Miracle-dz/UniFAR-FTUs huggingface dataset:
TNFR1 single nucleotide polymorphisms are not associated with cervical HPV-induced pre-malignant lesion but regulate in situ cervical TNFR1 expression

TNF-α is involved in HPV infection control by triggering cell signaling through binding in specific receptors TNFR1 and TNFR2. Genetic polymorphisms in these receptors may influence TNF-α signaling. Herein, we investigated TNFR1 rs767455 and rs2234649 single nucleotide polymorphisms, and TNFR1 protein expression in cervical squamous intraepithelial lesions (SIL) to identify their role in cervical pre-malignant development. SIL patients (n = 179) and healthy volunteers (n = 227) were enrolled for TNFR1 genotyping analysis by PCR-RFLP in blood samples and TNFR1 protein expression in cervical tissue by immunohistochemistry. No statistical differences regard genotypes and allelic frequencies for both polymorphisms were observed. Cervical TNFR1-expressing cells were rare in epithelium and basal layer regardless the groups. However, a progressive increase in infiltrating cells was observed in the stromal area, mainly in high SIL (HSIL) group compared to low SIL (LSIL, p < 0.001) and control (p < 0.001) groups. TNFR1-expressing cells frequency was higher in TNFR1 rs767455AG/GG (p < 0.001), and in rs2234649AA (p < 0.001) genotypes carries in HSIL subgroup. These data indicated that TNFR1-expression is abrogated in cervical epithelium, where HPV-induced pre-malignant lesion occurs, increasing its frequency in inflammatory cells in stroma, and is genetically controlled by TNFR1 rs767455AG/GG and rs234649AA genotypes. These biomarkers may be useful to identify cervical precancerous lesions progression.
Flexibility and Solvation of Amyloid-β Hydrophobic Core*

Amyloid fibril deposits found in Alzheimer disease patients are composed of amyloid-β (Aβ) protein forming a number of hydrophobic interfaces that are believed to be mostly rigid. We have investigated the μs-ms time-scale dynamics of the intra-strand hydrophobic core and interfaces of the fibrils composed of Aβ1–40 protein. Using solid-state 2H NMR line shape experiments performed on selectively deuterated methyl groups, we probed the 3-fold symmetric and 2-fold symmetric polymorphs of native Aβ as well as the protofibrils of D23N Iowa mutant, associated with an early onset of Alzheimer disease. The dynamics of the hydrophobic regions probed at Leu-17, Leu-34, Val-36, and Met-35 side chains were found to be very pronounced at all sites and in all polymorphs of Aβ, with methyl axis motions persisting down to 230–200 K for most of the sites. The dominant mode of motions is the rotameric side chain jumps, with the Met-35 displaying the most complex multi-modal behavior. There are distinct differences in the dynamics among the three protein variants, with the Val-36 site displaying the most variability. Solvation of the fibrils does not affect methyl group motions within the hydrophobic core of individual cross-β subunits but has a clear effect on the motions at the hydrophobic interface between the cross-β subunits, which is defined by Met-35 contacts. In particular, hydration activates transitions between additional rotameric states that are not sampled in the dry protein. Thus, these results support the existence of water-accessible cavity recently predicted by molecular dynamics simulations and suggested by cryo-EM studies.
Evaluation of 10 genotypes of sweetpotato for fries

Abstract The potential use of selected genotypes of sweetpotato for fries was evaluated. Moisture, fat, browning index, and beta‐carotene content of fries from 10 sweetpotato genotypes, Apomuden, Bohye, Nanungungu, Otoo, CIP442162, Patron, CIP440390, Obare, Dadanyuie, and Tu‐Purple, were determined by standard methods. Sensorial properties of the fries were further evaluated by an in‐house trained panel of eight members using standard methods. Fat content was highest in CIP442162 and low in Dadanyuie, while beta‐carotene content decreased by 44.27% in Bohye and 13.20% in Nanungungu after frying. Browning index was highest in the orange‐fleshed and purple genotypes, but this was mostly due to their flesh colors and not the frying conditions. Fries from orange‐fleshed genotypes, Apomuden and Nanungungu, were considered to be sweeter than the other genotypes. Detection of caramel and starch (rawness sensation) was very low for all genotypes assessed. Oily mouthcoat, moistness, and sogginess were detected in mostly the orange‐fleshed genotypes, particularly Apomuden and Nanungungu. Tu‐Purple, Bohye, and CIP440390 produced moderately crunchy fries and had the highest score for desirable attributes compared with the other genotypes. Tu‐Purple, Bohye, and CIP440390 could be explored in commercial production of fries for enhanced utilization of developed sweetpotato genotypes.
Candiduria in Hospitalized Patients and Identification of Isolated Candida Species by Morphological and Molecular Methods in Ilam, Iran

Background: Candiduria in hospitalized patients may represent contamination, colonization, or urinary tract infections. On the other hand, candidemia and upper urinary tract infection could be the complications of candiduria. The aim of this study was to determine candiduria in hospitalized patients and identify isolated Candida species by conventional and molecular methods. Methods: This cross-sectional study was conducted on hospitalized patients in Imam Khomeini and Mostafa Khomeini hospitals in Ilam, western Iran from Jan to Dec 2016. Urine samples of hospitalized patients were collected during a period of 4 months for diagnosis of candiduria. Primary identification was done by conventional methods. PCR profile was carried out using phenol-chloroform method and confirmed using restriction fragment length polymorphism (PCR-RFLP) technique by MspI restriction enzyme. Results: Candiduria was diagnosed in 18 (9.2%) cases from a total of 195 patients. Isolated yeasts were identified as C. albicans (n: 13), C. glabrata (n: 5), and C. parapsilosis (n: 1) in the one case both C. albicans and C. glabrata were isolated from a urine sample. Conclusion: Candida urinary tract infection is becoming increasingly common in hospitalized patients but, differentiation fungal colonization from infection and identification of etiologic agents for optimal treatment is necessary.
High Expression B3GAT3 Is Related with Poor Prognosis of Liver Cancer

Abstract Liver cancer is one of the most malignant tumors with poor prognosis. Finding molecular markers that can predict prognosis is very important for the treatment of liver cancer. The present research is trying to find a new biomarker for human liver cancer. The analysis of abnormal expression genes and prognosis value on liver cancer by Gene Expression Profiling Interactive Analysis (GEPIA) database, the Pathology Atlas of the Human Protein Atlas (HPA), and Kaplan Meier-plotter (KM plotter), proved that B3GAT3 might be one of the important candidates. Furthermore, we investigated the specific role of B3GAT3 on liver cancer through the transfection of B3GAT3 siRNA in HepG2 cells. The proliferation was detected using CCK8, and migration and invasion were determined using Transwell assay. Our results proved that knockdown of B3GAT3 inhibited the proliferation, migration, and invasion. Moreover, B3GAT3 knockdown inhibited the expression of EMT related proteins, N-cad, Snail, and Twist, while promoting the expression of E-cad, suggesting that B3GAT3 knockdown reversed the EMT process of liver cancer cells. In conclusion, overexpressed B3GAT3 promotes the process of tumor EMT, which is an independent prognostic marker to predict the prognosis of liver cancer and might be a potential new target for liver cancer therapy.
State transitions in the substantia nigra reticulata predict the onset of motor deficits in models of progressive dopamine depletion in mice

Parkinson’s disease (PD) is a progressive neurodegenerative disorder whose cardinal motor symptoms are attributed to dysfunction of basal ganglia circuits under conditions of low dopamine. Despite well-established physiological criteria to define basal ganglia dysfunction, correlations between individual parameters and motor symptoms are often weak, challenging their predictive validity and causal contributions to behavior. One limitation is that basal ganglia pathophysiology is studied only at end-stages of depletion, leaving an impoverished understanding of when deficits emerge and how they evolve over the course of depletion. In this study, we use toxin- and neurodegeneration-induced mouse models of dopamine depletion to establish the physiological trajectory by which the substantia nigra reticulata (SNr) transitions from the healthy to the diseased state. We find that physiological progression in the SNr proceeds in discrete state transitions that are highly stereotyped across models and correlate well with the prodromal and symptomatic stages of behavior.
Quantitative immunohistochemical assay with novel digital immunostaining for comparisons of PD-L1 antibodies

One obstacle in diagnostic pathology is the harmonization of one drug-one diagnostic tests for programmed death ligand-1 (PD-L1). There are many challenges in accurate comparisons of diagnostic tests, such as differences in the titer of each antibody, detection system and dynamic range of visualization. Our previously developed digital immunostaining technique is highly sensitive and quantitative with the ability to quantify particles that bind in a one-to-one fashion with antibody in each cell. Determining the differences in the titer of each antibody with digital immunostaining may be beneficial for future harmonized analysis. To demonstrate the accuracy of digital immunostaining, the present study compared the number of particles with ELISA and nCounter data from five cell lines. NCI-H460 exhib-ited the highest level of PD-L1 protein, followed by A549, PC-3, NCI-H1299, and NCI-H446 cells. In addition, the PD-L1 mRNA values determined by nCounter corresponded with the order of the protein levels determined by ELISA. The present study revealed that digital immunostaining for PD-L1 was highly associated with ELISA and nCounter data. Among the four antibodies tested, the titer of all but SP142 coincided with ELISA and nCounter data. These results indicated that our digital immunostaining technique may be beneficial for future harmonized analysis.
Environmental filtering predicts plant‐community trait distribution and diversity: Kettle holes as models of meta‐community systems

Abstract Meta‐communities of habitat islands may be essential to maintain biodiversity in anthropogenic landscapes allowing rescue effects in local habitat patches. To understand the species‐assembly mechanisms and dynamics of such ecosystems, it is important to test how local plant‐community diversity and composition is affected by spatial isolation and hence by dispersal limitation and local environmental conditions acting as filters for local species sorting.We used a system of 46 small wetlands (kettle holes)—natural small‐scale freshwater habitats rarely considered in nature conservation policies—embedded in an intensively managed agricultural matrix in northern Germany. We compared two types of kettle holes with distinct topographies (flat‐sloped, ephemeral, frequently plowed kettle holes vs. steep‐sloped, more permanent ones) and determined 254 vascular plant species within these ecosystems, as well as plant functional traits and nearest neighbor distances to other kettle holes.Differences in alpha and beta diversity between steep permanent compared with ephemeral flat kettle holes were mainly explained by species sorting and niche processes and mass effect processes in ephemeral flat kettle holes. The plant‐community composition as well as the community trait distribution in terms of life span, breeding system, dispersal ability, and longevity of seed banks significantly differed between the two habitat types. Flat ephemeral kettle holes held a higher percentage of non‐perennial plants with a more persistent seed bank, less obligate outbreeders and more species with seed dispersal abilities via animal vectors compared with steep‐sloped, more permanent kettle holes that had a higher percentage of wind‐dispersed species. In the flat kettle holes, plant‐species richness was negatively correlated with the degree of isolation, whereas no such pattern was found for the permanent kettle holes.Synthesis: Environment acts as filter shaping plant diversity (alpha and beta) and plant‐community trait distribution between steep permanent compared with ephemeral flat kettle holes supporting species sorting and niche mechanisms as expected, but we identified a mass effect in ephemeral kettle holes only. Flat ephemeral kettle holes can be regarded as meta‐ecosystems that strongly depend on seed dispersal and recruitment from a seed bank, whereas neighboring permanent kettle holes have a more stable local species diversity.
Comparative Characterization of Phosphatidic Acid Sensors and Their Localization during Frustrated Phagocytosis*

Phosphatidic acid (PA) is the simplest phospholipid naturally existing in living organisms, but it constitutes only a minor fraction of total cell lipids. PA has attracted considerable attention because it is a phospholipid precursor, a lipid second messenger, and a modulator of membrane shape, and it has thus been proposed to play key cellular functions. The dynamics of PA in cells and in subcellular compartments, however, remains an open question. The recent generation of fluorescent probes for PA, by fusing GFP to PA-binding domains, has provided direct evidence for PA dynamics in different intracellular compartments. Here, three PA sensors were characterized in vitro, and their preferences for different PA species in particular lipidic environments were compared. In addition, the localization of PA in macrophages during frustrated phagocytosis was examined using these PA sensors and was combined with a lipidomic analysis of PA in intracellular compartments. The results indicate that the PA sensors display some preferences for specific PA species, depending on the lipid environment, and the localization study in macrophages revealed the complexity of intracellular PA dynamics.
Complex Formation of Human Proelastases with Procarboxypeptidases A1 and A2*

The pancreas secretes digestive proenzymes typically in their monomeric form. A notable exception is the ternary complex formed by proproteinase E, chymotrypsinogen C, and procarboxypeptidase A (proCPA) in cattle and other ruminants. In the human and pig pancreas binary complexes of proCPA with proelastases were found. To characterize complex formation among human pancreatic protease zymogens in a systematic manner, we performed binding experiments using recombinant proelastases CELA2A, CELA3A, and CELA3B; chymotrypsinogens CTRB1, CTRB2, CTRC, and CTRL1; and procarboxypeptidases CPA1, CPA2, and CPB1. We found that proCELA3B bound not only to proCPA1 (KD 43 nm) but even more tightly to proCPA2 (KD 18 nm), whereas proCELA2A bound weakly to proCPA1 only (KD 152 nm). Surprisingly, proCELA3A, which shares 92% identity with proCELA3B, did not form stable complexes due to the evolutionary replacement of Ala241 with Gly. The polymorphic nature of position 241 in both CELA3A (∼4% Ala241 alleles) and CELA3B (∼2% Gly241 alleles) points to individual variations in complex formation. The functional effect of complex formation was delayed procarboxypeptidase activation due to increased affinity of the inhibitory activation peptide, whereas proelastase activation was unchanged. We conclude that complex formation among human pancreatic protease zymogens is limited to a subset of proelastases and procarboxypeptidases. Complex formation stabilizes the inhibitory activation peptide of procarboxypeptidases and thereby increases zymogen stability and controls activation.
Effect of the storage atmosphere on metabolomics of harvested tomatoes (Solanum lycopersicum L.)

Abstract Harvested tomatoes were stored under atmospheres that were normoxic, anoxic, or modified (altered O2 and CO2 concentrations). Each atmosphere was created by storing the tomatoes at 25°C for up to 8 days in different kinds of pouches. During storage, metabolites of the tomatoes were measured using metabolomics. We obtained score plots of the metabolites on eighth day of storage by principal component analysis. There was a tendency for groups to be divided on the basis of score plot according to the composition of each gas. PC1 and PC2 seemed to correspond to the influence of O2 and CO2 concentrations, respectively, and the total contribution rate of the two axes was 72%, so that we concluded that the metabolites were affected mainly by O2 and CO2 concentrations. The results indicate that metabolomics may be an effective tool to reveal the relationship between metabolic state of harvested fruits and the atmosphere.
Predicting the Antiretroviral Medication Adherence and CD4 Measure in Patients with HIV/AIDS Based on the Post Traumatic Stress Disorder and Depression

Background: Antiretroviral therapy has significantly reduced the prevalence of diseases and mortality rate caused by HIV; therefore, recognition of the factors affecting the antiretroviral therapy is of great importance. We aimed to investigate the relationship between antiretroviral medication adherence and CD4 with posttraumatic stress disorder (PTSD) and depression in patients with HIV. Methods: This was a descriptive, cross-sectional, quantitative, and correlational study. The statistical population included all of the patients with HIV in Shiraz, Fars Province, southwest of Iran in 2013, of whom 220 were selected from the Behavioral Diseases Consultation Center using the convenience sampling method. The measures included Mississippi Post Traumatic Stress Disorder Questionnaire, Beck-II Depression, and ACTG Adherence (ACTG). The results were analyzed using the Pearson correlation method and stepwise hierarchical multivariate regression. Results: Regression analysis showed that of two mediating variables (age & educational level), only age could predict 5% (P<0.001) and of two predictive variables (depression & PTSD) only PTSD could predict 53% (P<0.001) of medication adherence's variance. Moreover, of two mediating variables (age & disease duration), only age could predict 3% (P<0.004) and of two predictive variables (depression & PTSD) only PTSD could predict 4% (P<0.001) of CD4 variance. Conclusion: The posttraumatic stress disorder symptoms could predict the medication non-adherence and lower CD4 levels.
Effects of postharvest polyamine application and edible coating on maintaining quality of mango (Mangifera indica L.) cv. Langra during cold storage

Abstract Mango is a tropical fruit which is sensitive to chilling injury. The present work investigated the potential of edible coatings of chitosan and polyamine spermidine in increasing shelf life and quality of mango. The control fruits (treated with distilled water) and the mango fruits treated with different concentrations of chitosan (0.5%, 1.0%, and 2.0%) and spermidine (0.5, 1.0, and 2.0 mM) were studied to improve postharvest characteristics and quality maintenance during cold storage. Parameters such as firmness, weight loss, fungal contamination, total phenol, antioxidant activity, vitamin C, pH, total soluble solids (TSS), titratable acidity (TA), flavor index, color index, and ethylene production were measured after at harvest (0), 8, 16, and 24 days of storage at 15 ± 2°C and relative humidity of 85%–90%. Chitosan and spermidine delayed water loss, firmness, and fungal contamination. Application of chitosan containing ascorbic acid significantly increased phenolic content and antioxidant activity compared to the control plants. It also changed soluble solid content, TA, pH of pulp, and sugar content and decreased ethylene production. The obtained results suggested that chitosan (2%) and spermidine (2 mM) had potential to improve firmness and delay deterioration processes of “Langra” mango after harvest.
Physical, but not chemical, antiherbivore defense expression is related to the clustered spatial distribution of tropical trees in an Amazonian forest

Abstract The conspecific negative density dependence hypothesis states that mortality of young trees (seedlings and saplings) is higher near conspecific adults due to mechanisms such as allelopathy, intraspecific competition, and pest facilitation, explaining why in the tropics, most of plant species tend to be rare and live dispersed. However, there are some tree species that defy this expectation and grow in large clusters of conspecific juveniles and adults. We hypothesize that conspecifics living in clusters show higher and/or more variable defensive profiles than conspecifics with dispersed distributions. We evaluated our hypothesis by assessing the expression of physical leaf traits (thickness, and the resistance to punch, tear and shear) and leaf chemical defenses for six clustered and six non‐clustered tree species in Yasuní National Park, Ecuadorian Amazon. We ask ourselves whether (a) clustered species have leaves with higher physical resistance to damage and more chemical defenses variability than non‐clustered species; (b) saplings of clustered species may show higher physical resistance to damage and higher variation on chemical leaf defenses than their conspecific adults, and (c) saplings of non‐clustered species show lower resistance to physical damage and lower variation in chemical defenses compared to conspecific adults. Overall, our study did not support any of our hypotheses. Remarkably, we found that soluble metabolites were significantly species‐specific. Our study suggests that plants physical but not chemical leaf antiherbivore defenses may be a crucial strategy for explaining survivorship of clustered species. Trees in Yasuní may also fall along a suite of tolerance/escape/defense strategies based on limitations of each species physiological constraints for survival and establishment. We conclude that other mechanisms, such as those related to indirect defenses, soil nutrient exploitation efficiency, volatile organic compounds, delayed leaf‐greening, and seed dispersal mechanisms, shall be evaluated to understand conspecific coexistence in this forest.
Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data

Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species’ history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re‐analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species’ history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM.