Miracle-dz/UniFAR-FTUs huggingface dataset:
Antioxidant potential of all-trans retinoic acid (ATRA) and enhanced activity of liposome encapsulated ATRA against inflammation and tumor-directed angiogenesis

The purpose of this study was to investigate whether all-trans retinoic acid (ATRA) has antioxidant property. The study was also focused on its inhibitory effect on the acute and chronic inflammation and tumor-associated capillary formation in terms of angiogenesis in C57BL/6 mice after incorporated in liposome composed of distearoylphosphatidylcholine (DSPC/cholesterol). ATRA possesses a number of important biologic activities including oncostatic, antioxidant and immunostimulatory actions. Our study was designed to evaluate the antioxidant activity of free ATRA by nitric oxide scavenging, superoxide radical scavenging, hydroxyl radical scavenging and lipid peroxide scavenging assays. The ATRA showed significant scavenging activities in all these antioxidant assays comparable to the standard antioxidant. We have also evaluated the activity of encapsulated ATRA against anti-inflammatory activity in C57BL/6 mice. The paw oedema inhibition was found in carrageenan model as 55.56% and 66.67% for free ATRA and encapsulated ATRA treatment respectively and for formaldehyde model it was found to be 60.87% and 69.57% respectively compared with saline treated control mice. Encapsulated ATRA inhibited the tumor-associated capillary formation in mice induced by highly metastatic B16F10 melanoma cells significantly than the free ATRA did. In this study the inhibition of tumor-directed capillary formation was found to be 56.25% and 62.50% for free ATRA and encapsulated ATRA treatment respectively. In conclusion, ATRA showed a significant antioxidant property in vitro. Free ATRA has anti-inflammatory activity as proved by us in animal model of acute and chronic inflammation and antiangiogenesis activity. Furthermore, its activity was boosted by encapsulation in liposome.
Tissue proteomics in pancreatic cancer study: Discovery, emerging technologies, and challenges

Pancreatic cancer is a highly lethal disease that is difficult to diagnose and treat. The advances in proteomics technology, especially quantitative proteomics, have stimulated a great interest in applying this technology for pancreatic cancer study. A variety of tissue proteomics approaches have been applied to investigate pancreatic cancer and the associated diseases. These studies were carried out with various goals, aiming to better understand the molecular mechanisms underlying pancreatic tumorigenesis, to improve therapeutic treatment and to identify cancer associated protein signatures, signaling events as well as interactions between cancer cells and tumor microenvironment. Here, we provide an overview on the tissue proteomics studies of pancreatic cancer reported in the past few years in light of discovery and technology development.
Effects of long‐term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

To understand the fine‐scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long‐term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae‐Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88 706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic‐ (farmyard manure), mineral‐ and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co‐occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.
Activation of matrix metalloproteinases-9 after photothrombotic spinal cord injury model in rats.

OBJECTIVE Matrix metalloproteinases (MMPs), especially MMP-2 and MMP-9 have been known to play an important role in secondary inflammatory reaction after spinal cord injury (SCI). The aim of this study was to investigate the expression and activity of MMP-2 and MMP-9 and to determine their relationship with disruption of endothelial blood-barrier after photochemically induced SCI in rats. METHODS Female Sprague-Dawley rats, weighing between 250 and 300 g (aged 8 weeks) received focal spinal cord ischemia by photothrombosis using Rose Bengal. Expressions and activities of MMP-2 and MMP-9 were assessed by Western blot and gelatin zymography at various times from 6 h to 7 days. Endothelial blood-barrier integrity was assessed indirectly using spinal cord water content. RESULTS Zymography and Western blot analysis demonstrated rapid up-regulation of MMP-9 protein levels in spinal cord after ischemic onset. Expressions and activities of MMP-9 showed a significant increased at 6 h after the photothrombotic ischemic event, and reached a maximum level at 24 h after the insult. By contrast, activated MMP-2 was not detected at any time point in either the experimental or the control groups. When compared with the control group, a significant increase in spinal cord water content was detected in rats at 24 h after photothrombotic SCI. CONCLUSION Early up-regulation of MMP-9 might be correlated with increased water content in the spinal cord at 24 h after SCI in rats. Results of this study suggest that MMP-9 is the key factor involved in disruption of the endothelial blood-barrier of the spinal cord and subsequent secondary damage after photothrombotic SCI in rats.
A Pseudo-Outbreak of Pseudomonas putida and Stenotrophomonas maltophilia in a Bronchoscopy Unit

Background: Endoscopes represent the medical devices most commonly linked to health care-associated outbreaks and pseudo-outbreaks. Most of the recent outbreaks and pseudo-outbreaks have resulted from contaminated automated endoscope reprocessors (AER) or the use of damaged or malfunctioning bronchoscopes or contaminated equipment. Objectives: We investigated a pseudo-outbreak of Pseudomonas putida and Stenotrophomonas maltophilia recovered from bronchial washing (BW) specimens obtained during bronchoscopy in a bronchoscopy unit. Methods: Samples were obtained from environmental surfaces in the endoscopy suite, bronchoscopes, and bronchoscopic dispensable material, and specimens of cleaning solutions, cleaning brushes, the AER, and the ultrasound system were sent for bacterial culture. Medical records were reviewed to identify possible infections after a bronchoscopy. Results:P. putida and S. maltophilia were isolated from BW samples of 39 patients. The bronchoscopy models Olympus BF-1T160 and BF-160 were contaminated. Both bronchoscopes and other contaminated material (cleaning brushes, diluted cleaning solutions, and the sink) were isolated, but new cases continued to appear. The AER was recently installed, and new connections were used for the water lines and new tubes were connected to the AER. Initially, specimens were obtained from the external circuits and the internal walls of the AER. Finally, cultures were made from the filters on the water lines, and growth of P. putida and S. maltophilia was found. The investigation revealed that the BW specimens were contaminated because sterile saline was injected by means of the biopsy port of the bronchoscope and was recovered through the same channel by means of the proximal suction port. No patients developed clinical signs or symptoms of infection, but the positive cultures did lead to treatment of 21 patients. Conclusions: We described a pseudo-outbreak related to a contaminated bronchoscope because of inadequate installation of the AER for used new water lines and because the new tubes were connected to the AER. The antibacterial filters of the AER used tap water, and this may have contained low levels of microorganisms. No serious clinical complications derived from this pseudo-outbreak.
Optimized data aided training in MIMO systems

We evaluate the achievable capacity of training-based MIMO systems, when the channel is allowed to be re-estimated, e.g., a decision-directed system. A lower bound on the capacity is derived for the single user block fading MIMO model for systems based on superimposed pilots, which include conventional time-multiplexed pilot based systems as special cases. The system is optimized with respect to the proportion of time and power spent on training and data, respectively, and how the power should be allocated over the block. It is found that the capacity can be very close to the fundamental capacity of the non-coherent channel, especially when the channel coherence time is short, and that a significant gain compared to conventional receivers is achieved at the expense of a linear increase in complexity.
Diabetes, use of antidiabetic drugs, and the risk of glioma.

BACKGROUND Prior epidemiologic studies suggest inverse relations between diabetes and glioma risk, but the underlying mechanisms, including use of antidiabetic drugs, are unknown. METHODS We therefore performed a matched case-control analysis using the Clinical Practice Research Datalink (CPRD). We identified incident glioma cases diagnosed between 1995 and 2012 and matched each case with 10 controls on age, gender, calendar time, general practice, and years of active history in the CPRD. We performed conditional logistic regression to estimate odds ratios (ORs) with 95% CIs, adjusted for body mass index and smoking. RESULTS We identified 2005 cases and 20 050 controls. Diabetes was associated with decreased risk of glioma (OR = 0.74; 95% CI = 0.60-0.93), particularly glioblastoma (OR = 0.69; 95% CI = 0.51-0.94). Glioblastoma risk reduction was markedly pronounced among diabetic men (OR = 0.60; 95% CI = 0.40-0.90), most apparently for those with diabetes of long-term duration (OR for >5 vs 0 y = 0.46; 95% CI = 0.26-0.82) or poor glycemic control (OR for HbA1c ≥ 8 vs <6.5% = 0.20; 95% CI = 0.06-0.70). In contrast, the effect of diabetes on glioblastoma risk was absent among women (OR = 0.85; 95% CI = 0.53-1.36). No significant associations with glioma were found for use of metformin (OR for ≥ 30 vs 0 prescriptions = 0.72; 95% CI = 0.38-1.39), sulfonylureas (OR = 0.71; 95% CI = 0.39-1.30), or insulin (OR = 0.79; 95% CI = 0.37-1.69). CONCLUSIONS Antidiabetic treatment appears to be unrelated to glioma, but long-term diabetes duration and increased HbA1c both show decreased glioma risk. Stronger findings in men than women suggest low androgen levels concurrent with diabetes as a biologic mechanism.
Epigenetic Determinants of Erythropoiesis: Role of the Histone Methyltransferase SetD8 in Promoting Erythroid Cell Maturation and Survival

ABSTRACT Erythropoiesis, in which committed progenitor cells generate millions of erythrocytes daily, involves dramatic changes in the chromatin structure and transcriptome of erythroblasts, prior to their enucleation. While the involvement of the master-regulatory transcription factors GATA binding protein 1 (GATA-1) and GATA-2 in this process is established, the mechanistic contributions of many chromatin-modifying/remodeling enzymes in red cell biology remain enigmatic. We demonstrated that SetD8, a histone methyltransferase that catalyzes monomethylation of histone H4 at lysine 20 (H4K20me1), is a context-dependent GATA-1 corepressor in erythroid cells. To determine whether SetD8 controls erythroid maturation and/or function, we used a small hairpin RNA (shRNA)-based loss-of-function strategy in a primary murine erythroblast culture system. In this system, SetD8 promoted erythroblast maturation and survival, and this did not involve upregulation of the established regulator of erythroblast survival Bcl-xL. SetD8 catalyzed H4K20me1 at a critical Gata2 cis element and restricted occupancy by an enhancer of Gata2 transcription, Scl/TAL1, thereby repressing Gata2 transcription. Elevating GATA-2 levels in erythroid precursors yielded a maturation block comparable to that induced by SetD8 downregulation. As lowering GATA-2 expression in the context of SetD8 knockdown did not rescue erythroid maturation, we propose that SetD8 regulation of erythroid maturation involves multiple target genes. These results establish SetD8 as a determinant of erythroid cell maturation and provide a framework for understanding how a broadly expressed histone-modifying enzyme mediates cell-type-specific GATA factor function.
Le déterminisme de la couleur du bois de chêne : Etude sur les relations entre la couleur et des propriétés physiques, chimiques et anatomiques ainsi que des caractéristiques de croissance

Le but de cette these est d'ameliorer les connaissances actuelles concernant la couleur du bois. Deux volets ont ete developpes, premierement la description et la modelisation des relations entre la couleur et des parametres importants pour le sylviculteur tels que la largeur de cerne et l'âge et, deuxiemement, la comprehension du determinisme de la couleur du bois de chene. La couleur, mesuree avec un spectrophotometre sur des faces radiales de bois, est exprimee soit dans le volume l#*l#*h soit dans le volume l#*a#*b. Nous avons etudie les relations entre la couleur et les parametres suivants : largeur de cerne, largeur des bois initial et final, l'âge du bois, la densite du bois, l'etat de surface, les dimensions des vaisseaux du bois initial, la teneur en phenols et avec l'evolution des extractibles au cours du temps. L’evolution radiale (variation intra arbre) de la couleur peut etre mise en relation avec une transformation des ellagitanins au cours du vieillissement du bois. La clarte du bois de chene peut etre modelisee a l'aide des parametres age et largeur de cerne. En revanche, la modelisation de la teinte necessite des parametres plus explicites, tels que des variables chimiques.
Beliefs in an Unjust World: Mediating Ethnicity-Related Stressors and Psychological Functioning.

OBJECTIVE Racism is negatively associated with health. Explorations of cognitive reactions, such as beliefs in an unjust world (BUW), are needed to understand the associations between both perceived discrimination and own-group conformity pressures (OGCPS) and reduced psychological well-being. METHOD With a sample of 215 ethnic minority individuals, this study used structural equation modeling to explore BUW's mediating role between the two aforementioned forms of ethnicity-related stressors (ERS), anger rumination, and negative affect. RESULTS ERS were directly positively associated with BUW, anger rumination, and negative affect. BUW were directly and positively associated with both anger rumination and negative affect. Finally, BUW significantly mediated the direct relationships between both ethnicity-related stressors and anger rumination and negative affect. CONCLUSION Although addressing racism and OGCPS at a systemic level (e.g., policy, prejudice prevention) is needed to reduce ERS, these findings suggest that BUW is one point of possible clinical intervention for individuals who have experienced these stressors.
Oligodeoxynucleotide CpG 7909 Delivered as Intravenous Infusion Demonstrates Immunologic Modulation in Patients With Previously Treated Non-Hodgkin Lymphoma

Oligodeoxynucleotides containing CpG motifs (CpG ODN) can alter various immune cell subsets important in antibody therapy of malignancy. We undertook a phase I trial of CPG 7909 (also known as PF-3512676) in patients with previously treated lymphoma with the primary objective of evaluating safety across a range of doses, and secondary objectives of evaluating immunomodulatory effects and clinical effects. Twenty-three patients with previously treated non-Hodgkin lymphoma received up to 3 weekly 2-hour intravenous (IV) infusions of CPG ODN 7909 at dose levels 0.01 to 0.64 mg/kg. Evaluation of immunologic parameters and clinical endpoints occurred for 6 weeks. Infusion-related toxicity included grade 1 nausea, hypotension, and IV catheter discomfort. Serious adverse hematologic events observed more than once included anemia (2=Gr3, 2=Gr4), thrombocytopenia (4=Gr3), and neutropenia (2=Gr3), and were largely judged owing to progressive disease. Immunologic observations included: (1) The mean ratio of NK-cell concentrations compared with pretreatment at day 2 was 1.44 (95% CI=0.94-1.94) and at day 42 was 1.53 (95% CI=1.14-1.91); (2) NK activity generally increased in subjects; and (3) Antibody-dependent cellular cytotoxicity activity increased in select cohorts. No clinical responses were documented radiographically at day 42. Two subjects demonstrated late response. We conclude CpG 7909 can be safely given as a 2-hour IV infusion to patients with previously treated non-Hodgkin lymphoma at doses that have immunomodulatory effects.
Bone loss in C57BL/6J‐OlaHsd mice, a substrain of C57BL/6J carrying mutated alpha‐synuclein and multimerin‐1 genes

The inbred mouse strain C57BL/6 is commonly used for the generation of transgenic mouse and is a well established strain in bone research. Different vendors supply different substrains of C57BL/6J as wild‐type animals when genetic drift did not incur any noticeable phenotype. However, we sporadically observed drastic differences in the bone phenotype of “WT” C57BL/6J mice originating from different labs and speculated that these variations are attributable, at least in part, to the variation between C57BL/6J substrains, which is often overlooked. C57BL/6J‐OlaHsd is a commonly used substrain that despite a well defined deletion in the alpha‐synuclein (Snca) and multimerin‐1 (Mmrn1) genes, was reported to display no obvious phenotype and is used as WT control. Here, we compared the bone phenotype of C57BL/6J‐OlaHsd (6J‐OLA) to C57BL/6J‐RccHsd (6J‐RCC) and to the original C57BL/6J (6J‐JAX). Using μCT analysis, we found that 6J‐OLA mice display a significantly lower trabecular bone mass compared to 6J‐RCC and 6J‐JAX. PCR analysis revealed that both the Snca and Mmrn1 genes are expressed in bone tissue of 6J‐RCC animals but not of 6J‐OLA mutants, suggesting either one or both genes play a role in bone metabolism. In vitro analysis demonstrated increase in osteoclasts number and decreased osteoblast mineralization in cells derived from 6J‐OLA compared with 6J‐RCC. Our data may shed light on unexplained differences in basal bone measurements between different research centers and reiterate the importance of specifying the exact substrain type. In addition, our findings describe the physiological role for Mmrn1 and/or Snca in bone remodeling.
Familial predictors of treatment outcome in childhood anxiety disorders.

OBJECTIVE To determine whether family factors are predictive of outcome in children with anxiety disorders who are receiving cognitive-behavioral treatment. METHOD Participants were 61 children aged 8 to 12 years (mean = 10.0, SD = 1.4) with Axis I anxiety disorders who had been referred to a large Toronto children's hospital. Parents and children completed measures assessing family functioning, parenting stress, parental frustration, and parental psychopathology before and after treatment. Outcome measures included clinician-rated functioning (Children's Global Assessment Scale) and self- and parent-rated anxiety (Revised Children's Manifest Anxiety Scale). RESULTS Child ratings of family dysfunction and frustration predicted clinician-rated improvement (total R2 = 0.28, p < .001). Mother and father reports of family dysfunction, and maternal parenting stress, predicted mother-rated child improvement (total R2 = 0.18, p < .01). Father-rated somatization and child reports of family dysfunction and frustration predicted child-rated improvement (total R2 = 0.25, p < .001). Several family factors improved with treatment. CONCLUSION Family dysfunction appears to be related to less favorable treatment outcome in children with anxiety disorders.
Simultaneous, Single‐Cell Measurement of Messenger RNA, Cell Surface Proteins, and Intracellular Proteins

Nucleic acid content can be quantified by flow cytometry through the use of intercalating compounds; however, measuring the presence of specific sequences has hitherto been difficult to achieve by this methodology. The primary obstacle to detecting discrete nucleic acid sequences by flow cytometry is their low quantity and the presence of high background signals, rendering the detection of hybridized fluorescent probes challenging. Amplification of nucleic acid sequences by molecular techniques such as in situ PCR have been applied to single‐cell suspensions, but these approaches have not been easily adapted to conventional flow cytometry. An alternative strategy implements a Branched DNA technique, comprising target‐specific probes and sequentially hybridized amplification reagents, resulting in a theoretical 8,000‐ to 16,000‐fold increase in fluorescence signal amplification. The Branched DNA technique allows for the quantification of native and unmanipulated mRNA content with increased signal detection and reduced background. This procedure utilizes gentle fixation steps with low hybridization temperatures, leaving the assayed cells intact to permit their concomitant immunophenotyping. This technology has the potential to advance scientific discovery by correlating potentially small quantities of mRNA with many biological measurements at the single‐cell level. © 2016 by John Wiley & Sons, Inc.
Interpretation of Cloud-Climate Feedback as Produced by 14 Atmospheric General Circulation Models

Understanding the cause of differences among general circulation model projections of carbon dioxide-induced climatic change is a necessary step toward improving the models. An intercomparison of 14 atmospheric general circulation models, for which sea surface temperature perturbations were used as a surrogate climate change, showed that there was a roughly threefold variation in global climate sensitivity. Most of this variation is attributable to differences in the models' depictions of cloud-climate feedback, a result that emphasizes the need for improvements in the treatment of clouds in these models if they are ultimately to be used as climatic predictors.
Alpha taxonomy of the genus Kessleria Nowicki, 1864, revisited in light of DNA-barcoding (Lepidoptera, Yponomeutidae)

Abstract The taxonomy of Kessleria, a highly specialized montane genus of Yponomeutidae with larval host restriction to Saxifragaceae and Celastraceae (Saxifraga spp. – subgenus Kessleria; Saxifraga spp. and Parnassia spp. – subgenus Hofmannia), is revised based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 29 species in Europe (the two known species from Asia and North America are not treated herein). A full 658 bp fragment of COI was obtained from 135 specimens representing 24 species, a further seven sequences are >560 bp. Five new species are described: Kessleria cottiensis sp. n. (Prov. Torino, Italy; Dep. Hautes Alpes, France), Kessleria dimorpha sp. n. (Dep. Alpes-de-Haute-Provence, France), Kessleria alpmaritimae sp. n. (Dep. Alpes-Maritimes, France), Kessleria apenninica sp. n. (Prov. Rieti, Prov. L´Aquila, Italy), and Kessleria orobiae sp. n. (Prov. Bergamo, Italy).