adipocytes by varanadi kashayam and identification of potential bioactive molecules by UHPLC-Q-Orbitrap HRMS

Abstract Obesity is associated with chronic low-grade inflammation, characterised by the up-regulation of pro-inflammatory cytokines in obese adipose tissue. In this study, 3T3-L1 CM enhanced TNF-α and IL-1β in RAW 264.7 cells compared with LPS treated cells. However, treatment with Varanadi kashayam suppressed the inflammatory changes associated with RAW 264.7 cells. Subsequently, RAW CM used to stimulate adipocytes, resulting in decreased intracellular lipid content and reduced adipogenic markers after Varanadi kashayam treatment. The chemical profiling of Varanadi kashayam using UHPLC-Q-Orbitrap-HRMS identified 194 compounds by comparing their retention time, the experimentally measured exact mass of precursor, and fragmented ions, and fragmentation pattern with spectral library and reported literature. Collectively, Varanadi kashayam act as a potent anti-inflammatory and anti-adipogenic agent that could disrupt the crosstalk between adipocytes and macrophages. Hence it could be a better candidate for reducing inflammation associated with obese adipose tissue.
PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs

ABSTRACT Phased siRNAs (phasiRNAs) are a class of small interfering RNAs (siRNAs) which play essential roles in plant development and defence. However, only a few phasiRNAs have been extensively studied due to the difficulties in identifying and characterizing plant phasiRNAs by plant biologists. Herein, we describe a comprehensive and multi-functional web server termed PhasiRNAnalyzer, which is able to identify all crucial components in plant phasiRNA’s regulatory pathway (phase-initiator→PHAS gene→phasiRNA cluster→target gene). Currently, PhasiRNAnalyzer exhibits the following advantages: I) It is the most comprehensive platform which hosts 170 plant species with 256 genome data, 438 cDNA data and 271 degradome data. II) It can identify all crucial components in phasiRNA’s regulatory pathway, and verify the interactions between phasiRNAs and their target genes based on degradome data. III) It can perform differential expression analysis of phasiRNAs on each PHAS gene locus between different samples conveniently. IV) It provides the user-friendly interfaces and introduces several improvements, primarily by making more accurate and efficient analysis when dealing with deep sequencing data. In summary, PhasiRNAnalyzer is a comprehensive and systemic phasiRNA analysis server with high sensitivity and efficiency. It can be freely accessed at https://cbi.njau. edu.cn/PPSA/.
Impact of electrostatic potential on microcapsule-formation and physicochemical analysis of surface structure: Implications for therapeutic cell-microencapsulation

Cell-encapsulation is used for preventing therapeutic cells from being rejected by the host. The technology to encapsulate cells in immunoprotective biomaterials, such as alginate, commonly involves application of an electrostatic droplet generator for reproducible manufacturing droplets of similar size and with similar surface properties. As many factors influencing droplet formation are still unknown, we investigated the impact of several parameters and fitted them to equations to make procedures more reproducible and allow optimal control of capsule size and properties. We demonstrate that droplet size is dependent on an interplay between the critical electric potential (Uc,), the needle size, and the distance between the needle and the gelation bath, and that it can be predicted with the equations proposed. The droplet formation was meticulously studied and followed by a high-speed camera. The X-ray photoelectron analysis demonstrated optimal gelation and substitution of sodium with calcium on alginate surfaces while the atomic force microscopy analysis demonstrated a low but considerable variation in surface roughness and low surface stiffness. Our study shows the importance of documenting critical parameters to guarantee reproducible manufacturing of beads with constant and adequate size and preventing batch-to-batch variations.
Clinically diagnosed iron and iodine deficiencies and disorders in the entire population of US military service members from 1997 to 2015

Abstract Objective: Iron and/or iodine deficiencies can have multiple serious adverse health outcomes, but examination of incidence rates of these deficiencies has rarely been conducted in any large population. This study examined incidence rates, temporal trends and demographic factors associated with medically diagnosed iron and iodine deficiencies/disorders in US military service members (SM). Design: The Defense Medical Epidemiological Database (DMED) was queried for medical visits of active duty SM to obtain specific International Classification of Diseases, Version 9, codes involving clinically diagnosed iron and iodine deficiencies/disorders. Setting: Analysis of existing database (DMED). Participants: Entire population of US military SM from 1997 to 2015 (average n per year = 1 382 266, 15 % women). Results: Overall incidence rates for iron and iodine were 104 and 36 cases/100 000 person-years, respectively. Over the 19-year period, rates for iron disorders increased steadily (108 % for men, 177 % for women). Rates for iodine disorders also increased steadily for men (91 %), but, for women, there was an initial rise followed by a later decline. Overall, women’s rates were 12 and 10 times higher than men’s for iron and iodine, respectively. Compared with whites, blacks and those of other races had higher rates of deficiencies of both minerals. Incidence rates for iodine deficiency increased substantially with age. Conclusions: The overall incidence of clinically diagnosed iron and iodine deficiency among SM was low, but increased over the 19 years examined, and certain demographic groups were at significantly greater risk. Given the unexpected increases in incidence of these mineral disorders, increased surveillance may be appropriate. Clinical Trial Registration No. ISRCTN58987177 (http//:www.isrctn.com/ISRCTN58987177)
Identification of potential biomarkers associated with immune infiltration in the esophageal carcinoma tumor microenvironment

Abstract Tumor immune cell infiltration was significantly correlated with the progression and the effect of immunotherapy in cancers including esophageal carcinoma (ESCA). However, no biomarkers were identified which were associated with immune infiltration in ESCA. In the present study, a total of 128 common differentially expressed genes (DEGs) were identified between esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinomas (EAC). The results of gene ontology (GO) enrichment and Reactome pathway analysis displayed that the up-regulated DEGs were mainly involved in the regulation of extracellular matrix (ECM), while the down-regulated DEGs were mainly involved in the regulation of cornification and keratinocyte differentiation. The most significant module of up-regulated DEGs was selected by Molecular Complex Detection (MCODE). Top ten similar genes of COL1A2 were explored, then validation and the prognostic analysis of these genes displayed that COL1A2, COL1A1, COL3A1, ZNF469 and Periostin (POSTN) had the prognostic value which were up-regulated in ESCA. The expressions of COL1A2 and its four similar genes were mainly correlated with infiltrating levels of macrophages and dendritic cells (DCs) and showed strong correlations with diverse immune marker sets in ESCA. To summarize, COL1A2 and its four similar genes were identified as the potential biomarkers associated with immune infiltration in ESCA. These genes might be applied to immunotherapy for ESCA.
Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes

Significance Mitochondria are the powerhouses of eukaryotic cells. Pairs of molecular machines with a rotary action, called ATP synthase, are embedded in their inner membranes and produce adenosine triphosphate, ATP, the fuel of life. These dimers form long rows on cristae tips, helping to endow them with their characteristic and mobile tubular shape. Our structural analyses of bovine dimers show that some structural changes depend on catalysis and others are independent. The monomers pivot and translate at wedge-shaped structures in their membrane domains. The structures suggest how dimeric ATP synthases might interact and fashion themselves to the range of oligomeric arrangements observed in mitochondria, whilst allowing the ATP synthase to produce ATP under a wide range of physiological conditions. The ATP synthase complexes in mitochondria make the ATP required to sustain life by a rotary mechanism. Their membrane domains are embedded in the inner membranes of the organelle, and they dimerize via interactions between their membrane domains. The dimers form extensive chains along the tips of the cristae with the two rows of monomeric catalytic domains extending into the mitochondrial matrix at an angle to each other. Disruption of the interface between dimers by mutation affects the morphology of the cristae severely. By analysis of particles of purified dimeric bovine ATP synthase by cryo-electron microscopy, we have shown that the angle between the central rotatory axes of the monomeric complexes varies between ca. 76 and 95°. These particles represent active dimeric ATP synthase. Some angular variations arise directly from the catalytic mechanism of the enzyme, and others are independent of catalysis. The monomer–monomer interaction is mediated mainly by j subunits attached to the surface of wedge-shaped protein-lipid structures in the membrane domain of the complex, and the angular variation arises from rotational and translational changes in this interaction, and combinations of both. The structures also suggest how the dimeric ATP synthases might be interacting with each other to form the characteristic rows along the tips of the cristae via other interwedge contacts, molding themselves to the range of oligomeric arrangements observed by tomography of mitochondrial membranes, and at the same time allowing the ATP synthase to operate under the range of physiological conditions that influence the structure of the cristae.
Recent Advances in Plasma Deposition of Functional Coatings on Polymers

Plasma enhanced chemical vapor deposition (PECVD) is increasingly being applied for the fabrication of functional coatings on polymeric substrates. This presentation briefly reviews the energetics of plasma-surface interactions leading to the deposition of films for different applications such as optical coatings, barriers against gas and vapor permeation, and protective coatings for space. Particular emphasis is placed on the formation and characterization of a relatively wide (tens of nm) interfacial region (“interphase”) between the coating and the polymer, its role in adhesion, and in optical, mechanical and other functional porperties of thin film systems on plastic substrates.
Production of Class II MHC Proteins in Lentiviral Vector‐Transduced HEK‐293T Cells for Tetramer Staining Reagents

Class II major histocompatibility complex peptide (MHC‐IIp) multimers are precisely engineered reagents used to detect T cells specific for antigens from pathogens, tumors, and self‐proteins. While the related Class I MHC/peptide (MHC‐Ip) multimers are usually produced from subunits expressed in E. coli, most Class II MHC alleles cannot be produced in bacteria, and this has contributed to the perception that MHC‐IIp reagents are harder to produce. Herein, we present a robust constitutive expression system for soluble biotinylated MHC‐IIp proteins that uses stable lentiviral vector−transduced derivatives of HEK‐293T cells. The expression design includes allele‐specific peptide ligands tethered to the amino‐terminus of the MHC‐II β chain via a protease‐cleavable linker. Following cleavage of the linker, HLA‐DM is used to catalyze efficient peptide exchange, enabling high‐throughput production of many distinct MHC‐IIp complexes from a single production cell line. Peptide exchange is monitored using either of two label‐free methods, native isoelectric focusing gel electrophoresis or matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry of eluted peptides. Together, these methods produce MHC‐IIp complexes that are highly homogeneous and that form the basis for excellent MHC‐IIp multimer reagents. © 2021 Wiley Periodicals LLC.
Potential Antidiabetic Effects of Seaweed Extracts by Upregulating Glucose Utilization and Alleviating Inflammation in C2C12 Myotubes

Seaweed is known to have various health-promoting effects. However, the mechanisms underlying seaweed’s antidiabetic effects remain unclear. We investigated the potential antidiabetic effects of seaweed water extracts and further examined their mechanism(s) using C2C12 mouse skeletal muscle cells. Briefly, we screened the physiochemical properties of seven seaweed extracts by comparing the antioxidant and α-glucosidase inhibitory effects. Among them, three seaweed extracts, Undaria pinnatifida sporophyll (UPS), Codium fragile (CF), and Gracilaria verrucosa (GV), were selected for further testing of their possible antidiabetic effects with underlying mechanisms using C2C12 myotubes. Consistent with the superior α-glucosidase inhibition of the three seaweed extracts, the extracts also enhanced glucose utilization in myotubes compared to the control. The upregulated glucose uptake by the seaweed extracts was reversed by an AMP-activated protein kinase (AMPK) inhibitor, compound C, in the UPS- and CF-treated groups. Furthermore, all three seaweed extracts significantly promoted the phosphorylation of AMPK which was completely blocked by pretreating with compound C. In addition, all three extracts reduced lipopolysaccharide-simulated TNF-α production in C2C12 cells. Our results demonstrated that all three seaweed extracts exhibited antidiabetic properties through not only the inhibition of glucose absorption but also the promotion of glucose utilization. Moreover, the regulation of inflammatory cytokine production by the extracts suggested their potential anti-inflammatory property which might play a critical role in protecting insulin sensitivity in a chronic inflammatory state. Taken together, UPS, CF, and GV are a promising source to modulate the glucose absorption and utilization in muscle cells partially via the AMPK pathway.
Determinants of Hospital Variation in Cardiac Rehabilitation Enrollment During Coronary Artery Disease Episodes of Care.

BACKGROUND Cardiac rehabilitation (CR) is associated with improved outcomes for patients with coronary artery disease (CAD). However, CR enrollment remains low and there is a dearth of real-world data on hospital-level variation in CR enrollment. We sought to explore determinants of hospital variability in CR enrollment during CAD episodes of care: medical management of acute myocardial infarction (AMI-MM), percutaneous coronary intervention (PCI), and coronary artery bypass grafting (CABG). METHODS A cohort of 71 703 CAD episodes of care were identified from 33 hospitals in the Michigan Value Collaborative statewide multipayer registry (2015 to 2018). CR enrollment was defined using professional and facility claims and compared across treatment strategies: AMI-MM (n=18 678), PCI (n=41 986), and CABG (n=11 039). Hierarchical logistic regression was used to estimate effects of predictors and hospital risk-adjusted rates of CR enrollment. RESULTS Overall, 20 613 (28.8%) patients enrolled in CR, with significant differences by treatment strategy: AMI-MM=13.4%, PCI=29.0%, CABG=53.8% (P<0.001). There were significant differences in CR enrollment across age groups, comorbidity status, and payer status. At the hospital-level, there was over 5-fold variation in hospital risk-adjusted CR enrollment rates (9.8%-51.6%). Hospital-level CR enrollment rates were highly correlated across treatment strategy, with the strongest correlation between AMI-MM versus PCI (R2=0.72), followed by PCI versus CABG (R2=0.51) and AMI-MM versus CABG (R2=0.46, all P<0.001). CONCLUSIONS Substantial variation exists in CR enrollment during CAD episodes of care across hospitals. However, within-hospital CR enrollment rates were significantly correlated across all treatment strategies. These findings suggest that CR enrollment during CAD episodes of care is the product of hospital-specific rather than treatment-specific practice patterns.
76-year decline and recovery of aspen mediated by contrasting fire regimes: Long-unburned, infrequent and frequent mixed-severity wildfire

Quaking aspen (Populus tremuloides) is a valued, minor component on northeastern California landscapes. It provides a wide range of ecosystem services and has been in decline throughout the region for the last century. This decline may be explained partially by the lack of fire on the landscape due to heavier fire suppression, as aspen benefit from fire that eliminates conifer competition and stimulates reproduction through root suckering. However, there is little known about how aspen stand area changes in response to overlapping fire. Our study area in northeastern California on the Lassen, Modoc and Plumas National Forests has experienced recent large mixed-severity wildfires where aspen was present, providing an opportunity to study the re-introduction of fire. We observed two time periods; a 52-year absence of fire from 1941 to 1993 preceding a 24-year period of wildfire activity from 1993 to 2017. We utilized aerial photos and satellite imagery to delineate aspen stands and assess conifer cover percent. We chose aspen stands in areas where wildfires overlapped (twice-burned), where only a single wildfire burned, and areas that did not burn within the recent 24-year period. We observed these same stands within the first period of fire exclusion for comparison (i.e., 1941–1993). In the absence of fire, all aspen stand areas declined and all stands experienced increases in conifer composition. After wildfire, stands that burned experienced a release from conifer competition and increased in stand area. Stands that burned twice or at high severity experienced a larger removal of conifer competition than stands that burned once at low severity, promoting expansion of aspen stand area. Stands with less edge:area ratio also expanded in area more with fire present. Across both time periods, stand movement, where aspen stand footprints were mostly in new areas compared to footprints of previous years, was highest in smaller stands. In the fire exclusion period, smaller stands exhibited greater loss of area and changes in location (movement) than in the return of fire period, highlighting their vulnerability to loss via succession to conifers in the absence of disturbances that provide adequate growing space for aspen over time.
Theoretical Evaluation of Polyelectrolyte Layering during Layer-by-Layer Coating of Ultrafiltration Hollow Fiber Membranes

Layer-by-layer (LbL) modification of porous membranes for water filtration has become an active research field in the past few years. Different mechanisms regarding polyelectrolyte film growth, swelling and smoothing, transport through these films, etc., have been studied. Although there are conjectures, it is not yet fully understood where the polyelectrolyte layering takes place when modifying porous membranes, either within the pores or on top of the porous material. This study presents a theoretical approach to investigate the dominant layer buildup regime between pore-dominated vs. layer-dominated growth of polyelectrolytes on porous membranes without mechanically interfering or damaging the membrane material. For this, fouling mechanism processes are used as an analogy. The presented approach gives a new insight into layering conformation and might be helpful to investigate the interaction between the membrane surface and the PE film. Moreover, the MgSO4 rejection behavior of two types of modified membranes was investigated: one with an initial pore-dominated layer growth followed by a layer-dominated film growth; the other one with a completely layer-dominated film growth. The data confirm that a rejection for MgSO4 could only be achieved in the regime of layer-dominated film growth. Additionally, when layer-dominated film growth prevails from the early stages of the coating process, permeability values are higher at similar MgSO4 rejection rates compared to an initial pore-dominated and then layer-dominated film growth. Accordingly, the interaction between the membrane pore size and molecular weight of the polyelectrolytes in the coating solutions plays an important role during LbL coating.
Maximal surgical resection and adjuvant surgical technique to prolong the survival of adult patients with thalamic glioblastoma

The importance of maximal resection in the treatment of glioblastoma (GBM) has been reported in many studies, but maximal resection of thalamic GBM is rarely attempted due to high rate of morbidity and mortality. The purpose of this study was to investigate the role of surgical resection in adult thalamic glioblastoma (GBM) treatment and to identify the surgical technique of maximal safety resection. In case of suspected thalamic GBM, surgical resection is the treatment of choice in our hospital. Biopsy was considered when there was ventricle wall enhancement or multiple enhancement lesion in a distant location. Navigation magnetic resonance imaging, diffuse tensor tractography imaging, tailed bullets, and intraoperative computed tomography and neurophysiologic monitoring (transcranial motor evoked potential and direct subcortical stimulation) were used in all surgical resection cases. The surgical approach was selected on the basis of the location of the tumor epicenter and the adjacent corticospinal tract. Among the 42 patients, 19 and 23 patients underwent surgical resection and biopsy, respectively, according to treatment strategy criteria. As a result, the surgical resection group exhibited a good response with overall survival (OS) (median: 676 days, p < 0.001) and progression-free survival (PFS) (median: 328 days, p < 0.001) compared with each biopsy groups (doctor selecting biopsy group, median OS: 240 days and median PFS: 134 days; patient selecting biopsy group, median OS: 212 days and median PFS: 118 days). The surgical resection groups displayed a better prognosis compared to that of the biopsy groups for both the O6-methylguanine-DNA methyltransferase unmethylated (log-rank p = 0.0035) or methylated groups (log-rank p = 0.021). Surgical resection was significantly associated with better prognosis (hazard ratio: 0.214, p = 0.006). In case of thalamic GBM without ventricle wall-enhancing lesion or multiple lesions, maximal surgical resection above 80% showed good clinical outcomes with prolonged the overall survival compared to biopsy. It is helpful to use adjuvant surgical techniques of checking intraoperative changes and select the appropriate surgical approach for reducing the surgical morbidity.