Miracle-dz/UniFAR-FTUs huggingface dataset:
Closure between particulate matter concentrations measured ex situ by thermal–optical analysis and in situ by the CPMA–electrometer reference mass system

Abstract The thermal-optical analysis (TOA) of black carbon in particulate matter (PM) collected on filters has been recommended and used for the calibration of mass-concentration instruments. However, filter-based TOA calibrations have substantial practical limitations, requiring high sample flow rates (>10 litres per minute), long sampling times (up to 3 h), and subsequently manual filter processing with long analysis times (>15 min per filter). These limitations are avoided by in situ calibration techniques such as the centrifugal particle mass analyzer (CPMA)–electrometer reference mass system (CERMS). The CERMS is capable of producing and monitoring in situ reference mass concentrations below 1 µg m−3 and in real-time (∼1 Hz). Additional advantages of the CERMS are its improved repeatability (1.1%) over TOA (9–11%), and its measurement of a well-defined quantity: total post-CPMA suspended PM mass. In the present work, we demonstrate closure between these two techniques in terms of PM mass concentration for three different soot generators (viz., the Argonaut miniature inverted soot generator, Jing miniCAST, and National Research Council inverted-flame burner) under carefully controlled conditions. We also demonstrate the sensitivity of the CERMS by characterizing the limits of detection of a commercial laser-induced incandescence instrument and a photoacoustic instrument. Our data support the use of the CERMS with well-characterized PM sources to provide reference mass concentrations for the calibration of instruments measuring PM or black-carbon mass concentration.
A review of the subgenus Euprepiosaurus of Varanus (Squamata: Varanidae): morphological and molecular phylogeny, distribution and zoogeography, with an identification key for the members of the V. indicus and the V. prasinus species groups

We provide a synopsis of the currently recognized taxa within the subgenus Euprepiosaurus of Varanus, consisting of the V. indicus species group (in chronological order, V. indicus, V. doreanus, V. jobiensis, V. finschi, V. melinus, V. yuwonoi, V. caerulivirens, V. cerambonensis, V. juxtindicus, V. zugorum) and the V. prasinus species group (accordingly, V. prasinus, V. beccarii, V. kordensis, V. bogerti, V. keithhornei, V. telenesetes, V. macraei, V. boehmei, V. reisingeri). We summarize the taxonomic history of the species groups and highlight the morphology and distribution of the species in detail. Molecular genetic analyses confirm Euprepiosaurus and also the two contained species groups as monophyla. Our molecular (mitochondrial 16S rRNA gene) data further reinforce that V. beccarii, V. boehmei, V. keithhornei, and V. macraei are distinct species within the V. prasinus group. V. kordensis consistently proves to be a sister species to all remaining members of the V. prasinus species group studied by us. Comparatively low genetic distances argue for relatively recent speciation processes within the V. indicus group. The species status of V. caerulivirens and V. finschi is again corroborated. The analyses consistently place V. cerambonensis and V. melinus as sister species. It is further evident that both species groups within Euprepiosaurus still contain distinct unrecognized taxa. Finally, we discuss the phylogeny and zoogeography of Euprepiosaurus in the light of our data and provide an identification key for the species of this subgenus.
Response to Infection by Trypanosoma cruzi in a Murine Model

Cardiopathy is a common, irreversible manifestation of the chronic phase of Chagas disease; however, there is controversy as to how the causes for progression from the acute to the chronic phase are defined. In this work, the presence of the parasite is correlated with the occurrence of cell infiltration and fibrosis in cardiac tissues, as well as IgG detection and disease progression in a murine model. Fifty CD1 mice were infected intraperitoneally with Trypanosoma cruzi, while 30 control were administered with saline solution. Parasitemia levels were determined, and IgG titers were quantified by ELISA. At different times, randomly selected mice were euthanized, and the heart was recovered. Cardiac tissue slides were stained with HE and Masson trichrome stain. A significant increase in parasitemia levels was observed after 15 days post-infection (dpi), with a maximum of 4.1 × 106 parasites on 33 dpi, ending on 43 dpi; amastigote nests were observed on 15–62 dpi. Histological analysis revealed lymphocytic infiltration and fibrotic lesions from 8 dpi until the end of the study, on 100 dpi. The presence of plasma cells in the myocardium observed on 40–60 dpi, accompanied by seropositivity to ELISA on 40–100 dpi, was regarded as the hallmark of the transition phase. Meanwhile, the chronic phase, characterized by the absence of amastigotes, presence of cell infiltration, fibrotic lesions, and seropositivity, started on 62 dpi. A strong correlation between parasitemia and the presence of amastigote nests was found (r2 = 0.930), while correlation between the presence of fibrosis and of amastigote nests was weak (r2 = 0.306), and that between fibrosis and lymphocyte infiltration on 100 dpi was strong (r2 = 0.899). The murine model is suitable to study Chagas disease, since it can reproduce the chronic and acute phases of the human disease. The acute phase was determined to occur on 1–60 dpi, while the chronic phase starts on 62 dpi, and fibrotic damage is a consequence of the continuous inflammatory infiltration; on the other hand, fibrosis was determined to start on the acute phase, being more apparent in the chronic phase, when Chagas disease-related cardiopathy is induced.
Mifepristone as a Potential Therapy to Reduce Angiogenesis and P-Glycoprotein Associated With Glioblastoma Resistance to Temozolomide

Glioblastoma, the most common primary central nervous system tumor, is characterized by extensive vascular neoformation and an area of necrosis generated by rapid proliferation. The standard treatment for this type of tumor is surgery followed by chemotherapy based on temozolomide and radiotherapy, resulting in poor patient survival. Glioblastoma is known for strong resistance to treatment, frequent recurrence and rapid progression. The aim of this study was to evaluate whether mifepristone, an antihormonal agent, can enhance the effect of temozolomide on C6 glioma cells orthotopically implanted in Wistar rats. The levels of the vascular endothelial growth factor (VEGF), and P-glycoprotein (P-gp) were examined, the former a promoter of angiogenesis that facilitates proliferation, and the latter an efflux pump transporter linked to drug resistance. After a 3-week treatment, the mifepristone/temozolomide regimen had decreased the level of VEGF and P-gp and significantly reduced tumor proliferation (detected by PET/CT images based on 18F-fluorothymidine uptake). Additionally, mifepristone proved to increase the intracerebral concentration of temozolomide. The lower level of O6-methylguanine-DNA-methyltransferase (MGMT) (related to DNA repair in tumors) previously reported for this combined treatment was herein confirmed. After the mifepristone/temozolomide treatment ended, however, the values of VEGF, P-gp, and MGMT increased and reached control levels by 14 weeks post-treatment. There was also tumor recurrence, as occurred when administering temozolomide alone. On the other hand, temozolomide led to 100% mortality within 26 days after beginning the drug treatment, while mifepristone/temozolomide enabled 70% survival 60–70 days and 30% survived over 100 days, suggesting that mifepristone could possibly act as a chemo-sensitizing agent for temozolomide.
Monitoring Immune Responses in IgA Nephropathy: Biomarkers to Guide Management

IgA nephropathy (IgAN) is the commonest biopsy-reported primary glomerulonephritis worldwide. It has an incidence which peaks among young adults, and 30 to 40% of patients’ progress to end stage kidney disease within twenty years of diagnosis. Ten-year kidney survival rates have been reported to be as low as 35% in some parts of the world. The successful management of IgAN is limited by an incomplete understanding of the pathophysiology of IgAN and a poor understanding of how pathophysiology may vary both from patient to patient and between patient groups, particularly across races. This is compounded by a lack of rigorously designed and delivered clinical trials in IgAN. This is slowly changing, with a number of Phase 2 and 3 clinical trials of novel therapies targeting a number of different putative pathogenic pathways in IgAN due to report in the next 5 years. From our current, albeit limited, understanding of the pathophysiology of IgAN it is unlikely a single therapy will be effective in all patients with IgAN. The successful management of IgAN in the future is, therefore, likely to be reliant on targeted therapies, carefully selected based on an individualized understanding of a patient’s risk of progression and underlying pathophysiology. The potential role of biomarkers to facilitate personalization of prognostication and treatment of IgAN is immense. Here we review the progress made over the past decade in identifying and validating new biomarkers, with a particular focus on those that reflect immunological responses in IgAN.
Flexibility in Problem Solving: Analogical Transfer of Tool Use in Toddlers Is Immune to Delay

Solving problems that are perceptually dissimilar but require similar solutions is a key skill in everyday life. In adults, this ability, termed analogical transfer, draws on memories of relevant past experiences that partially overlap with the present task at hand. Thanks to this support from long-term memory, analogical transfer allows remarkable behavioral flexibility beyond immediate situations. However, little is known about the interaction between long-term memory and analogical transfer in development as, to date, they have been studied separately. Here, for the first time, effects of age and memory on analogical transfer were investigated in 2–4.5-olds in a simple tool-use setup. Children attempted to solve a puzzle box after training the correct solution on a different looking box, either right before the test or 24 h earlier. We found that children (N = 105) could transfer the solution regardless of the delay and a perceptual conflict introduced in the tool set. For children who failed to transfer (N = 54) and repeated the test without a perceptual conflict, the odds of success did not improve. Our findings suggest that training promoted the detection of functional similarities between boxes and, thereby, flexible transfer both in the short and the long term.
Baicalin Inhibits Influenza A Virus Infection via Promotion of M1 Macrophage Polarization

Background and Aims The natural compound baicalin (BA) possesses potent antiviral properties against the influenza virus. However, the underlying molecular mechanisms of this antiviral activity and whether macrophages are involved remain unclear. In this study, we, therefore, investigated the effect of BA on macrophages. Methods We studied macrophage recruitment, functional phenotypes (M1/M2), and the cellular metabolism via flow cytometry, qRT-PCR, immunofluorescence, a cell culture transwell system, and GC-MS–based metabolomics both in vivo in H1N1 A virus-infected mice and in vitro. Results BA treatment drastically reduced macrophage recruitment (CD11b+, F4/80+) by approximately 90% while maintaining the proportion of M1-polarized macrophages in the bronchoalveolar lavage fluid of infected mice. This BA-stimulated macrophage M1 phenotype shift was further verified in vitro in ANA-1 and primary peritoneal macrophages by measuring macrophage M1 polarization signals (CD86, iNOS, TNF-α, iNOS/Arg-1 ratio, and IL-1β cleavage). Meanwhile, we observed an activation of the IFN pathway (upregulation of IFN-β and IRF-3), an inhibition of influenza virus replication (as measured by the M gene), and distinct cellular metabolic responses in BA-treated cells. Conclusion BA triggered macrophage M1 polarization, IFN activation, and other cellular reactions, which are beneficial for inhibition of H1N1 A virus infection.
Age-Dependent Shift of AMPA Receptors From Synapses to Intracellular Compartments in Alzheimer’s Disease: Immunocytochemical Analysis of the CA1 Hippocampal Region in APP/PS1 Transgenic Mouse Model

Synapse loss occurs early in Alzheimer’s disease (AD) patients and animal models. Alterations at synaptic level are a major morphological correlate of the memory deficits and related symptoms of AD. Given the predominant roles of synaptic AMPA receptors (AMPARs) in excitatory synaptic transmission in the brain, changes in their dynamic regulation are also implicated in the pathophysiology of AD. Here, we used immunolocalization techniques to analyze the expression and subcellular distribution of AMPARs in the hippocampal region of APP/PS1 mouse model of AD. Immunoblots and histoblots revealed that the total amount of AMPARs and their regional expression pattern in the hippocampus was similar in APP/PS1 mice and in age-matched wild type mice. At the ultrastructural level, two synapse populations were examined using SDS-digested freeze-fracture replica labeling in the stratum radiatum in mice: (i) on spines of CA1 pyramidal cells; and (ii) on randomly found dendritic shafts of CA1 interneurons. While 1- and 6-months-old APP/PS1 mice exhibited no change, we observed a significant reduction at 12 months in AMPAR density at synapses in both pyramidal cells and interneurons, compared to wild-type. This reduction of AMPARs in dendritic spines was accompanied by a significant increase in AMPAR subunit proteins identified in intracellular compartments. Our data demonstrate an age-dependent reduction of synaptic AMPARs in APP/PS1 mice, which may contribute to impaired learning and memory at later stages of AD.
Docosahexaenoic Acid Modulates NK Cell Effects on Neutrophils and Their Crosstalk

Natural killer (NK) cells and neutrophils engage in crosstalk that is important in inflammation and likely also for resolution of inflammation. NK cells activate neutrophils and induce their infiltration to the inflamed sites but may also influence their apoptosis and their subsequent efferocytosis by macrophages. Several studies indicate that docosahexaenoic acid (DHA) can inhibit NK cell cytotoxicity but the effects of DHA on the ability of NK cells to engage in crosstalk with neutrophils and affect their functions have not been described. This study explored the kinetics of the effects of NK cells and NK cells pre-treated with DHA on neutrophil surface molecule expression and apoptosis, as well as the ability of NK cells to affect other neutrophil functions. In addition, the study explored the effects of neutrophils on NK cell phenotype and function. Primary NK cells were pre-incubated with or without DHA, then stimulated and co-cultured with freshly isolated neutrophils. When co-cultured with NK cells, neutrophils had higher expression levels of CD11b and CD47; secreted more IL-8, IL-1ra, and CXCL10; had increased phagocytic ability; and their apoptosis was increased early after initiation of the co-culture while dampened at a later time-point. Pre-incubation of NK cells with DHA attenuated NK cell-induced upregulation of CD11b and CD47 on neutrophils, had minor effects on NK cell induction of cytokine/chemokine secretion or their phagocytic ability. Neutrophils also affected the function of NK cells, lowering the frequency of NKp46+ and CXCR3+ NK cells and increasing the concentrations of IFN-γ, TNF-α, and GM-CSF in the co-cultures. Pre-incubation of NK cells with DHA further decreased the frequency of NKp46+ NK cells in the co-culture with neutrophils and decreased the concentrations of IFN-γ, CCL3 and GM-CSF. These findings indicate that NK cells have mostly pro-inflammatory effects on neutrophils and that DHA can attenuate some of these pro-inflammatory effects. Neutrophils had both anti- and pro-inflammatory effects on NK cells. When NK cells had been pre-treated with DHA, the anti-inflammatory effects were increased and some of the pro-inflammatory effects attenuated. Overall, the results suggest that DHA may lead to a more anti-inflammatory microenvironment for NK cell and neutrophil crosstalk.
Modulated Response of Aspergillus fumigatus and Stenotrophomonas maltophilia to Antimicrobial Agents in Polymicrobial Biofilm

Introduction: The complexity of biofilms constitutes a therapeutic challenge and the antimicrobial susceptibility of fungal-bacterial biofilms remains poorly studied. The filamentous fungus Aspergillus fumigatus (Af) and the Gram-negative bacillus Stenotrophomonas maltophilia (Sm) can form biofilms and can be co-isolated from the airways of cystic fibrosis (CF) patients. We previously developed an in vitro biofilm model which highlighted the antibiosis effect of Sm on Af, which was dependent on the bacterial fitness. The aim of the present study was to investigate the in vitro susceptibility of Af and Sm in mono- or polymicrobial biofilms to five antimicrobial agents alone and in two-drug combinations. Methods: Af and Sm clinical reference strains and two strains from CF sputa were tested through a planktonic and biofilm approaches. Af, Sm, or Af-Sm susceptibilities to amphotericin B (AMB), itraconazole (ITC), voriconazole (VRC), levofloxacin (LVX), and rifampicin (RFN) were evaluated by conventional planktonic techniques, crystal violet, XTT, qPCR, and viable plate count. Results: Af planktonic cells and biofilms in formation were more susceptible to AMB, ITC, and VRC than Af mature biofilms. Af mature biofilms were susceptible to AMB, but not to ITC and VRC. Based on viable plate count, a lower concentration of LVX and RFN was required to reduce Sm cell numbers on biofilms in formation compared with mature biofilms. The antibiosis effect of Sm on Af growth was more pronounced for the association of CF strains that exhibited a higher fitness than the reference strains. In Af-Sm biofilms, the fungal susceptibility to AMB was increased compared with Af biofilms. In contrast, the bacterial susceptibility to LVX decreased in Af-Sm biofilms and was fungal biomass-dependent. The combination of AMB (64 μg/mL) with LVX or RFN (4 μg/mL) was efficient to impair Af and Sm growth in the polymicrobial biofilm. Conclusion: Sm increased the Af susceptibility to AMB, whereas Af protected Sm from LVX. Interactions between Af and Sm within biofilms modulate susceptibility to antimicrobial agents, opening the way to new antimicrobial strategies in CF patients.
Identification of Four Immune Subtypes in Bladder Cancer Based on Immune Gene Sets

Molecular classification of bladder cancer is becoming increasingly important for its clinical management. And, the current classifications are primarily based on gene expression profiles. We identified four immunotypes of bladder cancer (referred to as C1–C4) based on gene expression profiles performed by immune-related gene sets in three independent data sets, and proved that this classification is effective and reproducible. We found that C2 is an immune-infiltrating type and C4 is an immune “desert” type. These types are characterized by the up- and downregulation of genes encoding numerous immune checkpoint proteins and HLA and regulating human immune cell subgroups. The survival rate was better for the C2 subtype than for other subtypes. We believe that this can be explained by the antitumor effects of CD4 memory T cells and CD8 T cells as well as their ability to circumvent M0 macrophage antitumor immunity. In addition, C2 was most sensitive to not only anti-PD-1 immunosuppressive therapy, but also conventional chemotherapeutics such as gemcitabine and bleomycin. The C4 subtype was most sensitive to the chemotherapy drugs cisplatin and doxorubicin. This theoretical framework may guide the personalized treatment of bladder cancer in the future. It is worth noting that the C2 immune infiltration type positively correlates with a variety of stromal components, such as enrichment of endothelial cells and fibroblasts, epithelial-mesenchymal transition, and angiogenesis, together with enrichment of seven kinds of stem cells. We further identified tumor-related JAK-STAT and other signaling pathways in the C2 subtype, along with important mutations in the proteins involved in these pathways, revealing the complex mechanism underlying tumor immune escape. Our results, and particularly the identification of hub genes specific to the C2 and C4 subtypes, provide a reference for the development of immunotherapeutic agents against bladder cancer.
Software as a Service Adoption in Micro, Small and Medium Enterprise in Indonesia: Examining the Environmental Factors

This research aims to identify factors affecting adoption of Software as a Service (SaaS) in Micro, Small and Medium Enterprises (MSME). The combination of technological organization environment (TOE) framework, institutional theory (INT), and diffusion of innovation (DOI theory) were used as the basis of environment factors that influence adoption of SaaS. Data were collected from 136 owners or directors of MSMEs around Indonesia representing MSMEs with diverse backgrounds. Through the use of PLS-SEM, this research confirms environmental factors affecting MSMEs in adopting SaaS technology. Furthermore, this research also discusses the influence of environmental factors in different organizational scales of MSMEs (micro, small, and medium).
Detection of Chemical Host–Guest Interactions Using a Quartz Tuning Fork Sensing System

In this paper, we investigate the potential of using quartz tuning fork (QTF) sensing system for detection of specific metal ions in aqueous solutions with sample volume of <inline-formula> <tex-math notation="LaTeX">$1~\mu \text{L}$ </tex-math></inline-formula>. Functionalized self-assembled monolayers (SAMs) of L-glutathione (LG) on gold-coated QTFs were used to sense specific analytes of CaCl<sub>2</sub> and HgCl<sub>2</sub>, whereas functionalized L-cysteine based SAMs used to sense PbCl<sub>2</sub>. The resonance frequency undergoes a shift in response to the interaction between functionalized QTF and target analyte. X-ray photoelectron spectroscopy was used to study the interaction of thiol groups between the functionalized SAM and gold coated on QTF surface. Our analysis revealed that active QTFs functionalized with LG are more sensitive to detection of CaCl<sub>2</sub> compared with HgCl<sub>2</sub>. The SAM-based QTF sensors were found to be capable of detecting low concentrations (<inline-formula> <tex-math notation="LaTeX">$10^{- {12}}$ </tex-math></inline-formula> M) of divalent analyte solutes with high sensitivity.