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Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref, Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref, Mahlet G Tadesse, Shiyue ZhOU, Rui Zhu, Yehia Mechref, Alessia Ferrarini, Cristina Di Poto, Yiming Zuo, Habtom W Ressom, Mohammad R Nezami Ranjbar, Ehwang Song, Minkun Wang, Rency S Varghese, Yunli Hu
Multi-omic approaches offer the opportunity to characterize complex diseases such as cancer at various molecular levels. In this paper, we present transcriptomic, proteomic/glycoproteomic, glycomic, and metabolomic (TPGM) data we acquired by analysis of liver tissues from hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. We evaluated changes in the levels of transcripts, proteins, glycans, and metabolites between tumor and cirrhotic tissues by statistical methods. We demonstrated the potential of multi-omic approaches and network analysis to investigate the interactions among these biomolecules in the progression of liver cirrhosis to HCC...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Cristina Di Poto, Alessia Ferrarini, Yi Zhao, Rency S Varghese, Chao Tu, Yiming Zuo, Minkun Wang, Mohammad R Nezami Ranjbar, Yue Luo, Chi Zhang, Chirag S Desai, Kirti Shetty, Mahlet G Tadesse, Habtom W Ressom
BACKGROUND: Metabolomics plays an important role in providing insight into the etiology and mechanisms of hepatocellular carcinoma (HCC). This is accomplished by a comprehensive analysis of patterns involved in metabolic alterations in human specimens. This study compares the levels of plasma metabolites in HCC cases versus cirrhotic patients and evaluates the ability of candidate metabolites in distinguishing the two groups. Also, it investigates the combined use of metabolites and clinical covariates for detection of HCC in patients with liver cirrhosis...
December 2, 2016: Cancer Epidemiology, Biomarkers & Prevention
Á Vojcek, G Pajor, D Alpár, R Mátics, L Pótó, K Szuhai, L Pajor
BACKGROUND: High hyperdiploid (HeH) pre-B pediatric acute lymphoblastic leukemia (B-pALL) is known to be heterogeneous by prognosis, but the stratification principals according to conventional cytogenetic analysis (CCA) are equivocal. PROCEDURE: Untreated bone marrow samples of 214 B-pALL patients were previously classified according to the modal numbers (iMN8) based on the gains of the chromosomes 4, 6, 10, 14, 17, 18, 21, and X as revealed by consecutive and correlated 2×4 color interphase fluorescence in situ hybridization, and at least five years of follow up data were analyzed...
January 2017: Leukemia Research
Qingyu Wu, Yongqiang Jin, Hongyin Li, Mingkui Zhang
BACKGROUND: Double outlet right ventricle (DORV) is a conotruncal anomaly that is a defining element of many types of complex congenital heart disease. Because of a big variety of pathology, there are still some controversies with respect to the definition, classification, and surgical treatment. We report our experience with surgical treatment for DORV (as defined by the "90% rule") with pulmonary outflow tract obstruction (POTO). METHODS: From July 2005 to July 2015, 90 patients underwent surgical treatment of DORV with POTO at the First Hospital of Tsinghua University...
November 2016: World Journal for Pediatric & Congenital Heart Surgery
Yiming Zuo, Yi Cui, Cristina Di Poto, Rency S Varghese, Guoqiang Yu, Ruijiang Li, Habtom W Ressom
Differential expression (DE) analysis is commonly used to identify biomarker candidates that have significant changes in their expression levels between distinct biological groups. One drawback of DE analysis is that it only considers the changes on single biomolecule level. Recently, differential network (DN) analysis has become popular due to its capability to measure the changes on biomolecular pair level. In DN analysis, network is typically built based on correlation and biomarker candidates are selected by investigating the network topology...
December 1, 2016: Methods: a Companion to Methods in Enzymology
Minkun Wang, Tsung-Heng Tsai, Cristina Di Poto, Alessia Ferrarini, Guoqiang Yu, Habtom W Ressom
BACKGROUND: A fundamental challenge in quantitation of biomolecules for cancer biomarker discovery is owing to the heterogeneous nature of human biospecimens. Although this issue has been a subject of discussion in cancer genomic studies, it has not yet been rigorously investigated in mass spectrometry based proteomic and metabolomic studies. Purification of mass spectometric data is highly desired prior to subsequent analysis, e.g., quantitative comparison of the abundance of biomolecules in biological samples...
2016: BMC Genomics
Gregory L Fisher, Anne L Bruinen, Nina Ogrinc Potočnik, John S Hammond, Scott R Bryan, Paul E Larson, Ron M A Heeren
We report a method for the unambiguous identification of molecules in biological and materials specimens at high practical lateral resolution using a new TOF-SIMS parallel imaging MS/MS spectrometer. The tandem mass spectrometry imaging reported here is based on the precise monoisotopic selection of precursor ions from a TOF-SIMS secondary ion stream followed by the parallel and synchronous collection of the product ion data. Thus, our new method enables simultaneous surface screening of a complex matrix chemistry with TOF-SIMS (MS(1)) imaging and targeted identification of matrix components with MS/MS (MS(2)) imaging...
June 21, 2016: Analytical Chemistry
Alberto Cassese, Shane R Ellis, Nina Ogrinc Potočnik, Elke Burgermeister, Matthias Ebert, Axel Walch, Arn M J M van den Maagdenberg, Liam A McDonnell, Ron M A Heeren, Benjamin Balluff
Mass spectrometry imaging (MSI) is a powerful molecular imaging technique. In microprobe MSI, images are created through a grid-wise interrogation of individual spots by mass spectrometry across a surface. Classical statistical tests for within-sample comparisons fail as close-by measurement spots violate the assumption of independence of these tests, which can lead to an increased false-discovery rate. For spatial data, this effect is referred to as spatial autocorrelation. In this study, we investigated spatial autocorrelation in three different matrix-assisted laser desorption/ionization MSI data sets...
June 7, 2016: Analytical Chemistry
Robert Chun, Noel Jabbour, Karthik Balakrishnan, Nancy Bauman, David H Darrow, Ravindhra Elluru, J Fredrik Grimmer, Jonathan Perkins, Gresham Richter, Jennifer Shin
IMPORTANCE: The field of vascular anomalies presents diverse challenges in diagnosis and management. Although many lesions involve the head and neck, training in vascular anomalies is not universally included in otolaryngology residencies and pediatric otolaryngology (POTO) fellowships. OBJECTIVE: To explore the education in, exposure to, and comfort level of otolaryngology trainees with vascular anomalies. DESIGN, SETTING, AND PARTICIPANTS: A survey was distributed to 39 POTO fellows and 44 residents in postgraduate year 5 who matched into POTO fellowships from April 22 through June 16, 2014...
July 1, 2016: JAMA Otolaryngology—Head & Neck Surgery
Katja Repnik, Silvo Koder, Pavel Skok, Ivan Ferkolj, Uroš Potočnik
Tumor necrosis factor α inhibitors (anti-TNF) have improved treatment of several complex diseases, including Crohn's disease (CD). However, the effect varies and approximately one-third of the patients do not respond. Since blood parameters as well as genetic factors have shown a great potential to predict response during treatment, the aim of the study was to evaluate response to anti-TNF treatment with adalimumab (ADA) between genes HFE and TF and haematological parameters in Slovenian refractory CD patients...
August 2016: Biochemical Genetics
Abigail R McEwen, Heileen Hsu-Kim, Nicholas A Robins, Nicole A Hagan, Susan Halabi, Olivo Barras, Daniel deB Richter, John J Vandenberg
Potosí, Bolivia, is the site of centuries of historic and present-day mining of the Cerro Rico, a mountain known for its rich polymetallic deposits, and was the site of large-scale Colonial era silver refining operations. In this study, the concentrations of several metal and metalloid elements were quantified in adobe brick, dirt floor, and surface dust samples from 49 houses in Potosí. Median concentrations of total mercury (Hg), lead (Pb), and arsenic (As) were significantly greater than concentrations measured in Sucre, Bolivia, a non-mining town, and exceeded US-based soil screening levels...
August 15, 2016: Science of the Total Environment
Matjaž Deželak, Katja Repnik, Silvo Koder, Ivan Ferkolj, Uroš Potočnik
Crohn's disease is often treated with the anti-tumor necrosis factor-α drug adalimumab. However, about 20%-40% of patients do not display adequate therapeutic response. We prospectively evaluated, during a routine therapy of Crohn's disease patients, the candidate autophagy-related genes ATG12 and ATG5 and the inflammation-related genes NFKB1, NFKBIA, and CRP as potential predictors of adalimumab treatment response (pharmacodynamics). The associations of haplotypes and SNPs in these genes with response to drug therapy, biochemical parameters, and body mass were determined at baseline and after 4, 12, 20, and 30 weeks of therapy...
May 2016: Omics: a Journal of Integrative Biology
Kunjing Pang, Hong Meng, Hao Wang, Shengshou Hu, Zhongdong Hua, Xiangbin Pan, Shoujun Li
OBJECTIVE: To explore the feasibility and value of a new categorization of double outlet right ventricular (DORV) on guiding the optimal choices of surgical approaches. METHODS: Five hundred and twenty one DORV patients diagnosed by echocardiography, angiocardiography and CT at Fuwai Hospital from May 2003 to September 2014 were enrolled in this retrospective study. Congenital DORV was categorized according to three basic factors as follows: the positional relationships of great arteries (normal relation or abnormal relation), the relationships of the ventricular septal defect (VSD) to the great arteries (committed VSD or remote VSD), the presence or absence of pulmonary outflow tract obstruction (POTO)...
November 2015: Zhonghua Xin Xue Guan Bing za Zhi
Mohammad R Nezami Ranjbar, Cristina Di Poto, Yue Wang, Habtom W Ressom
BACKGROUND: Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, there are no software tools specifically designed for analysis of GC-SIM-MS data. In this paper, we introduce a new R/Bioconductor package called SIMAT for quantitative analysis of the levels of targeted analytes...
August 19, 2015: BMC Bioinformatics
Frederik Helsen, Pieter De Meester, Jan Van Keer, Charlien Gabriels, Alexander Van De Bruaene, Paul Herijgers, Filip Rega, Bart Meyns, Marc Gewillig, Els Troost, Werner Budts
BACKGROUND: Pulmonary outflow tract obstruction (POTO) reduces systemic atrioventricular valve (SAVV) regurgitation severity in congenitally corrected transposition of the great arteries (ccTGA). Therefore, pulmonary artery banding is proposed as a palliative intervention. We aimed to investigate the effect of native or surgically induced POTO on event-free survival, defined as the composite of all-cause mortality, heart transplantation, or congestive heart failure (CHF). METHODS AND RESULTS: Patients with ccTGA (n=62; median age 27...
October 1, 2015: International Journal of Cardiology
Mohammad R Nezami Ranjbar, Yue Luo, Cristina Di Poto, Rency S Varghese, Alessia Ferrarini, Chi Zhang, Naglaa I Sarhan, Hanan Soliman, Mahlet G Tadesse, Dina H Ziada, Rabindra Roy, Habtom W Ressom
This study evaluates changes in metabolite levels in hepatocellular carcinoma (HCC) cases vs. patients with liver cirrhosis by analysis of human blood plasma using gas chromatography coupled with mass spectrometry (GC-MS). Untargeted metabolomic analysis of plasma samples from participants recruited in Egypt was performed using two GC-MS platforms: a GC coupled to single quadruple mass spectrometer (GC-qMS) and a GC coupled to a time-of-flight mass spectrometer (GC-TOFMS). Analytes that showed statistically significant changes in ion intensities were selected using ANOVA models...
2015: PloS One
Romain Potier, Olivier Reineau
A 14.5-yr-old female kinkajou (Potos flavus) was diagnosed with cholelithiasis after an episode of vomiting; diagnostics included biochemical analysis and abdominal ultrasound exam. Despite antimicrobial treatment, cholelithiasis led to cholecystitis. A cholecystotomy was performed to remove choleliths and inspissated bile. Morphological and spectroscopic properties of the choleliths were similar to those of gallstones from the brown pigment family and Streptococcus sp. and Escherichia coli were isolated from the bile...
March 2015: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
Toshihiro Tokiwa, Kosuke Tsugo, Shohei Nakamura, Kensuke Taira, Yumi Une
Roundworms of the genus Baylisascaris are natural parasites primarily of wild carnivores, and they can occasionally cause infection in humans and animals. Infection results in visceral larva migrans and/or neural larva migrans, which can be severe or fatal in some animals. Recently, Baylisascaris nematodes isolated from kinkajous (Potos flavus) and previously referred to as Baylisascaris procyonis were renamed as Baylisascaris potosis; however, data regarding the pathogenicity of B. potosis towards animals and humans are lacking...
October 2015: Parasitology International
Tsung-Heng Tsai, Ehwang Song, Rui Zhu, Cristina Di Poto, Minkun Wang, Yue Luo, Rency S Varghese, Mahlet G Tadesse, Dina Hazem Ziada, Chirag S Desai, Kirti Shetty, Yehia Mechref, Habtom W Ressom
Associating changes in protein levels with the onset of cancer has been widely investigated to identify clinically relevant diagnostic biomarkers. In the present study, we analyzed sera from 205 patients recruited in the United States and Egypt for biomarker discovery using label-free proteomic analysis by LC-MS/MS. We performed untargeted proteomic analysis of sera to identify candidate proteins with statistically significant differences between hepatocellular carcinoma (HCC) and patients with liver cirrhosis...
July 2015: Proteomics
Gina Retschnig, Geoffrey R Williams, Richard Odemer, Janina Boltin, Cornelia Di Poto, Marion M Mehmann, Peter Retschnig, Pius Winiger, Peter Rosenkranz, Peter Neumann
Interactions between pesticides and parasites are believed to be responsible for increased mortality of honey bee (Apis mellifera) colonies in the northern hemisphere. Previous efforts have employed experimental approaches using small groups under laboratory conditions to investigate influence of these stressors on honey bee physiology and behaviour, although both the colony level and field conditions play a key role for eusocial honey bees. Here, we challenged honey bee workers under in vivo colony conditions with sublethal doses of the neonicotinoid thiacloprid, the miticide tau-fluvalinate and the endoparasite Nosema ceranae, to investigate potential effects on longevity and behaviour using observation hives...
November 2015: Environmental Microbiology
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