Miracle-dz/UniFAR-FTUs huggingface dataset:
Uracil-DNA Glycosylase UNG Promotes Tet-mediated DNA Demethylation*

In mammals, active DNA demethylation involves oxidation of 5-methylcytosine (5mC) into 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by Tet dioxygenases and excision of these two oxidized bases by thymine DNA glycosylase (TDG). Although TDG is essential for active demethylation in embryonic stem cells and induced pluripotent stem cells, it is hardly expressed in mouse zygotes and dispensable in pronuclear DNA demethylation. To search for other factors that might contribute to demethylation in mammalian cells, we performed a functional genomics screen based on a methylated luciferase reporter assay. UNG2, one of the glycosylases known to excise uracil residues from DNA, was found to reduce DNA methylation, thus activating transcription of a methylation-silenced reporter gene when co-transfected with Tet2 into HEK293T cells. Interestingly, UNG2 could decrease 5caC from the genomic DNA and a reporter plasmid in transfected cells, like TDG. Furthermore, deficiency in Ung partially impaired DNA demethylation in mouse zygotes. Our results suggest that UNG might be involved in Tet-mediated DNA demethylation.
Venoarterial versus venovenous extracorporeal membrane oxygenation in congenital diaphragmatic hernia: the Extracorporeal Life Support Organization Registry, 1990-1999.

BACKGROUND/PURPOSE Venoarterial (VA) extracorporeal membrane oxygenation (ECMO) traditionally has been the mode of support used in congenital diaphragmatic hernia (CDH). A few studies report success using venovenous (VV) ECMO. The purpose of this study is to compare outcomes in CDH patients treated with VA and VV. METHODS The authors queried the Extracorporeal Life Support Organization Registry for newborns with CDH treated with ECMO from January 1, 1990 through December 31, 1999. They analyzed the pre-ECMO data, ECMO course, and complications. RESULTS VA was utilized in 2,257 (86%) and VV in 371 (14%) patients. The pre-ECMO status was similar, with greater use of nitric oxide, surfactant, and pressors in VV. Survival rate was similar (58.4% for VV and 52.2% for VA, P =.057). VA was associated with more seizures (12.3% v 6.7%, P =.0024) and cerebral infarction (10.5% v 6.7%, P =.03). Sixty-four treatments were converted from VV to VA (VV-->VA). Survival rate in VV-->VA was not significantly different than VA (43.8% v 52.2%, respectively; P =.23). VV-->VA and VA patients had similar neurologic complications. CONCLUSIONS CDH patients treated with VV and VA have similar survival rates. VA had more neurologic complications. The authors identified no disadvantage to the use of VV as an initial mode of ECMO for CDH, although some infants may need conversion to VA.
Gustatory responses of neurons in the nucleus of the solitary tract of behaving rats.

1. The activity of 117 single neurons was recorded in the rostral nucleus of the solitary tract (NST) and tested with each of four standard chemical stimuli [sucrose, NaCl, citric acid, and quinine HCl (QHCl)] and distilled water in awake, behaving rats. In 101 of these neurons, at least one sapid stimulus elicited a significant taste response. The mean spontaneous rate of the taste neurons was 4.1 +/- 5.8 (SD) spike/s. The mean response magnitudes were as follows: sucrose, 10.6 +/- 11.7; NaCl, 8.6 +/- 14.6; citric acid, 6.2 +/- 7.8; and QHCl, 2.4 +/- 6.6 spikes/s. 2. On the basis of their largest response, 42 taste neurons were classified as sucrose-best, 25 as NaCl-best, 30 as citric acid-best, and 4 as QHCl-best. The mean spontaneous rates for these categories were 4.9 +/- 6.2 for sucrose-best cells, 5.8 +/- 7.4 for NaCl-best, 1.6 +/- 2.0 for citric acid-best, and 5.8 +/- 6.0 spikes/s for QHCl-best. The spontaneous rate of the citric acid-best neurons was significantly lower than that of the other categories. 3. At the standard concentrations, 45 taste cells (44.6%) responded significantly to only one of the gustatory stimuli. Of the 30 acid-best neurons, 23 (76.7%) responded only to citric acid. For sucrose-best cells, specific sensitivity was less common (18/42, 42.9%), and for NaCl-best neurons, it was relatively uncommon (3/25, 12%). One of the 4 QHCl-best neurons was specific. In a concentration series, more than one-half of the 19 specific neurons tested responded to only one chemical at any strength. 4. The mean entropy for the excitatory responses of all gustatory neurons was 0.60. Citric acid-best cells showed the least breadth of responsiveness (0.49), sucrose-best cells were somewhat broader (0.56), but NaCl-best and QHCl-best cells were considerably less selective (0.77 and 0.79, respectively). Inhibition was observed infrequently and never reached the criterion for significance. 5. In the hierarchical cluster analysis, the four largest clusters segregated neurons primarily by best-stimulus category. The major exception to this was a group of sucrose-best neurons that also responded to NaCl and were grouped with the NaCl-best neurons. In a two-dimensional space, the specific taste neurons, those that responded to only one of the four standard sapid stimuli, remained in well-separated groups. These specific groups, however, were joined in a ring-like formation by other neurons that responded to more than one of the sapid stimuli. (ABSTRACT TRUNCATED AT 400 WORDS)
The mRNAs of Prekallikrein, Factors XI and XII, and Kininogen, Components of the Contact Phase Cascade Are Differentially Expressed in Multiple Non-hepatic Human Tissues

Summary Recently RT-PCR studies had demonstrated the expression of plasma prekallikrein (PPK) mRNA in extrahepatic tissues. The questions arose whether that is illegitimate or regular expression, and whether the mRNAs of blood coagulation factors XI and XII, and high molecular weight kininogen, components of the contact activation cascade of blood coagulation are also expressed in non-hepatic tissues. These questions were addressed in the present study by employing quantitative RT-PCR. The relative mRNA levels of the respective proteins determined in 16 human tissues indicate legitimate extrahepatic transcription of at least three of the genes. Transcription of all genes was highest in the liver, but only PPK mRNA was detected in all 16 tissues, especially high levels in pancreas, kidney, testis, spleen and prostate. We conclude from these results that PPK is synthesized in significant amounts in non-hepatic tissues and that this locally synthesized PPK may have special local functions.
Expression of the deleted in colorectal cancer gene is related to prognosis in DNA diploid and low proliferative colorectal adenocarcinoma.

PURPOSE Whether or not the deleted in colorectal cancer (DCC) gene is implicated in metastases or in predicting prognosis in patients with colorectal cancer has not previously been substantiated. Our aims were to investigate DCC expression in primary colorectal cancers and in metastases to identify any prognostic significance. PATIENTS AND METHODS DCC expression was examined immunohistochemically in 195 primary colorectal adenocarcinomas and in 23 paired primary tumors and lymph node metastases. DNA content and S-phase fraction were measured by flow cytometry. RESULTS The absence of DCC expression was observed in 55 primary tumors (28%). DCC negativity was significantly related to poor prognosis in patients with DNA diploid tumors (P =.03) and those with a low S-phase fraction (< 5%, P =.02) but not in patients with nondiploid tumors or those with a higher S-phase fraction. Furthermore, DCC expression retained its prognostic significance in the diploid subgroup after adjusting for sex, age, site, stage, growth pattern, and differentiation (P =.01). DCC expression was similar in primary tumors and their metastases. CONCLUSION The absence of DCC predicted a poor outcome in the patients with diploid tumors and those tumors with a low S-phase fraction. Immunohistochemistry may be considered as a practical test to assess prognosis in this subgroup of patients.
Effects of mould remediation on school teachers' health

The follow-up study of the health of teachers (n = 56) of three mould damage schools were done with self-administered symptom questionnaire before and 1 year after the remediation of school buildings. Technical and microbiological investigations were done parallel at the same time. In the beginning of the study symptoms of allergic rhinitis, sinusitis, conjunctivitis and fatigue were high compared to normal population and 1 year after the intervention a decrease in fatigue (OR = 0.4) and headache (OR = 0.2) was observed. An association between female gender and sinusitis was found before the remediation (OR = 8.1). Age over 40 years was a risk factor for voice problems and more than 10 working years at the same school were associated with increased risk for conjunctivitis (OR = 8.5) and headache (OR = 5.4). Other exposure situations such as mould problems at home and mould exposure during leisure time also have an effect on teachers' health. Significant reduction was found in symptoms of fatigue and headache after the cessation of exposure, while respiratory symptoms need much longer time to relieve after the remediation. Age, female gender, atopy, long-term exposure time and other exposure situations might be the risk factors for prolonged symptoms among mould exposed teachers.
Antimicrobial susceptibility pattern and SCCmec types of methicillin-resistant coagulase-negative staphylococci from subclinical bovine mastitis in Hatay, Turkey

Abstract Eighty-nine isolates of coagulase-negative staphylococci (CoNS) of eight species from subclinical bovine mastitis were screened for the phenotypic and genotypic methicilline-resistance. In addition, all methicillin-resistant (MR) isolates indicating the mecA gene were examined by PCR for the antimicrobial susceptibility patterns, and staphylococcal cassette chromosome mec (SCCmec) types were also determined by multiplex PCR. A total of 21 (23.6%) CoNS isolates were found to be resistant to oxacillin in broth microdilution assay. All isolates phenotypically resistant to oxacillin did not have the mecA gene, which was only found in 14.6% (13) of the isolates. Most MR-CoNS isolates were highly resistant to erythromycin (92.3%), fusidic acid (84.6%), penicillin (76.9%), and rifampycin (61.5%), and susceptible to mupirocin (100%), tetracycline (100%), vancomycin (100%), clindamycin (92.3%), and sulfamethoxazole-trimethoprim (69.2%). In conclusion, a high rate of antimicrobial resistance among MR-CoNS isolated from food producing animals emphasises the need for periodic surveillance of their resistance.
Effect of Orthodontic Treatment on Salivary Immunoglobulin A Levels among a group of healthy Egyptian Children

It has been reported that the immune system undergoes changes due to various factors, inflammation, surgery, medication, age and gender. The aim of this study was to investigate changes of salivary IgA (S-IgA) among healthy subjects undergoing active orthodontic treatment with fixed and removable appliance. The levels of S- IgA were determined before, 3 and 6 months after active orthodontic treatment. A total of 38 healthy individuals (aged 8-14 years) were enrolled in the study. They were divided into two equal groups. Group A were treated with fixed orthodontic appliances and group B were treated with removable orthodontic appliances. Two milliliters of saliva were collected from all participants before ,three and six months after treatment. Salivary IgA levels were measured by the ELISA technique. Results: The average values of S-IgA in the saliva of group A and group B three and six months after treatment were (160.4 ±3.5 and162.0±3.3 µg/ml) and (145.8 ±6.0 and 146.7±5.2 µg/ml), respectively. The average values of S-IgA in the saliva in both group A and group B showed statistically significant higher values after treatment than before. The average values of S-IgA in group A showed statistically significant higher values than those of group B. There was no significant differences between both groups regarding age and sex. Conclusions: The average values of S-IgA in both group A and group B showed statistically significant higher values after treatment than before. The average values of S-IgA in group A showed statistically significant higher values than those of group B. Removable and fixed orthodontic appliances appeared to be a local immunogenic factor, which provided a stronger stimulus for oral secretory immunity. There isa significant positive correlation between S-IgA and
A Multi-Species TaqMan PCR Assay for the Identification of Asian Gypsy Moths (Lymantria spp.) and Other Invasive Lymantriines of Biosecurity Concern to North America

Preventing the introduction and establishment of forest invasive alien species (FIAS) such as the Asian gypsy moth (AGM) is a high-priority goal for countries with extensive forest resources such as Canada. The name AGM designates a group of closely related Lymantria species (Lepidoptera: Erebidae: Lymantriinae) comprising two L. dispar subspecies (L. dispar asiatica, L. dispar japonica) and three closely related Lymantria species (L. umbrosa, L. albescens, L. postalba), all considered potential FIAS in North America. Ships entering Canadian ports are inspected for the presence of suspicious gypsy moth eggs, but those of AGM are impossible to distinguish from eggs of innocuous Lymantria species. To assist regulatory agencies in their identification of these insects, we designed a suite of TaqMan® assays that provide significant improvements over existing molecular assays targeting AGM. The assays presented here can identify all three L. dispar subspecies (including the European gypsy moth, L. dispar dispar), the three other Lymantria species comprising the AGM complex, plus five additional Lymantria species that pose a threat to forests in North America. The suite of assays is built as a “molecular key” (analogous to a taxonomic key) and involves several parallel singleplex and multiplex qPCR reactions. Each reaction uses a combination of primers and probes designed to separate taxa through discriminatory annealing. The success of these assays is based on the presence of single nucleotide polymorphisms (SNPs) in the 5’ region of mitochondrial cytochrome c oxidase I (COI) or in its longer, 3’ region, as well as on the presence of an indel in the “FS1” nuclear marker, generating North American and Asian alleles, used here to assess Asian introgression into L. dispar dispar. These assays have the advantage of providing rapid and accurate identification of ten Lymantria species and subspecies considered potential FIAS.
High frequency of polyandry in a lek mating system

The adaptive significance of polyandry by female birds in the absence of direct benefits remains unclear. We determined the frequencies of polyandrous mating and multiple paternity in the ruff, a lekking shorebird with a genetic dimorphism in male mating behavior. More than half of female ruffs mate with, and have clutches fertilized by, more than one male. Individual females mate with males of both behavioral morphs more often than expected. Polyandrous mating was more likely following copulation interference, but interference was uncommon. The multiple paternity rate of ruffs is the highest known for avian lekking species and for shorebirds. The general hypothesis that pair-bond constraints are the major selective factor favoring multiple mating in birds does not predict our findings. Active genetic diversification, which has been widely dismissed as a functional explanation for polyandrous mating in birds, may apply with respect to the behavioral polymorphism in ruffs because of a Mendelian genetic basis for male behavioral morph determination and aspects of male--male cooperation and female choice. However, rates of multiple paternity in other species of lekking birds are higher than generally realized, and the potential benefits of diversification in general deserve further consideration. Copyright 2002.
The Effect of Cash Flow on Investment: An Empirical Test of the Balance Sheet Channel

This paper tests the balance sheet theory, where the status of balance sheets affects the economy's response to monetary and other shocks. The theory predicts a positive effect of cash flow on investment, given fundamental determinants of investment. I use an empirical method developed by Gilchrist and Himmelberg (1995, 1999), which has previously only been used to study very large, publicly traded firms. In contrast, this paper uses a large Swedish data set with many smaller firms, where balance sheet effects are likely to be especially important. I find that a firm's cash flow has a positive impact on its investment, controlling for any information in cash flow about investment opportunities. As predicted by the balance sheet channel, the estimated effect of cash flow on investment is especially large for firms which, a priori, are more likely to be financially constrained (low-dividend, small and non-group firms). Moreover, the investment-cash flow sensitivity is significantly larger and more persistent during the first half of the sample period, which includes a severe banking crisis and recession, than during the second half.
Down‐regulation of survivin alleviates experimental arthritis

Survivin is a proto‐oncogene that regulates cell division and apoptosis. It is a molecular marker of cancer. Recently, survivin has emerged as a feature of RA, associated with severe joint damage and poor treatment response. The present study examined if inhibition of survivin affects experimental arthritis, which was induced in mBSA‐immunized mice by an injection of mBSA in the knee joint or developed spontaneously in collagen type II‐immunized mice. The inhibition of survivin transcription by a lentivirus shRNA construct alleviated joint inflammation and reduced bone damage. The inhibition of survivin reduced the levels of metalloproteinases, β‐catenin, and vimentin, limiting the invasive capacity of synovia, while no inhibition of osteoclastogenesis could be found. The inhibition of survivin led to a p53‐independent reduction of T cell proliferation and favored the transcription and activity of Blimp‐1, which limited IL‐2 production and facilitated formation of regulatory Foxp3+CD4+ and effector CD8+ T cells. The study shows that the inhibition of survivin is sufficient to reduce joint inflammation and bone damage in preclinical models of arthritis. Antiarthritic effects of survivin inhibition are related to p53‐independent control of lymphocyte proliferation.
Leakage Current Paths in Isolated AlGaN/GaN Heterostructures

Electrical characterization of AlGaN/GaN heterojunctions isolated by Ar-implantation identified three conduction regimes. These include an Ohmic regime below 100 V associated with conduction across the implanted area itself as well as an exponential regime above 400 V associated with a conduction across the buffer or buried interfaces with the substrate. While the extraction of activation energies found an average of roughly 0.85 eV for the Ohmic regime, activation energies above 400 V were consistent with a Poole-Frenkel conduction mechanism. Variations in epitaxial structure, lateral and vertical electric field enabled the distinction between a conduction path in the top layers of the structure and a conduction path which is at least partially vertical across the structure. In addition, time-dependent measurements showed a capacitive effect for conduction across the buffer at room temperature. Having identified the performance limiting conduction path through the buffer layers, these experimental results can also be used as a tool for epitaxy assessment very early on in the production process.
The "Spark Spread:" An Equilibrium Model of Cross-Commodity Price Relationships in Electricity

This paper presents a competitive rational expectations model of spot and forward prices for multiple commodities that can be stored and/or converted. As a result of the conversion option, an equilibrium theory of basis spreads across commodities is derived. This extends the \theory of storage" models to include goods which are not directly storable. In particular, we consider \upstream" (e.g., natural gas and other fuels) and \downstream" commodities (e.g., electricity). We show that many of the most intriguing empirical features of electricity prices follow naturally from the underlying economics of supply and demand. For example, the model produces meanreverting prices, price-dependent heteroscedasticity, skewness and unstable electricityfuel correlations. The general model can incorporate other speci cations such as a commodity with multiple uses (e.g., oil and its re ned products) or a single commodity at multiple locations (e.g., natural gas). The \Spark Spread:" An Equilibrium Model of Cross-Commodity Price Relationships in Electricity
The Sgs1 Helicase of Saccharomyces cerevisiae Inhibits Retrotransposition of Ty1 Multimeric Arrays

ABSTRACT Ty1 retrotransposons in the yeast Saccharomyces cerevisiae are maintained in a genetically competent but transpositionally dormant state. When located in the ribosomal DNA (rDNA) locus, Ty1 elements are transcriptionally silenced by the specialized heterochromatin that inhibits rDNA repeat recombination. In addition, transposition of all Ty1 elements is repressed at multiple posttranscriptional levels. Here, we demonstrate that Sgs1, a RecQ helicase required for genome stability, inhibits the mobility of Ty1 elements by a posttranslational mechanism. Using an assay for the mobility of Ty1 cDNA via integration or homologous recombination, we found that the mobility of both euchromatic and rDNA-Ty1 elements was increased 32- to 79-fold in sgs1Δ mutants. Increased Ty1 mobility was not due to derepression of silent rDNA-Ty1 elements, since deletion of SGS1 reduced the mitotic stability of rDNA-Ty1 elements but did not stimulate their transcription. Furthermore, deletion of SGS1 did not significantly increase the levels of total Ty1 RNA, protein, or cDNA and did not alter the level or specificity of Ty1 integration. Instead, Ty1 cDNA molecules recombined at a high frequency in sgs1Δmutants, resulting in transposition of heterogeneous Ty1 multimers. Formation of Ty1 multimers required the homologous recombination protein Rad52 but did not involve recombination between Ty1 cDNA and genomic Ty1 elements. Therefore, Ty1 multimers that transpose at a high frequency in sgs1Δ mutants are formed by intermolecular recombination between extrachromosomal Ty1 cDNA molecules before or during integration. Our data provide the first evidence that the host cell promotes retrotransposition of monomeric Ty1 elements by repressing cDNA recombination.