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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...
August 31, 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...
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
Antonella Di Poto, Massimiliano Papi, Sheetal Trivedi, Alessandro Maiorana, Paola Gavazzo, Massimo Vassalli, Franklin D Lowy, Marco De Spirito, Lucio Montanaro, Marcello Imbriani, Carla Renata Arciola, Livia Visai
Staphylococcus epidermidis is the leading etiologic agent of device-related infections. S. epidermidis is able to bind, by means of the adhesins of its cell wall, the host matrix proteins filming the artificial surfaces. Thence, bacteria cling to biomaterials and infection develops. The effect of temperature on integrity, structure, and biological activity of the collagen-binding adhesin (SdrF) of S. epidermidis has been here investigated. By cloning in E. coli XL1-Blue, a recombinant of the SdrF binding domain B (rSdrFB), carrying an N-terminal polyhistidine, was obtained...
July 2015: Applied Microbiology and Biotechnology
Luisa Poto, Jacopo Gabrieli, Simon Crowhurst, Claudio Agostinelli, Andrea Spolaor, Warren R L Cairns, Giulio Cozzi, Carlo Barbante
Ombrotrophic peatlands are remarkable repositories of high-quality climatic signals because their only source of nutrients is precipitation. Although several analytical techniques are available for analysing inorganic components in peat samples, they generally provide only low-resolution data sets. Here we present a new analytical approach for producing high-resolution data on main and trace elements from ombrotrophic peat cores. Analyses were carried out on a 7-m-long peat core collected from Danta di Cadore, North-Eastern Italy (46° 34' 16″ N, 12° 29' 58″ E)...
January 2015: Analytical and Bioanalytical Chemistry
Vidal Haddad Junior
The cosmopolitan beetles of the Paederus genus (potós) cause a severe dermatitis when the insect is crushed against the skin of exposed areas (the cervical region is the most affected). Toxins (pederin and others) from the hemolymph of the insect cause plaques and/or bizarre, linear lesions with erythema, edema, blisters, pustules, crusts and exulcerations. There may be a burning sensation and severe conjunctivitis. Lesions disappear after 10 days and may leave hyperchromic macules. Treatment is made with topical corticosteroids and intensive washing...
November 2014: Anais Brasileiros de Dermatologia
Donát Alpár, Gábor Pajor, Péter Varga, Béla Kajtár, László Pótó, Róbert Mátics, Agnes Vojcek, Gábor Ottoffy, Károly Szuhai, László Pajor
BACKGROUND: Pathogenesis of the non-random accumulation of extra chromosomes in the low and high hyperdiploid (HeL, HeH) pre-B pediatric acute lymphoblastic leukemia (B-pALL) is largely unknown, and has been clarified with respect only to tetrasomic chromosomes. We analyzed the hierarchy of changes in chromosome number and chromosomal instability, as well as clonal heterogeneity and evolution, in the untreated bone marrow cell samples from 214 B-pALL patients. PROCEDURE: Applying relocation, 2 × 4 color interphase fluorescence in situ hybridization was used to detect copy number alterations (CNAs) of the most commonly involved chromosomes, 4, 6, 10, 14, 17, 18, 21, and X...
December 2014: Pediatric Blood & Cancer
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