bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding
Authors: Schoofs Till , Rohde Christian , Hebestreit Katja , Klein Hans-Ulrich , Göllner Stefanie , Schulze Isabell , Lerdrup Mads , Dietrich Nikolaj , Agrawal-Singh Shuchi , Witten Anika , Stoll Monika , Lengfelder Eva , Hofmann Wolf-Karsten , Schlenke Peter , Büchner Thomas , Hansen Klaus , Berdel Wolfgang E. , Rosenbauer Frank , Dugas Martin , Müller-Tidow Carsten 
Published: November 2012

Abstract
The origin of aberrant DNA methylation in cancer remains largely unknown. In the present study, we elucidated the DNA methylome in primary acute promyelocytic leukemia (APL) and the role of promyelocytic leukemia–retinoic acid receptor α (PML-RARα) in establishing these patterns. Cells from APL patients showed increased genome-wide DNA methylation with higher variability than healthy CD34+ cells, promyelocytes, and remission BM cells. A core set of differentially methylated regions in APL was identified. Age at diagnosis, Sanz score, and Flt3-mutation status characterized methylation subtypes. Transcription factor–binding sites (eg, the c-myc–binding sites) were associated with low methylation. However, SUZ12- and REST-binding sites identified in embryonic stem cells were preferentially DNA hypermethylated in APL cells. Unexpectedly, PML-RARα–binding sites were also protected from aberrant DNA methylation in APL cells. Consistent with this, myeloid cells from preleukemic PML-RARα knock-in mice did not show altered DNA methylation and the expression of PML-RARα in hematopoietic progenitor cells prevented differentiation without affecting DNA methylation. Treatment of APL blasts with all-trans retinoic acid also did not result in immediate DNA methylation changes. The results of the present study suggest that aberrant DNA methylation is associated with leukemia phenotype but is not required for PML-RARα–mediated initiation of leukemogenesis.
Early T-cell progenitors are the major granulocyte precursors in the adult mouse thymus
Authors: De Obaldia Maria Elena , Bell J. Jeremiah , Bhandoola Avinash 
Published: November 2012

AbstractThe mouse thymus supports T-cell development, but also contains non–T-cell lineages such as dendritic cells, macrophages, and granulocytes that are necessary for T-cell repertoire selection and apoptotic thymocyte clearance. Early thymic progenitors (ETPs) are not committed to the T-cell lineage, as demonstrated by both in vitro and in vivo assays. Whether ETPs realize non–T-cell lineage potentials in vivo is not well understood and indeed is controversial. In the present study, we investigated whether ETPs are the major precursors of any non–T-lineage cells in the thymus. We analyzed the development of these populations under experimental circumstances in which ETPs are nearly absent due to either abrogated thymic settling or inhibition of early thymic development by genetic ablation of IL-7 receptorα or Hes1. Results obtained using multiple in vivo approaches indicate that the majority of thymic granulocytes derive from ETPs. These data indicate that myelolymphoid progenitors settle the thymus and thus clarify the pathways by which stem cells give rise to downstream blood cell lineages.
Expression of KCNQ1OT1, CDKN1C, H19, and PLAGL1 and the methylation patterns at the KvDMR1 and H19/IGF2 imprinting control regions is conserved between human and bovine
Authors: Robbins Katherine Marie , Chen Zhiyuan , Wells Kevin Dale , Rivera Rocío Melissa 
Published: November 2012

Abstract

Background
Beckwith-Wiedemann syndrome (BWS) is a loss-of-imprinting pediatric overgrowth syndrome. The primary features of BWS include macrosomia, macroglossia, and abdominal wall defects. Secondary features that are frequently observed in BWS patients are hypoglycemia, nevus flammeus, polyhydramnios, visceromegaly, hemihyperplasia, cardiac malformations, and difficulty breathing. BWS is speculated to occur primarily as the result of the misregulation of imprinted genes associated with two clusters on chromosome 11p15.5, namely the KvDMR1 and H19/IGF2. A similar overgrowth phenotype is observed in bovine and ovine as a result of embryo culture. In ruminants this syndrome is known as large offspring syndrome (LOS). The phenotypes associated with LOS are increased birth weight, visceromegaly, skeletal defects, hypoglycemia, polyhydramnios, and breathing difficulties. Even though phenotypic similarities exist between the two syndromes, whether the two syndromes are epigenetically similar is unknown. In this study we use control Bos taurus indicus X Bos taurus taurus F1 hybrid bovine concepti to characterize baseline imprinted gene expression and DNA methylation status of imprinted domains known to be misregulated in BWS. This work is intended to be the first step in a series of experiments aimed at determining if LOS will serve as an appropriate animal model to study BWS.

Results
The use of F1 B. t. indicus x B. t. taurus tissues provided us with a tool to unequivocally determine imprinted status of the regions of interest in our study. We found that imprinting is conserved between the bovine and human in imprinted genes known to be associated with BWS. KCNQ1OT1 and PLAGL1 were paternally-expressed while CDKN1C and H19 were maternally-expressed in B. t. indicus x B. t. taurus F1 concepti. We also show that in bovids, differential methylation exists at the KvDMR1 and H19/IGF2 ICRs.

Conclusions
Based on these findings we conclude that the imprinted gene expression of KCNQ1OT1, CDKN1C, H19, and PLAGL1 and the methylation patterns at the KvDMR1 and H19/IGF2 ICRs are conserved between human and bovine. Future work will determine if LOS is associated with misregulation at these imprinted loci, similarly to what has been observed for BWS.
First survey and functional annotation of prohormone and convertase genes in the pig
Authors: Porter Kenneth I , Southey Bruce R , Sweedler Jonathan V , Rodriguez-Zas Sandra L 
Published: November 2012

AbstractBackgroundThe pig is a biomedical model to study human and livestock traits. Many of these traits are controlled by neuropeptides that result from the cleavage of prohormones by prohormone convertases. Only 45 prohormones have been confirmed in the pig. Sequence homology can be ineffective to annotate prohormone genes in sequenced species like the pig due to the multifactorial nature of the prohormone processing. The goal of this study is to undertake the first complete survey of prohormone and prohormone convertases genes in the pig genome. These genes were functionally annotated based on 35 gene expression microarray experiments. The cleavage sites of prohormone sequences into potentially active neuropeptides were predicted.ResultsWe identified 95 unique prohormone genes, 2 alternative calcitonin-related sequences, 8 prohormone convertases and 1 cleavage facilitator in the pig genome 10.2 assembly and trace archives. Of these, 11 pig prohormone genes have not been reported in the UniProt, UniGene or Gene databases. These genes areintermedin,cortistatin,insulin-like 5,orexigenic neuropeptide QRFP,prokineticin 2,prolactin-releasing peptide,parathyroid hormone 2,urocortin,urocortin 2,urocortin 3, andurotensin 2-related peptide. In addition, a novelneuropeptide Swas identified in the pig genome correcting the previously reported pig sequence that is identical to the rabbit sequence. Most differentially expressed prohormone genes were under-expressed in pigs experiencing immune challenge relative to the un-challenged controls, in non-pregnant relative to pregnant sows, in old relative to young embryos, and in non-neural relative to neural tissues. The cleavage prediction based on human sequences had the best performance with a correct classification rate of cleaved and non-cleaved sites of 92% suggesting that the processing of prohormones in pigs is similar to humans. The cleavage prediction models did not find conclusive evidence supporting the production of the bioactive neuropeptidesurocortin 2,urocortin 3,torsin family 2 member A,tachykinin 4,islet amyloid polypeptide, andcalcitonin receptor-stimulating peptide2 in the pig.ConclusionsThe present genomic and functional characterization supports the use of the pig as an effective animal model to gain a deeper understanding of prohormones, prohormone convertases and neuropeptides in biomedical and agricultural research.
A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome
Authors: Capurso Daniel , Xiong Hao , Segal Mark R 
Published: November 2012

Abstract

Background
Applying supervised learning/classification techniques to epigenomic data may reveal properties that differentiate histone modifications. Previous analyses sought to classify nucleosomes containing histone H2A/H4 arginine 3 symmetric dimethylation (H2A/H4R3me2s) or H2A.Z using human CD4+ T-cell chromatin immunoprecipitation sequencing (ChIP-Seq) data. However, these efforts only achieved modest accuracy with limited biological interpretation. Here, we investigate the impact of using appropriate data pre-processing —deduplication, normalization, and position- (peak-) finding to identify stable nucleosome positions — in conjunction with advanced classification algorithms, notably discriminatory motif feature selection and random forests. Performance assessments are based on accuracy and interpretative yield.

Results
We achieved dramatically improved accuracy using histone modification features (99.0%; previous attempts, 68.3%) and DNA sequence features (94.1%; previous attempts, <60%). Furthermore, the algorithms elicited interpretable features that withstand permutation testing, including: the histone modifications H4K20me3 and H3K9me3, which are components of heterochromatin; and the motif TCCATT, which is part of the consensus sequence of satellite II and III DNA. Downstream analysis demonstrates that satellite II and III DNA in the human genome is occupied by stable nucleosomes containing H2A/H4R3me2s, H4K20me3, and/or H3K9me3, but not 18 other histone methylations. These results are consistent with the recent biochemical finding that H4R3me2s provides a binding site for the DNA methyltransferase (Dnmt3a) that methylates satellite II and III DNA.

Conclusions
Classification algorithms applied to appropriately pre-processed ChIP-Seq data can accurately discriminate between histone modifications. Algorithms that facilitate interpretation, such as discriminatory motif feature selection, have the added potential to impart information about underlying biological mechanism.
Isolimonic acid interferes with Escherichia coli O157:H7 biofilm and TTSS in QseBC and QseA dependent fashion
Authors: Vikram Amit , Jesudhasan Palmy R , Pillai Suresh D , Patil Bhimanagouda S 
Published: November 2012

Abstract

Background

E. coli O157:H7 (EHEC) is an important human pathogen. The antibiotic treatment of EHEC reportedly results in release of Shiga toxin and is therefore discouraged. Consequently, alternative preventive or therapeutic strategies for EHEC are required. The objective of the current study was to investigate the effect of citrus limonoids on cell-cell signaling, biofilm formation and type III secretion system in EHEC.

Results
Isolimonic acid and ichangin were the most potent inhibitors of EHEC biofilm (IC25=19.7 and 28.3 μM, respectively) and adhesion to Caco-2 cells. The qPCR analysis revealed that isolimonic acid and ichangin repressed LEE encoded genes by ≈3 to 12 fold. In addition, flhDC was repressed by the two limonoids (≈3 to 7 fold). Further studies suggested that isolimonic acid interferes with AI-3/epinephrine activated cell-cell signaling pathway. Loss of biofilm inhibitory activity of isolimonic acid in ΔqseBC mutant, which could be restored upon complementation, suggested a dependence on functional QseBC. Additionally, overexpression of qseBC in wild type EHEC abated the inhibitory effect of isolimonic acid. Furthermore, the isolimonic acid failed to differentially regulate ler in ΔqseA mutant, while plasmid borne expression of qseA in ΔqseA background restored the repressive effect of isolimonic acid.

Conclusions
Altogether, results of study seem to suggest that isolimonic acid and ichangin are potent inhibitors of EHEC biofilm and TTSS. Furthermore, isolimonic acid appears to interfere with AI-3/epinephrine pathway in QseBC and QseA dependent fashion.
Prevalence and risk factors of gastroesophageal reflux symptoms in a Chinese retiree cohort
Authors: Chen Tiantian , Lu Ming , Wang Xiaofeng , Yang Yajun , Zhang Juan , Jin Li , Ye Weimin 
Published: November 2012

Abstract

Background
Data about prevalence of gastroesophageal reflux diseases (GERD) from Asian populations are still scarce. To provide additional data on prevalence of GERD and investigate its potential risk factors, we performed this cross-sectional study in the Taizhou Retiree Cohort.

Methods
After physical examination, the participants were asked whether they suffered with heartburn or acid regurgitation in the last 12 months by trained interviewers, and if yes, the severity and frequency of the symptoms were recorded. Odds ratios (ORs) with 95% confidence intervals (CIs) for the associations of obesity and other risk factors with GERD were derived from logistic regression models.

Results
8831 retirees completed the questionnaire and physical examination. In total 150 (1.7%) reported the symptoms occurring at least once per week within the last 12 months before the interview. Compared with subjects without GERD, having a history of diabetes mellitus (OR 2.2, 95% CI 1.4-3.5), hypertension (OR 1.4, 95% CI 1.0-2.1), gastritis (OR 8.2, 95% CI 5.8-11.5), peptic ulcer (OR 3.3, 95% CI 1.8-6.1) and high triglyceride level (≥1.81mmol/L) (OR 2.0, 95% CI 1.2-3.4) were associated with a significantly increased risk of GERD. However, there was no significant association between body mass index, waist-to-hip ratio or waist alone, smoking, consumption of alcohol & tea, and the occurrence of reflux symptoms.

Conclusions
Compared with Western populations, the prevalence of GERD in this Chinese retiree cohort is low. A history of diabetes mellitus, hypertension, gastritis, peptic ulcer or hypertriglyceridaemia increases GERD risk in this population.
Abdominal aortic aneurysm in patients affected by intermittent claudication: prevalence and clinical predictors
Authors: Giugliano Giuseppe , Laurenzano Eugenio , Rengo Carlo , De Rosa Giovanna , Brevetti Linda , Sannino Anna , Perrino Cinzia , Chiariotti Lorenzo , Schiattarella Gabriele Giacomo , Serino Federica , Ferrone Marco , Scudiero Fernando , Carbone Andreina , Sorropago Antonio , Amato Bruno , Trimarco Bruno , Esposito Giovanni 
Published: November 2012

Abstract

Background
Abdominal aortic aneurysm (AAA) is a frequent cause of death among elderly. Patients affected by lower extremity peripheral arterial disease (LE-PAD) seem to be particularly at high risk for AAA. We aimed this study at assessing the prevalence and the clinical predictors of the presence of AAA in a homogeneous cohort of LE-PAD patients affected by intermittent claudication.

Methods
We performed an abdominal ultrasound in 213 consecutive patients with documented LE-PAD (ankle/brachial index ≤0.90) attending our outpatient clinic for intermittent claudication. For each patient we registered cardiovascular risk factors and comorbidities, and measured neutrophil count.

Results
The ultrasound was inconclusive in 3 patients (1.4%), thus 210 patients (169 males, 41 females, mean age 65.9 ± 9.8 yr) entered the study. Overall, AAA was present in 19 patients (9.0%), with a not significant higher prevalence in men than in women (10.1% vs 4.9%, p = 0.300). Patients with AAA were older (71.2 ± 7.0 vs 65.4 ± 9.9 years, p = 0.015), were more likely to have hypertension (94.7% vs 71.2%, p = 0.027), and greater neutrophil count (5.5 [4.5 – 6.2] vs 4.1 [3.2 – 5.5] x103/μL, p = 0.010). Importantly, the c-statistic for neutrophil count (0.73, 95% CI 0.60 – 0.86, p =0.010) was higher than that for age (0.67, CI 0.56–0.78, p = 0.017). The prevalence of AAA in claudicant patients with a neutrophil count ≥ 5.1 x103/μL (cut-off identified at ROC analysis) was as high as 29.0%.

Conclusions
Prevalence of AAA in claudicant patients is much higher than that reported in the general population. Ultrasound screening should be considered in these patients, especially in those with an elevated neutrophil count.
Endovascular treatment of lower extremity arteries is associated with an improved outcome in diabetic patients affected by intermittent claudication
Authors: Giugliano Giuseppe , Perrino Cinzia , Schiano Vittorio , Brevetti Linda , Sannino Anna , Schiattarella Gabriele Giacomo , Gargiulo Giuseppe , Serino Federica , Ferrone Marco , Scudiero Fernando , Carbone Andreina , Bruno Antonio , Amato Bruno , Trimarco Bruno , Esposito Giovanni 
Published: November 2012

Abstract

Background
Lower extremity peripheral arterial disease (LE-PAD) is a highly prevalent condition among diabetic patients, associated with reduced walking capacity and a high incidence of cardiovascular events. Endovascular revascularization of lower extremities arteries improves walking performance and quality of life of diabetic patients affected by intermittent claudication, but few studies evaluated the impact of revascularization on cardiovascular outcome in this high-risk population. Accordingly, in the present study we evaluated if leg-ischemia resolution by effective lower limbs percutaneous revascularization can also impact cardiovascular outcome in a homogeneous group of diabetic patients affected by intermittent claudication.

Methods
236 diabetic patients affected by LE-PAD at stage II of Fontaine’s classification, with ankle/brachial index ≤0.90 and one or more hemodynamically significant stenosis in at least one artery of the ileo-femoro-popliteal axis were enrolled in the study. According to the Trans-Atlantic Inter Society Consensus II recommendations, 123 (52.1%) underwent percutaneous transluminal angioplasty (PTA group), while 113 (47.9%) underwent conservative medical therapy only (MT group). The incidence of major cardiovascular events (cardiovascular death, myocardial infarction, ischemic stroke, coronary or carotid revascularization) was prospectively analyzed with Kaplan-Meier curves and the risk of developing a cardiovascular event calculated by Cox analyses.

Results
No baseline difference in cardiovascular risk factors were observed between the PTA and MT groups, except for a lower prevalence of males in PTA group (74.8% vs. 85.8%, p=0.034). Furthermore, patients in the PTA group showed a worse walking capacity as expressed by maximum walking distance (108.7 ± 300.9 vs 378.4 ± 552.3 meters, p<0.001). During a median follow-up of 20 months (12.0-29.0), the incidence of cardiovascular events was markedly lower in patients in the PTA group with respect to patients in the MT group (7.3% vs. 22.1%, p=0.001), and patients of the MT group had at Cox analysis a 3.9 increased risk with respect to PTA group, after adjustment for potential confounding factors (95% CI 1.1-15.3, p=0.049).

Conclusions
The present study shows that lower limbs revascularization of diabetic patients affected by intermittent claudication, in addition to improve walking performance, is associated with a reduction in the incidence of future major cardiovascular events.
Major postoperative complications and survival for colon cancer elderly patients
Authors: Grosso Giuseppe , Biondi Antonio , Marventano Stefano , Mistretta Antonio , Calabrese Giorgio , Basile Francesco 
Published: November 2012

Abstract

Background
Increased life expectancy has led to elevating the mean age of the patients at the time of diagnosis of colon cancer and subsequent treatment. Differences in complication rates and outcome between elderly and younger patients have been investigated.

Methods
We retrospectively analysed a database containing the information of patients who underwent surgery for stage I-III colorectal cancer from January 2004 to January 2012 at our institution and compared demographic, cancer-related, and outcomes data of 235 elderly patients with 211 patients ≤65 years old.

Results
Intraoperative complications did not differ between young and old patients whereas some differences have been found in postoperative and late complications: elderly patients suffered more by ileus (P = 0.024), peritonitis or septic shock (P = 0.017), pelvic abscess (P = 0.028), wound infection (P = 0.031), and incisional/port herniation (P = 0.012) compared with younger patients. Moreover, elderly patients suffered by systemic complications such as cardiovascular (4.7% vs. 1.4%, P = 0.049), renal (4.7% vs. 0.5%, P = 0.006), and respiratory (10.6% vs. 5.2%, P = 0.036). The multivariate analysis assessing the odds of having a complication revealed that older age (Odd Ratio [OR] 2.75, 95% Confidential Interval [CI]: 1.67-4.52) and open surgery (OR 1.63, 95% CI: 1.01-2.62) are significantly and independently associated with having a complication.

Conclusions
In our series, elderly patients have presented a slight higher incidence of comorbidities that may affect the incidence rates of postoperative complications. These results have implications in increasing the hospital stay as well as a higher rate of death.
Sexual asthenia: Tradamixina versus Tadalafil 5 mg daily
Authors: Iacono Fabrizio , Prezioso Domenico , Illiano Ester , Romeo Giuseppe , Ruffo Antonio , Amato Bruno 
Published: November 2012

Abstract

Background
Reduced libido is widely considered the most prominent symptomatic reflection of low testosterone (T) levels in men. Testosterone deficiency (TD) afflicts approximately 30% of men aged 40-79 years. This study seeks to evaluate the effect of a new natural compound “tradamixina “in order to improve male sexual function in elderly men, particularly libido and possible erectile dysfunction, versus administration of tadalafil 5 mg daily.

Methods
Seventy patients (67.3± 3.7 years) with stable marital relations and affected by reduced libido, with or without erectile dysfunction were recruited. They were randomly separated in 2 groups A-B of 35. Group A was administered twice a day a new compound “Tradamixina” (150 mg of Alga Ecklonia Bicyclis, 396 mg of Tribulus Terrestris and 144 mg of D-Glucosamine and N-Acetyl-D-Glucosamine) for two months, while Group B was administered tadalafil 5 mg daily, for two months. At visit and after 60 days of treatment patients were evaluated by means of detailed medical and sexual history, clinical examination, laboratory investigations (Total and Free T), instrumental examination (NPTR- nocturnal penile tumescence and rigidity test- with Rigiscan). Patients completed a self-administered IIEF questionnaire (The international index of erectile function) and SQoLM questionnaire (Sexual quality of life Questionnarie-Male). The results pre and post treatment were compared by Student t test (p<0.005).

Results
After 2 months of treatment in group A serum TT levels (230±18 ng/dl vs 671±14 ng/dl ) and FT levels(56± 2.4 pg/ml vs 120± 3.9pg/ml) increased, while in group B serum TT levels (245±12 ng/dl vs 247±15 ng/dl ) and FT levels(53± 0.3 pg/ml vs 55± 0.5pg/ml) increased not statistically significant. The patient’s numbers with negative NPTR improved after treatment in group A and B (15 vs 18 and 13 vs 25 respectively). The IIEF total score in group A increased after treatment with tradamixina (15±1.5 vs 29.77±1.2); the IIEF total score in group B increased slightly (12±1.3 vs 23.40±1.2). The SQoLM total score improved in both groups (A:16±2,3 vs 33±4,1 and B: 16±3,4 vs 31±2,1).

Conclusion
The treatment twice a day with “Tradamixina” for 2 months improved libido in elderly men without side effects of Tadalafil.