Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular mechanisms underpinning phosphorus-use efficiency in rice.

Orthophosphate (H2 PO4- , Pi) is an essential macronutrient integral to energy metabolism as well as a component of membrane lipids, nucleic acids, including ribosomal RNA, and therefore essential for protein synthesis. The Pi concentration in the solution of most soils worldwide is usually far too low for maximum growth of crops, including rice. This has prompted the massive use of inefficient, polluting, and nonrenewable phosphorus (P) fertilizers in agriculture. We urgently need alternative and more sustainable approaches to decrease agriculture's dependence on Pi fertilizers. These include manipulating crops by (a) enhancing the ability of their roots to acquire limiting Pi from the soil (i.e. increased P-acquisition efficiency) and/or (b) increasing the total biomass/yield produced per molecule of Pi acquired from the soil (i.e. increased P-use efficiency). Improved P-use efficiency may be achieved by producing high-yielding plants with lower P concentrations or by improving the remobilization of acquired P within the plant so as to maximize growth and biomass allocation to developing organs. Membrane lipid remodelling coupled with hydrolysis of RNA and smaller P-esters in senescing organs fuels P remobilization in rice, the world's most important cereal crop.
Isolation of Neutrophils from the Bronchoalveotar Lavage ( BAL ) of Patients with Adult Respiratory Distress Syndrome ( ARDS )

Increasing evidence suggests that the metabolism of arachidonic acid (AA) may be different in inflammatory cells isolated from blood or migrating into tissues. To explore the possibility that changes in AA metabolism between blood and tissue inflammatory cells could be due in part to a different content or distribution of AA in glycerollpid classes, we studied these parameters in six human inflammatory cells isolated from blood (eosinophils, monocytes, neutrophils, and platelets) or from the lung tissue (mast cells and macrophages). Lung cells generally had a higher total cellular content of AA than that found in the blood cells. In addition, both mast cells and macrophages had a large endogenous pool of AA associated with triglycerides (TG), containing 45 and 22% of their total cellular AA, respectively. To address the hypothesis that cells migrating into the lung had a higher cellular level of AA and a larger AA pool in TG, we studied neutrophils isolated from the bronchoalveolar Iavage (BAL) of patients with adult respiratory distress syndrome. BAL neutrophils had a fourfold increase in cellular AA as compared with blood neutrophils and contained 25% of their AA in TG versus 3% in blood neutrophils. BAL neutrophils also had a higher number of cytoplasmic lipid bodies (8 + 3/cell) relative to blood neutrophils (2 + 1/cell). High concentrations of free AA were also found in the cell-free BAL fluid of adult respiratory distress syndrome patients. To explore whether changes in BAL neutrophils may be due to the exposure of the cells to high concentrations of exogenous AA found in BAL, we incubated blood neutrophils in culture with AA (10-100 p,M) for 24 h. Neutrophils supplemented with AA had a 10-fold increase in the amount of AA associated with TG and a sixfold increase in the number of lipid bodies. In addition, supplementation with AA induced a dose-dependent formation of hypodense cells. Taken together, these data indicate that human inflammatory cells undergo a fundamental and consistent remodeling of AA pools as they mature or enter the lung from the blood. These biochemical and morphological changes can be mimicked in vitro by exposing the cells to high levels of AA. This mechanism may be responsible for the changes in AA mobilization and eicosanoid metabolism observed in tissue inflammatory cells.
Adaptive interactions between zinc oxide nanoparticles and Chlorella sp.

The effects of ZnO nanoparticles (NPs) interacting with single-celled green algae, Chlorella sp. , have been found to be bilateral. Specifically, our electron microscopy, plant cell, and fluorescence assays showed that the adsorption and aggregation of ZnO NPs compromised algal cell morphology, viability, and membrane integrity, resulting from zinc ion dissolution as well as possible mechanical cell damage induced by the NPs. Conversely, algal cells displayed a remarkable capability of self-protection by minimizing their surface area through aggregation mediated by the oppositely charged metal ions and suppressing zinc ion release from the NPs through exudation, as evidenced by inductively coupled plasma mass spectrometry, zeta potential, and attenuated total reflectance-Fourier transform infrared spectroscopy. This study illustrates the adaptive nature and complexity in potential ecological response to discharged nanomaterials.
Reliability and accuracy of the tape measurement method with a nearest reading of 5 mm in the assessment of leg length discrepancy.

INTRODUCTION The aim of this study was to determine the reliability and accuracy of the tape measurement method (TMM) with a nearest reading of 5 mm in assessing leg length discrepancy (LLD). METHODS This was a cross-sectional study conducted on 35 patients with LLD and 13 patients without LLD. Two blinded surgeons measured the lower limbs from the anterior superior iliac spine to the medial malleolus using TMM with a nearest reading of 5 mm. Computed tomography (CT) scanograms of the lower limbs of 22 patients were conducted by two blinded radiologists. Intraclass correlation coefficient (ICC) with 95 percent confidence interval was calculated to assess the interobserver reliability of TMM. The accuracy of TMM was assessed by comparison with CT as the gold standard. RESULTS The interobserver reliability of LLD measurement using both TMM and CT scanogram was high, with ICCs of 0.924 and 0.971, respectively. No significant mean difference on paired sample t-test was observed for both TMM and CT scanogram. Compared to CT scanogram, TMM had good accuracy, with an ICC of 0.805. When the mean TMM readings by two observers were compared to those derived from CT scanogram, the ICC was found to be 0.847, with a mean difference of 1.95 (range -3.17 to 7.07) mm. CONCLUSION There was excellent agreement in the LLD measurements between the two surgeons using TMM, between the two radiologists using CT sonogram, and between the TMM and CT measurements. This study showed that one TMM with the nearest reading of 5 mm was reliable and accurate in measuring LLD.
Relationship between serum vitamin D and forced expiratory volume in patients with chronic obstructive pulmonary disease (COPD).

BACKGROUND Vitamin D deficiency seems to be associated with pulmonary function deterioration. The present study was designed to investigate the relationship between serum vitamin D and forced expiratory volume in patients with chronic obstructive pulmonary disease (COPD). METHODS From September 2011 to April 2012 eighty consecutive patients with COPD presented to an outpatient clinic of Babol University- Teaching Hospital entered to the study. Diagnosis of COPD was confirmed according to clinical findings and pulmonary function test. Serum 25-hydroxyvitamin D (25-OHD) was assessed by chemiluminuscence method and postbronchodilator forced expiratory volume in 1s (FEV1) was measured in all patients. The objective of this study was to determine the relationship between serum 25-OHD concentrations and FEV1 value. The patients were classified according to serum 25- OHD concentrations as less 10ng/ml, 10-19.9; 20-29.9; 30-39.9; and 40ng/ml or higher. The mean values of FEV1 for each class of serum 25-OHD were determined and compared. RESULTS The mean age of patients was 67.4±11.5 years. The mean FEV1 volume in serum 25-OHD deficient COPD was lower than sufficient COPD (1.550±0.55 vs 1.650±-0.58, p=0.45). Mean FEV1 values increased from 1.55±0.55 L in patients with mean serum 25-OHD <20 ng/ml to 1.94±0.74 L in COPD patients with mean serum 25-OHD ±>40 ng/ml. There was a dose-response pattern of relationship between FEV1 and serum 25-OHD. However, the relationship did not reach to a statistically significant level. CONCLUSION These findings indicated a relationship between serum 25-OHD concentration and FEV1 volume in patients with COPD and suggest optimization of serum vitamin D levels in COPD.
Genetic variation in C20orf54, PLCE1 and MUC1 and the risk of upper gastrointestinal cancers in Caucasian populations

Recently, two large genome-wide association studies, conducted in Chinese populations, have reported associations between upper gastrointestinal cancer and the rs2274223, rs13042395 and rs4072037 polymorphisms in PLCE1, C20orf54 and MUC1, respectively. We aimed to determine whether similar associations existed for Caucasian populations. We genotyped two population-based, case–control studies of upper gastrointestinal cancer; the first study included 290 gastric cancer (GC) cases and 376 controls and the second study included 306 GC cases, 107 oesophageal adenocarcinoma cancer cases, 52 oesphageal squamous cell cancer cases and 211 controls. Odds ratios (OR) and 95% confidence intervals (CIs) were computed from logistic models and adjusted for confounding variables. The rs4072037 polymorphism in MUC1 was associated with a reduced risk of GC of intestinal histological type (OR 0.4; 95% CI 0.2–0.9) and a reduced risk of oesophageal squamous cell cancer (OR 0.5; 95% CI 0.2–1.0), but not oesphageal adenocarcinoma. Similarly, rs2274223 in PLCE1 was associated with a reduced risk of oesophageal squamous cell cancer (OR 0.5; 95% CI 0.3–1.0), but not oesphageal adenocarcinoma. We observed no association between rs13042395 in Corf54 and the risk of gastric or oesphageal cancer in either of the two studies. Our findings for rs4072037 and the risk of GC are in agreement with one previous report for a Caucasian population. To the best of our knowledge, this is the first study to report an association between rs2274223 and rs4072037 and the risk of oesophageal squamous cell carcinoma in a Caucasian population.
Influence of nanotube preparation in Aquatic Bioassays

Knowledge gaps in nanomaterial fate and toxicity currently limit the ability of risk assessments to characterize the environmental implications of nanomaterials. This problem is further complicated by the lack of standardized characterization and preparation methodologies for researchers to gain the needed information to assist risk assessors. In the present study, data were generated to determine if multiwalled nanotube (MWNT) fate and toxicity are altered by engineered surface modifications or by different dispersal methods. While dissolved organic matter was a good dispersing agent of MWNTs in water, the humic acid fraction was a more effective dispersant than the fulvic acid fraction. When stabilized in organic matter, the functional group attached to the MWNT controlled its toxicity. Underivatized MWNTs induced relatively moderate toxicity to Ceriodaphnia dubia after 96 h (25 ± 19% survival at 26 mg/L), while hydrophilic groups (hydroxyl, carboxyl) reduced this toxicity (93 ± 12% survival at 48 mg/L). However, other functional groups (alkyl, amine) increased toxicity (0 ± 0% survival at <15 mg/L). In dispersal method studies, sonication of MWNTs increased fragmentation relative to magnetic stirring. The sonication treatment of MWNTs also slightly reduced the mortality of C. dubia in the water column but increased toxicity in the sediment to Leptocheirus plumulosus and Hyalella azteca. Findings in the present study indicate that nanotubes engineered for specific applications need to be managed independently and that laboratory methods to disperse and test nanotubes in bioassays need to be standardized to obtain repeatable results for comparison of materials.
Immunomodulation mediated through Leishmania donovani protein disulfide isomerase by eliciting CD8+ T-cell in cured visceral leishmaniasis subjects and identification of its possible HLA class-1 restricted T-cell epitopes

Protein disulphide isomerase (PDI) is one of the key enzymes essential for the survival of Leishmania donovani in the host. Our study suggested that PDI is associated with the generation of Th1-type of cellular responses in treated Visceral leishmaniasis (VL) subjects. The stimulation of Peripheral blood mononuclear cells (PBMCs) with recombinant Protein Disulphide Isomerase upregulated the reactive oxygen species generation, Nitric oxide release, IL12 and IFN-γ production indicating its pivotal role in protective immune response. Further, a pre-stimulation of PBMCs with Protein disulphide isomerase induced a strong IFN-γ response through CD8+ T cells in treated VL subjects. These findings also supported through the evidence that this antigen was processed and presented by major histocompatibility complex class I (MHC-1) dependent pathway and had an immunoprophylactic potential which can induce CD8+ T cell protective immune response in MHC class I dependent manner against VL. To find out the possible epitopes that might be responsible for CD8+ T cell specific IFN-γ response, computational approach was adopted. Six novel promiscuous epitopes were predicted to be highly immunogenic and can be presented by 32 different HLA allele to CD8+ T cells. Further investigation will explore more about their immunological relevance and usefulness as vaccine candidates.
Nephrotoxic serum nephritis in mice with a genetic deficiency in complement.

Complement-containing progeny from the hybridization of B10.D2-old line females with B10.D2-new line males were used to study the role of the complement system in immune tissue injury. Small differences in the severity of nephrotoxic serum nephritis were found following the injection of nephrotoxic serum which implicate the late acting complement components as intensifiers of tissue injury.
Characterization of a unique dihydropyrimidinone, ethyl 4‐(4′‐heptanoyloxyphenyl)‐6‐methyl‐3,4‐dihydropyrimidin‐2‐one‐5‐carboxylate, as an effective antithrombotic agent in a rat experimental model

Objectives To evaluate the potential of a novel dihydropyrimidinone, ethyl 4‐(4′‐heptanoyloxyphenyl)‐6‐methyl‐3,4‐dihydropyrimidin‐2‐one‐5‐carboxylate (H‐DHPM), as a calcium channel blocker, endowed with the ability to inhibit platelet aggregation effectively.
Regulation of dorsal gene expression in Xenopus by the ventralizing homeodomain gene Vox.

Patterning in the vertebrate embryo is controlled by an interplay between signals from the dorsal organizer and the ventrally expressed BMPs. Here we examine the function of Vox, a homeodomain-containing gene that is activated by the ventralizing signal BMP-4. Inhibition of BMP signaling using a dominant negative BMP receptor (DeltaBMPR) leads to the ectopic activation of dorsal genes in the ventral marginal zone, and this activation is prevented by co-injection of Vox. chordin is the most strongly activated of those genes that are up-regulated by DeltaBMPR and is the gene most strongly inhibited by Vox expression. We demonstrate that Vox acts as a transcriptional repressor, showing that the activity of native Vox is mimicked by a Vox-repressor fusion (VoxEnR) and that a Vox-activator fusion (VoxG4A) acts as an antimorph, causing the formation of a partial secondary axis when expressed on the ventral side of the embryo. Although Vox can ectopically activate BMP-4 expression in whole embryos, we see no activation of BMP-4 by VoxG4A, demonstrating that this activation is indirect. Using a hormone-inducible version of VoxG4A, we find that a critical time window for Vox function is during the late blastula period. Using this construct, we demonstrate that only a subset of dorsal genes is directly repressed by Vox, revealing that there are different modes of regulation for organizer genes. Since the major direct target for Vox repression is chordin, we propose that Vox acts in establishing a BMP-4 morphogen gradient by restricting the expression domain of chordin.
Coagulase‐negative staphylococcal sepsis as a predictor of bronchopulmonary dysplasia

Aim: To determine whether sepsis caused by coagulase‐negative staphylococci (CoNS) is a risk factor for developing bronchopulmonary dysplasia (BPD) in premature newborns. Methods: All newborns born at ±30 wk of gestation at Örebro University Hospital during 1994–2001 with clinical sepsis caused by CoNS (group A, n= 22) or by other bacteria (group B, n= 17) were included and compared with premature newborns without sepsis (group C, n= 53). Clinical sepsis was defined as a positive blood culture (monoculture) plus clinical symptoms and laboratory findings. BPD was defined as treatment with oxygen >21% for at least 28 d. Results: The incidence of BPD differed between the three groups, as follows: CoNS sepsis (A) 64%, other sepsis (B) 41% and control (C) 24%. The difference between the control group and the sepsis groups was highly significant (p= 0.006). In a univariate model the crude estimates of relative risk (RR) for occurrence of BPD increased with presence of sepsis and particularly with presence of sepsis with CoNS (A: RR 2.6, 95% CI 1.5–4.6, p= 0.001; B: RR 1.7, CI 0.8–3.5, p= 0.17). When regression was performed with two additional predictive variables in multivariate models including sepsis, gestational age and mechanical ventilation (group A: RR 1.5, CI 1.1–2.0, p= 0.004; group B: RR 0.9, CI 0.6–1.4, p= 0.67), the estimates were lower.
Effects of adrenaline administration on the interrenal gland of the newt, Triturus carnifex: Evidence of intraadrenal paracrine interactions

The existence of paracrine control of steroidogenic activity by adrenochromaffin cells in Triturus carnifex was investigated by in vivo adrenaline (A) administration. The effects were evaluated by examination of the ultrastructural morphological and morphometrical features of the tissues as well as the serum levels of aldosterone, noradrenaline (NA), and adrenaline. In March and July, adrenaline administration reduced aldosterone release (from 187.23 ± 2.93 pg/ml to 32.28 ± 1.85 pg/ml in March; from 314.60 ± 1.34 pg/ml to 87.51 ± 2.57 pg/ml in July) from steroidogenic cells. The cells showed clear signs of lowered activity: they appeared full of lipid, forming large droplets. Moreover, adrenaline administration decreased the mean total number of secretory granules in the chromaffin cells in July (from 7.74 ± 0.74 granules/μm2 to 5.14 ± 1.55 granules/μm2). In this period T. carnifex chromaffin cells contain almost exclusively NA granules (NA: 7.42 ± 0.86 granules/μm2; A: 0.32 ± 0.13 granules/μm2). Adrenaline administration reduced noradrenaline content (4.36 ± 1.40 granules/μm2) in the chromaffin cells, enhancing noradrenaline secretion (from 640.19 ± 1.65 pg/ml to 1030.16 ± 3.03 pg/ml). In March, adrenaline administration did not affect the mean total number of secretory vesicles (from 7.24 ± 0.18 granules/μm2 to 7.25 ± 1.97 granules/μm2). In this period the chromaffin cells contain both catecholamines, noradrenaline (3.88 ± 0.13 granules/μm2), and adrenaline (3.36 ± 0.05 granules/μm2), in almost equal quantities; adrenaline administration reduced adrenaline content (1.74 ± 0.84 granules/μm2), increasing adrenaline release (from 681.27 ± 1.83 pg/ml to 951.77 ± 4.11 pg/ml). The results of this study indicate that adrenaline influences the steroidogenic cells, inhibiting aldosterone release. Adrenaline effects on the chromaffin cells (increase of noradrenaline or adrenaline secretion) vary according to the period of chromaffin cell functional cycle. The existence of intraadrenal paracrine interactions in T. carnifex is discussed. J. Morphol. 261:18–25, 2004. © 2004 Wiley‐Liss, Inc.
Deep vein thrombosis in stroke. The use of plasma D-dimer level as a screening test in the rehabilitation setting.

BACKGROUND AND PURPOSE Venous thromboembolism is a leading cause of morbidity and mortality during the acute recovery period after stroke. This study investigated the utility of plasma D-dimer level as a diagnostic test for deep vein thrombosis (DVT) in patients hospitalized for stroke rehabilitation. METHOD Plasma samples were drawn from 105 nonambulatory rehabilitation patients with recent ischemic or hemorrhagic stroke and assayed for D-dimer with an enzyme-linked immunosorbent method. Samples were drawn within 24 hours of venous duplex ultrasound (VDU) screening for DVT. Optimal discriminant analysis was used to determine whether plasma D-dimer level, age, sex, days after stroke onset, stroke etiology. National Institutes of Health Stroke Scale score, and ambulatory status could correctly classify patients' DVT status. RESULTS Fourteen of 105 patients had DVT identified by VDU scan. Of all attributes, only D-dimer level had significant ability to discriminate between patients with or without DVT (P < .0001). The optimal cut point for predicting DVT was D-dimer = 1591 ng/mL, resulting in 79% sensitivity, 78% specificity, 35% positive predictive value, and 96% negative predictive value. Reducing the D-dimer cut point to 1092 ng/mL improved both sensitivity and negative predictive value to 100% but reduced specificity to 66% and positive predictive value to 31%. CONCLUSIONS A D-dimer level < or = 1092 ng/mL can exclude the presence of DVT in stroke rehabilitation patients. When a D-dimer level > 1092 ng/mL occurs, further diagnostic testing is necessary to confirm DVT. Plasma D-dimer level is a simple and inexpensive screening test for DVT during stroke rehabilitation.
A genetic factor for age-related cataract: identification and characterization of a novel galactokinase variant, "Osaka," in Asians.

Galactokinase (GALK) deficiency is an autosomal recessive disorder characterized by hypergalactosemia and cataract formation. Through mass screening of newborn infants, we identified a novel and prevalent GALK variant (designated here as the "Osaka" variant) associated with an A198V mutation in three infants with mild GALK deficiency. GALK activity and the amount of immunoreactive protein in the mutant were both 20% of normal construct in expression analysis. The K(m) values for galactose and ATP-Mg(2+) in erythrocytes with homozygous A198V were similar to those of the healthy adult control subjects. A population study for A198V revealed prevalences of 4.1% in Japanese and 2.8% in Koreans, lower incidence in Taiwanese and Chinese, no incidence in blacks and whites from the United States, and a significantly high frequency (7.8%; P < .023) in Japanese individuals with bilateral cataract. This variant probably originated in Japanese and Korean ancestors and is one of the genetic factors that causes cataract in elderly individuals.